diff --git a/.gitignore b/.gitignore index 3fb4a86..53b6cd5 100644 --- a/.gitignore +++ b/.gitignore @@ -4,7 +4,6 @@ .DS_Store semantic.cache bin/ -catalog-v001.xml *.tmp *.tmp.obo diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 378a967..e9c06f9 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -22,6 +22,7 @@ These are the current imports in OGMS | iao | http://purl.obolibrary.org/obo/iao.owl | mirror | | ido | http://purl.obolibrary.org/obo/ido.owl | filter | | omo | http://purl.obolibrary.org/obo/omo.owl | mirror | +| cob | http://purl.obolibrary.org/obo/cob.owl | slme | ## Components Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index cc5b8f7..cf3cd42 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -16,7 +16,7 @@ # 3. [Update repo to latest ODK](update_repo) # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 04d4c89977807b1ad2521b6386e797df708e1d2805834dc0af9cc669ff68d53d +CONFIG_HASH= 1fc11db5bb385926b27aa9fa890f57825a32f749e19de3b6ec2c22720f272f95 # ---------------------------------------- @@ -194,7 +194,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = ro obi bfo iao ido omo +IMPORTS = ro obi bfo iao ido omo cob IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -571,6 +571,14 @@ mirror-omo: | $(TMPDIR) $(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl +## ONTOLOGY: cob +.PHONY: mirror-cob +.PRECIOUS: $(MIRRORDIR)/cob.owl +mirror-cob: | $(TMPDIR) + curl -L $(OBOBASE)/cob.owl --create-dirs -o $(TMPDIR)/cob-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/cob-download.owl -o $(TMPDIR)/$@.owl + + $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 16d739d..69c9ccc 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -7,5 +7,6 @@ + \ No newline at end of file diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl index ebff232..144becb 100644 --- a/src/ontology/imports/bfo_import.owl +++ b/src/ontology/imports/bfo_import.owl @@ -7,14 +7,21 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2025-07-02") +Annotation(owl:versionInfo "2026-06-07") Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -26,6 +33,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) ############################ @@ -92,6 +100,14 @@ AnnotationAssertion(rdfs:label "ent AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) AnnotationAssertion(rdfs:label "continuant"@en) SubClassOf( ) +DisjointClasses( ) + +# Class: (occurrent) + +AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ) # Class: (independent continuant) @@ -108,6 +124,53 @@ AnnotationAssertion( "independent continuant"@en) SubClassOf( ) DisjointClasses( ) +DisjointClasses( ) + +# Class: (process) + +AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion( "a process of meiosis"@en) +AnnotationAssertion( "a process of sleeping"@en) +AnnotationAssertion( "the course of a disease"@en) +AnnotationAssertion( "the flight of a bird"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "your process of aging."@en) +AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion( "an atom of element X has the disposition to decay to an atom of element Y"@en) +AnnotationAssertion( "certain people have a predisposition to colon cancer"@en) +AnnotationAssertion( "children are innately disposed to categorize objects in certain ways."@en) +AnnotationAssertion( "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en) +AnnotationAssertion( "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type."@en) +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion( "the disposition of your blood to coagulate"@en) +AnnotationAssertion( "the function of your reproductive organs"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (quality) + +AnnotationAssertion( "the ambient temperature of this portion of air"@en) +AnnotationAssertion( "the color of a tomato"@en) +AnnotationAssertion( "the length of the circumference of your waist"@en) +AnnotationAssertion( "the mass of this piece of gold."@en) +AnnotationAssertion( "the shape of your nose"@en) +AnnotationAssertion( "the shape of your nostril"@en) +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) # Class: (specifically dependent continuant) @@ -124,6 +187,28 @@ AnnotationAssertion( "the smell of this portion of mozzarella"@en) AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) SubClassOf( ) +DisjointClasses( ) + +# Class: (role) + +AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion( "the priest role"@en) +AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion( "the role of a building in serving as a military target"@en) +AnnotationAssertion( "the role of a stone in marking a property boundary"@en) +AnnotationAssertion( "the role of subject in a clinical trial"@en) +AnnotationAssertion( "the student role"@en) +AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) # Class: (material entity) diff --git a/src/ontology/imports/cob_import.owl b/src/ontology/imports/cob_import.owl new file mode 100644 index 0000000..caf3665 --- /dev/null +++ b/src/ontology/imports/cob_import.owl @@ -0,0 +1,393 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2026-06-10") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (definition) + +AnnotationAssertion(rdfs:label "definition") + +# Annotation Property: (editor note) + +AnnotationAssertion(rdfs:label "editor note"@en) + +# Annotation Property: (term replaced by) + +AnnotationAssertion(rdfs:label "term replaced by"@en) + + +############################ +# Object Properties +############################ + +# Object Property: (part of) + +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion(rdfs:label "part of"@en) + +# Object Property: (has part) + +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion(rdfs:label "has part"@en) + +# Object Property: (realizes) + +AnnotationAssertion( "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process"@en) +AnnotationAssertion(rdfs:label "realizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (is about) + +AnnotationAssertion(rdfs:label "is about"@en) +ObjectPropertyDomain( ) + +# Object Property: (has specified input) + +AnnotationAssertion( "The inverse property of is specified input of") +AnnotationAssertion(rdfs:label "has specified input"@en) +ObjectPropertyDomain( ) + +# Object Property: (has specified output) + +AnnotationAssertion( "The inverse property of is specified output of") +AnnotationAssertion(rdfs:label "has specified output"@en) +ObjectPropertyDomain( ) + +# Object Property: (is specified output of) + +AnnotationAssertion( "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion(rdfs:label "is specified output of"@en) +ObjectPropertyRange( ) + +# Object Property: (characteristic of) + +AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) +AnnotationAssertion(rdfs:label "characteristic of"@en) + +# Object Property: (has characteristic) + +AnnotationAssertion( "Inverse of characteristic_of"@en) +AnnotationAssertion(rdfs:label "has characteristic"@en) + +# Object Property: (participates in) + +AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion(rdfs:label "participates in"@en) + +# Object Property: (has participant) + +AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) +AnnotationAssertion(rdfs:label "has participant"@en) + +# Object Property: (is concretized as) + +AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) +AnnotationAssertion(rdfs:label "is concretized as"@en) + +# Object Property: (concretizes) + +AnnotationAssertion( "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) +AnnotationAssertion(rdfs:label "concretizes"@en) + +# Object Property: (has output) + +AnnotationAssertion( "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.") +AnnotationAssertion(rdfs:label "has output"@en) + + + +############################ +# Classes +############################ + +# Class: (process) + +AnnotationAssertion(rdfs:label "process"@en) + +# Class: (disposition) + +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) + +# Class: (realizable entity) + +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) + +# Class: (role) + +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion(rdfs:label "material entity"@en) + +# Class: (immaterial entity) + +AnnotationAssertion(rdfs:label "immaterial entity"@en) + +# Class: (proton) + +AnnotationAssertion( "Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.") +AnnotationAssertion(rdfs:label "proton") +SubClassOf( ) + +# Class: (atomic nucleus) + +AnnotationAssertion( "A nucleus is the positively charged central portion of an atom, excluding the orbital electrons.") +AnnotationAssertion( "Some people may be uncomfortable calling every proton an atomic nucleus"@en) +AnnotationAssertion( "This is equivalent to CHEBI:33252"@en) +AnnotationAssertion(rdfs:label "atomic nucleus") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (subatomic particle) + +AnnotationAssertion( "A particle smaller than an atom.") +AnnotationAssertion(rdfs:label "subatomic particle") +SubClassOf( ) +DisjointClasses( ) + +# Class: (cell) + +AnnotationAssertion( "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") +AnnotationAssertion( "CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc."@en) +AnnotationAssertion( "We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism."@en) +AnnotationAssertion(rdfs:label "cell") +SubClassOf( ) + +# Class: (atom) + +AnnotationAssertion( "A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it."@en) +AnnotationAssertion( "This atom is closely related to ChEBI's atom, but not exactly equivalent to."@en) +AnnotationAssertion(rdfs:label "atom"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + +# Class: (molecule) + +AnnotationAssertion( "A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom."@en) +AnnotationAssertion( "This molecular entity is different than ChEBI's 'molecular entity'."@en) +AnnotationAssertion( "We would like to have cardinality restrictions on the logic, but there are some technical limitations."@en) +AnnotationAssertion(rdfs:label "molecule"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (gross anatomical part) + +AnnotationAssertion( "A part of a multicellular organism that is a collection of cell components that are not all contained in one cell."@en) +AnnotationAssertion(rdfs:label "gross anatomical part"@en) +SubClassOf( ) + +# Class: (organism) + +AnnotationAssertion( "A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome"@en) +AnnotationAssertion( "'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'."@en) +AnnotationAssertion( "Includes virus - we will later have a class for cellular organisms."@en) +AnnotationAssertion(rdfs:label "organism"@en) +SubClassOf( ) + +# Class: (completely executed planned process) + +AnnotationAssertion(rdfs:label "completely executed planned process"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (complex of molecules) + +AnnotationAssertion( "A complex of two or more molecules that are not covalently bound."@en) +AnnotationAssertion(rdfs:label "complex of molecules"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (planned process) + +AnnotationAssertion( "A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification."@en) +AnnotationAssertion(rdfs:label "planned process"@en) +SubClassOf( ) + +# Class: (material processing) + +AnnotationAssertion( "A completely executed planned process that intends to output material entities from input material entities"@en) +AnnotationAssertion(rdfs:label "material processing"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (characteristic) + +AnnotationAssertion(rdfs:label "characteristic"@en) + +# Class: (cellular_component) + +AnnotationAssertion( "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex).") +AnnotationAssertion(rdfs:label "cellular_component") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) + +# Class: (protein-containing complex) + +AnnotationAssertion( "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.") +AnnotationAssertion( "This is not covalently bonded, which conflicts with changes to the parent definition."@en) +AnnotationAssertion(rdfs:label "protein-containing complex") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (virion component) + +AnnotationAssertion( "Any constituent part of a virion, a complete fully infectious extracellular virus particle.") +AnnotationAssertion(rdfs:label "virion component") +SubClassOf( ) + +# Class: (cellular anatomical entity) + +AnnotationAssertion( "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion( "Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes."@en) +AnnotationAssertion( "Overlaps with some cellular components from GO"@en) +AnnotationAssertion(rdfs:label "cellular anatomical entity") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (data item) + +AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) +AnnotationAssertion( "Pier: 'data, information or knowledge'. OR 'representation'"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) + +# Class: (directive information entity) + +AnnotationAssertion( "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en) +AnnotationAssertion(rdfs:label "directive information entity"@en) +SubClassOf( ) + +# Class: (plan specification) + +AnnotationAssertion( "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en) +AnnotationAssertion(rdfs:label "plan specification"@en) +SubClassOf( ) + +# Class: (plan) + +AnnotationAssertion( "A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process."@en) +AnnotationAssertion(rdfs:label "plan"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (data transformation) + +AnnotationAssertion( "A completely executed planned process that produces output data from input data."@en) +AnnotationAssertion(rdfs:label "data transformation"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (protein) + +AnnotationAssertion( "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.") +AnnotationAssertion(rdfs:label "protein") +SubClassOf( ) + +# Class: (amino acid chain) + +AnnotationAssertion( "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.") +AnnotationAssertion(rdfs:label "amino acid chain") +SubClassOf( ) + +# Class: (material anatomical entity) + +AnnotationAssertion( "Anatomical entity that has mass.") +AnnotationAssertion(rdfs:label "material anatomical entity") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +SubClassOf( ) + +# Class: (immaterial anatomical entity) + +AnnotationAssertion( "Anatomical entity that has no mass.") +AnnotationAssertion(rdfs:label "immaterial anatomical entity") +SubClassOf( ) +SubClassOf( ) + +# Class: (anatomical entity) + +AnnotationAssertion( "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.") +AnnotationAssertion(rdfs:label "anatomical entity") +EquivalentClasses( ObjectUnionOf( )) + + +) \ No newline at end of file diff --git a/src/ontology/tmp/.gitkeep b/src/ontology/imports/cob_terms.txt similarity index 100% rename from src/ontology/tmp/.gitkeep rename to src/ontology/imports/cob_terms.txt diff --git a/src/ontology/imports/external_import.owl b/src/ontology/imports/external_import.owl index 9efb65c..8454551 100644 --- a/src/ontology/imports/external_import.owl +++ b/src/ontology/imports/external_import.owl @@ -10,13 +10,16 @@ Ontology( Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class(owl:Thing)) Declaration(ObjectProperty()) @@ -27,7 +30,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl index 372463c..613be7c 100644 --- a/src/ontology/imports/iao_import.owl +++ b/src/ontology/imports/iao_import.owl @@ -5,6 +5,7 @@ Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) +Prefix(xsp:=) Prefix(foaf:=) Prefix(rdfs:=) Prefix(swrl:=) @@ -15,9 +16,9 @@ Prefix(oboInOwl:=) Ontology( - -Annotation(dc:source ) -Annotation(owl:versionInfo "2025-07-02") + +Annotation(dc:source ) +Annotation(owl:versionInfo "2026-06-07") Declaration(Class(obo:APOLLO_SV_00000008)) Declaration(Class(obo:APOLLO_SV_00000032)) @@ -60,6 +61,8 @@ Declaration(Class(obo:BFO_0000146)) Declaration(Class(obo:BFO_0000147)) Declaration(Class(obo:BFO_0000148)) Declaration(Class(obo:BFO_0000182)) +Declaration(Class(obo:COB_0000035)) +Declaration(Class(obo:COB_0000082)) Declaration(Class(obo:IAO_0000001)) Declaration(Class(obo:IAO_0000003)) Declaration(Class(obo:IAO_0000005)) @@ -232,6 +235,7 @@ Declaration(Class(obo:IAO_0000646)) Declaration(Class(obo:IAO_0000647)) Declaration(Class(obo:IAO_0000648)) Declaration(Class(obo:IAO_0000650)) +Declaration(Class(obo:IAO_0000651)) Declaration(Class(obo:IAO_0000701)) Declaration(Class(obo:IAO_0000702)) Declaration(Class(obo:IAO_0000703)) @@ -240,6 +244,7 @@ Declaration(Class(obo:IAO_0000705)) Declaration(Class(obo:IAO_0000706)) Declaration(Class(obo:IAO_0000707)) Declaration(Class(obo:IAO_0000708)) +Declaration(Class(obo:IAO_0001000)) Declaration(Class(obo:IAO_0020000)) Declaration(Class(obo:IAO_0020001)) Declaration(Class(obo:IAO_0020010)) @@ -268,7 +273,6 @@ Declaration(Class(obo:IAO_8000017)) Declaration(Class(obo:IAO_8000018)) Declaration(Class(obo:IAO_8000019)) Declaration(Class(obo:IAO_8000020)) -Declaration(Class(obo:OBI_0000011)) Declaration(Class(obo:OBI_0000066)) Declaration(Class(obo:OBI_0000471)) Declaration(Class(obo:OBI_0200000)) @@ -288,6 +292,7 @@ Declaration(ObjectProperty(obo:BFO_0000054)) Declaration(ObjectProperty(obo:BFO_0000055)) Declaration(ObjectProperty(obo:BFO_0000066)) Declaration(ObjectProperty(obo:BFO_0000067)) +Declaration(ObjectProperty(obo:IAO_0000011)) Declaration(ObjectProperty(obo:IAO_0000039)) Declaration(ObjectProperty(obo:IAO_0000135)) Declaration(ObjectProperty(obo:IAO_0000136)) @@ -359,6 +364,7 @@ Declaration(NamedIndividual(obo:IAO_0000421)) Declaration(NamedIndividual(obo:IAO_0000423)) Declaration(NamedIndividual(obo:IAO_0000428)) Declaration(NamedIndividual(obo:OMO_0001000)) +Declaration(NamedIndividual(obo:OMO_0001002)) Declaration(AnnotationProperty(protege:defaultLanguage)) Declaration(AnnotationProperty(obo:BFO_0000179)) Declaration(AnnotationProperty(obo:BFO_0000180)) @@ -398,6 +404,22 @@ Declaration(AnnotationProperty(obo:IAO_0010000)) Declaration(AnnotationProperty(obo:IAO_0100001)) Declaration(AnnotationProperty(obo:OMO_0001001)) Declaration(AnnotationProperty(obo:OMO_0002000)) +Declaration(AnnotationProperty(obo:OMO_0002001)) +Declaration(AnnotationProperty(obo:OMO_0003000)) +Declaration(AnnotationProperty(obo:OMO_0003001)) +Declaration(AnnotationProperty(obo:OMO_0003002)) +Declaration(AnnotationProperty(obo:OMO_0003003)) +Declaration(AnnotationProperty(obo:OMO_0003004)) +Declaration(AnnotationProperty(obo:OMO_0003005)) +Declaration(AnnotationProperty(obo:OMO_0003006)) +Declaration(AnnotationProperty(obo:OMO_0003007)) +Declaration(AnnotationProperty(obo:OMO_0003008)) +Declaration(AnnotationProperty(obo:OMO_0003009)) +Declaration(AnnotationProperty(obo:OMO_0003010)) +Declaration(AnnotationProperty(obo:OMO_0003011)) +Declaration(AnnotationProperty(obo:OMO_0003012)) +Declaration(AnnotationProperty(obo:OMO_0003014)) +Declaration(AnnotationProperty(obo:OMO_0004000)) Declaration(AnnotationProperty(obo:RO_0001900)) Declaration(AnnotationProperty(dc:contributor)) Declaration(AnnotationProperty(dc:coverage)) @@ -407,6 +429,7 @@ Declaration(AnnotationProperty(dc:description)) Declaration(AnnotationProperty(dc:format)) Declaration(AnnotationProperty(dc:identifier)) Declaration(AnnotationProperty(dc:language)) +Declaration(AnnotationProperty(dc:license)) Declaration(AnnotationProperty(dc:member)) Declaration(AnnotationProperty(dc:publisher)) Declaration(AnnotationProperty(dc:relation)) @@ -415,10 +438,15 @@ Declaration(AnnotationProperty(dc:source)) Declaration(AnnotationProperty(dc:subject)) Declaration(AnnotationProperty(dc:title)) Declaration(AnnotationProperty(dc:type)) +Declaration(AnnotationProperty(terms:contributor)) +Declaration(AnnotationProperty(terms:created)) Declaration(AnnotationProperty(terms:license)) +Declaration(AnnotationProperty(terms:source)) +Declaration(AnnotationProperty(oboInOwl:SynonymTypeProperty)) Declaration(AnnotationProperty(oboInOwl:created_by)) Declaration(AnnotationProperty(oboInOwl:creation_date)) Declaration(AnnotationProperty(oboInOwl:hasBroadSynonym)) +Declaration(AnnotationProperty(oboInOwl:hasDbXref)) Declaration(AnnotationProperty(oboInOwl:hasExactSynonym)) Declaration(AnnotationProperty(oboInOwl:hasNarrowSynonym)) Declaration(AnnotationProperty(oboInOwl:hasRelatedSynonym)) @@ -429,6 +457,7 @@ Declaration(AnnotationProperty(rdfs:seeAlso)) Declaration(AnnotationProperty(foaf:homepage)) Declaration(AnnotationProperty(foaf:mbox)) Declaration(AnnotationProperty(foaf:page)) +Declaration(Datatype(xsd:date)) ############################ # Annotation Properties ############################ @@ -508,7 +537,7 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000115 "PERSON:Daniel Schober"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000115 "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy obo:IAO_0000115 obo:iao.owl) @@ -544,6 +573,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000118 "OBO Operations committee") AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000118 "PERSON:Daniel Schober"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000118 "GROUP:OBI:"@en) AnnotationAssertion(rdfs:comment obo:IAO_0000118 "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") +AnnotationAssertion(rdfs:isDefinedBy obo:IAO_0000118 obo:iao.owl) AnnotationAssertion(rdfs:label obo:IAO_0000118 "alternative label"@en) # Annotation Property: obo:IAO_0000119 (definition source) @@ -577,13 +607,14 @@ AnnotationAssertion(rdfs:label obo:IAO_0000232 "curator note"@en) # Annotation Property: obo:IAO_0000233 (term tracker item) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000233 "term tracker item"@en) -AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000233 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) +AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000233 "the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588"@en) AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000233 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000233 "An IRI or similar locator for a request or discussion of an ontology term."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000233 "A URL for a request or discussion of an ontology term."@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000233 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000233 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) AnnotationAssertion(rdfs:comment obo:IAO_0000233 "The 'tracker item' can associate a tracker with a specific ontology term."@en) AnnotationAssertion(rdfs:label obo:IAO_0000233 "term tracker item"@en) +AnnotationPropertyRange(obo:IAO_0000233 xsd:anyURI) # Annotation Property: obo:IAO_0000234 (ontology term requester) @@ -837,10 +868,164 @@ AnnotationAssertion(dc:contributor obo:OMO_0002000 ) AnnotationAssertion(rdfs:label obo:OMO_0002000 "defined by construct") +# Annotation Property: obo:OMO_0002001 (preferred label for community) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0002001 "The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease \"A\" and another one \"B\" (but they are the same thing).") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0002001 "A provenance property that denotes a synonym to be the preferred one for a specific community.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0002001 ) +AnnotationAssertion(terms:contributor obo:OMO_0002001 ) +AnnotationAssertion(terms:created obo:OMO_0002001 "2025-06-02"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0002001 "preferred label for community") + +# Annotation Property: obo:OMO_0003000 (abbreviation) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003000 "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003000 "A synonym type for describing abbreviations or initialisms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003000 ) +AnnotationAssertion(terms:contributor obo:OMO_0003000 ) +AnnotationAssertion(terms:created obo:OMO_0003000 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003000 "abbreviation") +SubAnnotationPropertyOf(obo:OMO_0003000 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003001 (ambiguous synonym) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003001 "A synonym type for describing ambiguous synonyms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003001 ) +AnnotationAssertion(terms:contributor obo:OMO_0003001 ) +AnnotationAssertion(terms:created obo:OMO_0003001 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003001 "ambiguous synonym") +SubAnnotationPropertyOf(obo:OMO_0003001 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003002 (dubious synonym) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003002 "A synonym type for describing dubious synonyms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003002 ) +AnnotationAssertion(terms:contributor obo:OMO_0003002 ) +AnnotationAssertion(terms:created obo:OMO_0003002 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003002 "dubious synonym") +SubAnnotationPropertyOf(obo:OMO_0003002 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003003 (layperson synonym) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003003 "EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym)") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003003 "A synonym type for describing layperson or colloquial synonyms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003003 ) +AnnotationAssertion(terms:contributor obo:OMO_0003003 ) +AnnotationAssertion(terms:created obo:OMO_0003003 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003003 "layperson synonym") +SubAnnotationPropertyOf(obo:OMO_0003003 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003004 (plural form) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003004 "CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003004 "A synonym type for describing pluralization synonyms") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003004 ) +AnnotationAssertion(terms:contributor obo:OMO_0003004 ) +AnnotationAssertion(terms:created obo:OMO_0003004 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003004 "plural form") +SubAnnotationPropertyOf(obo:OMO_0003004 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003005 (UK spelling synonym) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003005 "CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym)") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003005 "A synonym type for describing UK spelling variants") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003005 ) +AnnotationAssertion(terms:contributor obo:OMO_0003005 ) +AnnotationAssertion(terms:created obo:OMO_0003005 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003005 "UK spelling synonym") +SubAnnotationPropertyOf(obo:OMO_0003005 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003006 (misspelling) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003006 "A synonym type for common misspellings") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003006 ) +AnnotationAssertion(terms:contributor obo:OMO_0003006 ) +AnnotationAssertion(terms:created obo:OMO_0003006 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003006 "misspelling") +SubAnnotationPropertyOf(obo:OMO_0003006 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003007 (misnomer) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003007 "A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003007 ) +AnnotationAssertion(terms:contributor obo:OMO_0003007 ) +AnnotationAssertion(terms:created obo:OMO_0003007 "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003007 "misnomer") +SubAnnotationPropertyOf(obo:OMO_0003007 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003008 (previous name) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003008 "MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol.") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003008 "A synonym type for names that have been used as primary labels in the past.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003008 ) +AnnotationAssertion(terms:contributor obo:OMO_0003008 ) +AnnotationAssertion(terms:created obo:OMO_0003008 "2023-07-25"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003008 "previous name") +SubAnnotationPropertyOf(obo:OMO_0003008 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003009 (legal name) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003009 "The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003009 "A synonym type for the legal entity name") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003009 ) +AnnotationAssertion(terms:contributor obo:OMO_0003009 ) +AnnotationAssertion(terms:created obo:OMO_0003009 "2023-07-27"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003009 "legal name") +SubAnnotationPropertyOf(obo:OMO_0003009 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003010 (International Nonproprietary Name) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003010 "CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) \"paracetamol\". In some cases such as this one, the INN might be the same as the ontology's primary label") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003010 "The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003010 ) +AnnotationAssertion(terms:contributor obo:OMO_0003010 ) +AnnotationAssertion(terms:created obo:OMO_0003010 "2023-09-30"^^xsd:date) +AnnotationAssertion(oboInOwl:hasExactSynonym obo:OMO_0003010 "INN") +AnnotationAssertion(rdfs:label obo:OMO_0003010 "International Nonproprietary Name") +SubAnnotationPropertyOf(obo:OMO_0003010 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003011 (latin term) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003011 "nasopharynx (UBERON:0001728) has the latin name \"pars nasalis pharyngis") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003011 "A synonym type for describing Latin term synonyms.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003011 ) +AnnotationAssertion(terms:contributor obo:OMO_0003011 ) +AnnotationAssertion(terms:created obo:OMO_0003011 "2023-10-12"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003011 "latin term") +SubAnnotationPropertyOf(obo:OMO_0003011 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003012 (acronym) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003012 "NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003012 "A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003012 ) +AnnotationAssertion(terms:contributor obo:OMO_0003012 ) +AnnotationAssertion(terms:created obo:OMO_0003012 "2023-11-01"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003012 "acronym") +SubAnnotationPropertyOf(obo:OMO_0003012 oboInOwl:SynonymTypeProperty) + +# Annotation Property: obo:OMO_0003014 (has ontology hierarchical property) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003014 "The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: ` a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`.") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003014 "Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003014 ) +AnnotationAssertion(terms:contributor obo:OMO_0003014 ) +AnnotationAssertion(terms:created obo:OMO_0003014 "2025-09-17"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003014 "has ontology hierarchical property") + +# Annotation Property: obo:OMO_0004000 (has symbol) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0004000 "A serial number such as \"12324X\"; a stop sign; a written proper name such as \"OBI") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0004000 "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0004000 ) +AnnotationAssertion(terms:contributor obo:OMO_0004000 ) +AnnotationAssertion(terms:created obo:OMO_0004000 "2024-03-25"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0004000 "has symbol") + # Annotation Property: obo:RO_0001900 (temporal interpretation) AnnotationAssertion(obo:IAO_0000115 obo:RO_0001900 "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.") -AnnotationAssertion(rdfs:label obo:RO_0001900 "temporal interpretation"@en) +AnnotationAssertion(rdfs:label obo:RO_0001900 "temporal interpretation") # Annotation Property: oboInOwl:hasBroadSynonym (has broad synonym) @@ -851,6 +1036,15 @@ AnnotationAssertion(rdfs:label oboInOwl:hasBroadSynonym "has broad synonym"@en) AnnotationAssertion(rdfs:seeAlso oboInOwl:hasBroadSynonym "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") SubAnnotationPropertyOf(oboInOwl:hasBroadSynonym obo:IAO_0000118) +# Annotation Property: oboInOwl:hasDbXref (has cross-reference) + +AnnotationAssertion(obo:IAO_0000112 oboInOwl:hasDbXref "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string") +AnnotationAssertion(obo:IAO_0000115 oboInOwl:hasDbXref "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.") +AnnotationAssertion(obo:IAO_0000233 oboInOwl:hasDbXref ) +AnnotationAssertion(terms:contributor oboInOwl:hasDbXref ) +AnnotationAssertion(terms:created oboInOwl:hasDbXref "2024-03-18"^^xsd:date) +AnnotationAssertion(rdfs:label oboInOwl:hasDbXref "has cross-reference") + # Annotation Property: oboInOwl:hasExactSynonym (has exact synonym) AnnotationAssertion(obo:IAO_0000115 oboInOwl:hasExactSynonym "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") @@ -970,6 +1164,17 @@ AnnotationAssertion(rdfs:comment obo:BFO_0000067 "Paraphrase of definition: a re AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000067 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000067 "contains process"@en) +# Object Property: obo:IAO_0000011 (is directed towards) + +AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000011 "One of my mental representations is directed towards the Pacific Ocean."@en) +AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000011 obo:IAO_0000125) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000011 "A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000011 "person: William Hogan"@en) +AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000011 "https://ceur-ws.org/Vol-1515/regular10.pdf") +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000011 ) +AnnotationAssertion(rdfs:comment obo:IAO_0000011 "In the definition source, the relation is called 'is_about'. To avoid confusion with the existing \"is about\" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion."@en) +AnnotationAssertion(rdfs:label obo:IAO_0000011 "is directed towards"@en) + # Object Property: obo:IAO_0000039 (has measurement unit label) AnnotationAssertion(rdfs:label obo:IAO_0000039 "has measurement unit label"@en) @@ -1209,56 +1414,53 @@ SubObjectPropertyOf(obo:IAO_0000583 obo:BFO_0000051) ObjectPropertyDomain(obo:IAO_0000583 obo:IAO_0000582) ObjectPropertyRange(obo:IAO_0000583 ObjectIntersectionOf(obo:IAO_0000109 ObjectComplementOf(obo:IAO_0000416))) -# Object Property: obo:OBI_0000293 (has_specified_input) +# Object Property: obo:OBI_0000293 (has specified input) -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000293 "has_specified_input") -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000293 "has_specified_input"@en) +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000293 "has specified input") AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000293 "see is_input_of example_of_usage"@en) AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000293 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000293 "The inverse property of is_specified_input_of"@en) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000293 "The inverse property of is specified input of") AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000293 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Bjoern Peters") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Larry Hunter") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000293 "PERSON: Melanie Coutot") AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000293 obo:obi.owl) -AnnotationAssertion(rdfs:label obo:OBI_0000293 "has_specified_input"@en) -EquivalentObjectProperties(obo:OBI_0000293 ObjectInverseOf(obo:OBI_0000295)) +AnnotationAssertion(rdfs:label obo:OBI_0000293 "has specified input"@en) SubObjectPropertyOf(obo:OBI_0000293 obo:RO_0000057) -ObjectPropertyDomain(obo:OBI_0000293 obo:OBI_0000011) +InverseObjectProperties(obo:OBI_0000293 obo:OBI_0000295) +ObjectPropertyDomain(obo:OBI_0000293 obo:COB_0000035) -# Object Property: obo:OBI_0000295 (is_specified_input_of) +# Object Property: obo:OBI_0000295 (is specified input of) -AnnotationAssertion(rdfs:label obo:OBI_0000295 "is_specified_input_of"@en) +AnnotationAssertion(rdfs:label obo:OBI_0000295 "is specified input of"@en) -# Object Property: obo:OBI_0000299 (has_specified_output) +# Object Property: obo:OBI_0000299 (has specified output) -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000299 "has_specified_output") -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000299 "has_specified_output"@en) +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000299 "has specified output") AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000299 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000299 "The inverse property of is_specified_output_of"@en) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000299 "The inverse property of is specified output of") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Bjoern Peters") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Larry Hunter") AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000299 "PERSON: Melanie Courtot") AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000299 obo:obi.owl) -AnnotationAssertion(rdfs:label obo:OBI_0000299 "has_specified_output"@en) -EquivalentObjectProperties(obo:OBI_0000299 ObjectInverseOf(obo:OBI_0000312)) +AnnotationAssertion(rdfs:label obo:OBI_0000299 "has specified output"@en) SubObjectPropertyOf(obo:OBI_0000299 obo:RO_0000057) -ObjectPropertyDomain(obo:OBI_0000299 obo:OBI_0000011) +InverseObjectProperties(obo:OBI_0000299 obo:OBI_0000312) +ObjectPropertyDomain(obo:OBI_0000299 obo:COB_0000035) -# Object Property: obo:OBI_0000312 (is_specified_output_of) +# Object Property: obo:OBI_0000312 (is specified output of) -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000312 "is_specified_output_of") -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000312 "is_specified_output_of"@en) +AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000312 "is specified output of") AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000312 obo:IAO_0000122) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000312 "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000312 "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000312 "Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000312 "PERSON:Bjoern Peters") AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000312 obo:obi.owl) -AnnotationAssertion(rdfs:label obo:OBI_0000312 "is_specified_output_of"@en) +AnnotationAssertion(rdfs:label obo:OBI_0000312 "is specified output of"@en) SubObjectPropertyOf(obo:OBI_0000312 obo:RO_0000056) -ObjectPropertyRange(obo:OBI_0000312 obo:OBI_0000011) +ObjectPropertyRange(obo:OBI_0000312 obo:COB_0000035) # Object Property: obo:RO_0000052 (characteristic of) @@ -1309,7 +1511,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:RO_0000057 "this process has participant AnnotationAssertion(obo:IAO_0000115 obo:RO_0000057 "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) AnnotationAssertion(obo:IAO_0000116 obo:RO_0000057 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) AnnotationAssertion(obo:IAO_0000118 obo:RO_0000057 "has_participant"@en) -AnnotationAssertion(dc:source obo:RO_0000057 "http://www.obofoundry.org/ro/#OBO_REL:has_participant") +AnnotationAssertion(terms:source obo:RO_0000057 "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label obo:RO_0000057 "has participant"@en) ObjectPropertyDomain(obo:RO_0000057 obo:BFO_0000003) ObjectPropertyRange(obo:RO_0000057 obo:BFO_0000002) @@ -1318,19 +1520,19 @@ ObjectPropertyRange(obo:RO_0000057 obo:BFO_0000002) AnnotationAssertion(obo:IAO_0000112 obo:RO_0000058 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) AnnotationAssertion(obo:IAO_0000112 obo:RO_0000058 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0000058 "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000058 "A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes."@en) AnnotationAssertion(rdfs:label obo:RO_0000058 "is concretized as"@en) InverseObjectProperties(obo:RO_0000058 obo:RO_0000059) ObjectPropertyDomain(obo:RO_0000058 obo:BFO_0000031) -ObjectPropertyRange(obo:RO_0000058 obo:BFO_0000020) +ObjectPropertyRange(obo:RO_0000058 ObjectUnionOf(obo:BFO_0000015 obo:BFO_0000020)) # Object Property: obo:RO_0000059 (concretizes) AnnotationAssertion(obo:IAO_0000112 obo:RO_0000059 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) AnnotationAssertion(obo:IAO_0000112 obo:RO_0000059 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) -AnnotationAssertion(obo:IAO_0000115 obo:RO_0000059 "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) +AnnotationAssertion(obo:IAO_0000115 obo:RO_0000059 "A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant."@en) AnnotationAssertion(rdfs:label obo:RO_0000059 "concretizes"@en) -ObjectPropertyDomain(obo:RO_0000059 obo:BFO_0000020) +ObjectPropertyDomain(obo:RO_0000059 ObjectUnionOf(obo:BFO_0000015 obo:BFO_0000020)) ObjectPropertyRange(obo:RO_0000059 obo:BFO_0000031) # Object Property: obo:RO_0000079 (function of) @@ -1461,7 +1663,7 @@ AnnotationAssertion(obo:IAO_0000116 obo:RO_0001025 "Location as a relation betwe AnnotationAssertion(obo:IAO_0000116 obo:RO_0001025 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) AnnotationAssertion(obo:IAO_0000118 obo:RO_0001025 "located_in"@en) AnnotationAssertion(obo:RO_0001900 obo:RO_0001025 obo:RO_0001901) -AnnotationAssertion(dc:source obo:RO_0001025 "http://www.obofoundry.org/ro/#OBO_REL:located_in") +AnnotationAssertion(terms:source obo:RO_0001025 "http://www.obofoundry.org/ro/#OBO_REL:located_in") AnnotationAssertion(rdfs:label obo:RO_0001025 "located in"@en) TransitiveObjectProperty(obo:RO_0001025) ObjectPropertyDomain(Annotation(obo:IAO_0000116 "This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.") obo:RO_0001025 obo:BFO_0000004) @@ -1575,8 +1777,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000008 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000119 obo:APOLLO_SV_00000008 "http://en.wikipedia.org/wiki/Software_development") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000008 "A planned process resulting in a software product involving the creation of source code."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000008 "software development"@en) -EquivalentClasses(obo:APOLLO_SV_00000008 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectUnionOf(obo:IAO_0000010 obo:IAO_0000096)))) -SubClassOf(obo:APOLLO_SV_00000008 obo:OBI_0000011) +EquivalentClasses(obo:APOLLO_SV_00000008 ObjectIntersectionOf(obo:COB_0000035 ObjectSomeValuesFrom(obo:OBI_0000299 ObjectUnionOf(obo:IAO_0000010 obo:IAO_0000096)))) +SubClassOf(obo:APOLLO_SV_00000008 obo:COB_0000035) # Class: obo:APOLLO_SV_00000032 (count) @@ -1594,8 +1796,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000033 "Mathias Brochhausen" AnnotationAssertion(obo:IAO_0000119 obo:APOLLO_SV_00000033 "http://en.wikipedia.org/wiki/Counting") AnnotationAssertion(obo:IAO_0000600 obo:APOLLO_SV_00000033 "The planned process of finding the number of elements in a finite set of objects."@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000033 "counting"@en) -EquivalentClasses(obo:APOLLO_SV_00000033 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 obo:APOLLO_SV_00000032))) -SubClassOf(obo:APOLLO_SV_00000033 obo:OBI_0000011) +EquivalentClasses(obo:APOLLO_SV_00000033 ObjectIntersectionOf(obo:COB_0000035 ObjectSomeValuesFrom(obo:OBI_0000299 obo:APOLLO_SV_00000032))) +SubClassOf(obo:APOLLO_SV_00000033 obo:COB_0000035) # Class: obo:APOLLO_SV_00000522 (source code repository) @@ -1627,8 +1829,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:APOLLO_SV_00000796 "William R. Hogan"@en AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000796 "data set creation"@en) AnnotationAssertion(obo:IAO_0000118 obo:APOLLO_SV_00000796 "dataset creation"@en) AnnotationAssertion(rdfs:label obo:APOLLO_SV_00000796 "dataset creating"@en) -EquivalentClasses(obo:APOLLO_SV_00000796 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000100))) -SubClassOf(obo:APOLLO_SV_00000796 obo:OBI_0000011) +EquivalentClasses(obo:APOLLO_SV_00000796 ObjectIntersectionOf(obo:COB_0000035 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000100))) +SubClassOf(obo:APOLLO_SV_00000796 obo:COB_0000035) # Class: obo:BFO_0000001 (entity) @@ -1705,6 +1907,7 @@ AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000004 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000004 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000004 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:comment obo:BFO_0000004 "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000004 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000004 "independent continuant"@en) SubClassOf(obo:BFO_0000004 obo:BFO_0000002) @@ -1794,6 +1997,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000015 "your process of aging."@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000115 obo:BFO_0000015 "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) AnnotationAssertion(obo:IAO_0000116 obo:BFO_0000015 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000015 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:comment obo:BFO_0000015 "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000015 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000015 "process"@en) SubClassOf(obo:BFO_0000015 obo:BFO_0000003) @@ -1882,6 +2086,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000020 "the smell of this portion o AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000115 obo:BFO_0000020 "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) Annotation(rdfs:comment "per discussion with Barry Smith") obo:IAO_0000116 obo:BFO_0000020 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000020 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:comment obo:BFO_0000020 "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same."@en) AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000020 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000020 "specifically dependent continuant"@en) SubClassOf(obo:BFO_0000020 obo:BFO_0000002) @@ -2033,6 +2238,7 @@ AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000031 "the pdf file on your laptop AnnotationAssertion(obo:IAO_0000112 obo:BFO_0000031 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000115 obo:BFO_0000031 "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) AnnotationAssertion(Annotation(obo:IAO_0010000 ) obo:IAO_0000602 obo:BFO_0000031 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ") +AnnotationAssertion(rdfs:comment obo:BFO_0000031 "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time."@en) AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000031 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000031 "generically dependent continuant"@en) SubClassOf(obo:BFO_0000031 obo:BFO_0000002) @@ -2225,6 +2431,21 @@ AnnotationAssertion(rdfs:isDefinedBy obo:BFO_0000182 obo:bfo.owl) AnnotationAssertion(rdfs:label obo:BFO_0000182 "history"@en) SubClassOf(obo:BFO_0000182 obo:BFO_0000015) +# Class: obo:COB_0000035 (completely executed planned process) + +AnnotationAssertion(obo:IAO_0000111 obo:COB_0000035 "completely executed planned process"@en) +AnnotationAssertion(obo:IAO_0000412 obo:COB_0000035 obo:cob.owl) +AnnotationAssertion(rdfs:label obo:COB_0000035 "completely executed planned process"@en) +SubClassOf(obo:COB_0000035 obo:COB_0000082) + +# Class: obo:COB_0000082 (planned process) + +AnnotationAssertion(obo:IAO_0000111 obo:COB_0000082 "planned process"@en) +AnnotationAssertion(obo:IAO_0000115 obo:COB_0000082 "A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification."@en) +AnnotationAssertion(obo:IAO_0000412 obo:COB_0000082 obo:cob.owl) +AnnotationAssertion(rdfs:label obo:COB_0000082 "planned process"@en) +SubClassOf(obo:COB_0000082 obo:BFO_0000015) + # Class: obo:IAO_0000001 (conditional specification) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000001 "conditional specification"@en) @@ -2432,12 +2653,12 @@ AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000025 "group:OBI"@en) AnnotationAssertion(rdfs:label obo:IAO_0000025 "programming language"@en) SubClassOf(obo:IAO_0000025 obo:IAO_0000104) -# Class: obo:IAO_0000027 (data item) +# Class: obo:IAO_0000027 (data entity) -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000027 "data item"@en) +AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000027 "data entity"@en) AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000027 "Data items include counts of things, analyte concentrations, and statistical summaries."@en) AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000027 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000027 "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000027 "An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000027 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000027 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000027 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) @@ -2453,7 +2674,8 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000027 "PERSON: Alan Ruttenberg"@en AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000027 "PERSON: Chris Stoeckert"@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000027 "PERSON: Jonathan Rees"@en) AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000027 "data"@en) -AnnotationAssertion(rdfs:label obo:IAO_0000027 "data item"@en) +AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000027 "data item"@en) +AnnotationAssertion(rdfs:label obo:IAO_0000027 "data entity"@en) SubClassOf(obo:IAO_0000027 obo:IAO_0000030) # Class: obo:IAO_0000028 (symbol) @@ -2799,12 +3021,13 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000098 "PERSON: Alan Ruttenberg"@en AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000098 "PlanAndPlannedProcess Branch"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000098 "OBI branch derived"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000098 "OBI_0000187"@en) +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000098 ) AnnotationAssertion(rdfs:label obo:IAO_0000098 "data format specification"@en) SubClassOf(obo:IAO_0000098 obo:IAO_0000033) -# Class: obo:IAO_0000100 (data set) +# Class: obo:IAO_0000100 (homogenous data collection) -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000100 "data set"@en) +AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000100 "homogenous data collection"@en) AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000100 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en) AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000100 obo:IAO_0000125) AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000100 "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en) @@ -2812,10 +3035,10 @@ AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000100 "2009/10/23 Alan Ruttenberg. AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000100 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.") AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000100 "person:Allyson Lister"@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000100 "person:Chris Stoeckert"@en) -AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000100 "OBI_0000042"@en) +AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000100 "data set"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000100 "group:OBI"@en) -AnnotationAssertion(rdfs:label obo:IAO_0000100 "data set"@en) -SubClassOf(obo:IAO_0000100 obo:IAO_0000027) +AnnotationAssertion(rdfs:label obo:IAO_0000100 "homogenous data collection"@en) +SubClassOf(obo:IAO_0000100 obo:IAO_0001000) # Class: obo:IAO_0000101 (image) @@ -3618,7 +3841,7 @@ AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000443 obo:IAO_0000120) AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000443 "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing") AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000443 "Person:Alan Ruttenberg") AnnotationAssertion(rdfs:label obo:IAO_0000443 "data item extraction from journal article") -SubClassOf(obo:IAO_0000443 obo:OBI_0000011) +SubClassOf(obo:IAO_0000443 obo:COB_0000035) SubClassOf(obo:IAO_0000443 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000013)) SubClassOf(obo:IAO_0000443 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000027)) @@ -3631,7 +3854,7 @@ AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000444 "https://en.wikipedia.org/wi AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000444 ) AnnotationAssertion(obo:IAO_0000234 obo:IAO_0000444 "VEuPathDB"@en) AnnotationAssertion(rdfs:label obo:IAO_0000444 "publishing process"@en) -SubClassOf(obo:IAO_0000444 obo:OBI_0000011) +SubClassOf(obo:IAO_0000444 obo:COB_0000035) # Class: obo:IAO_0000445 (document in preparation for publication) @@ -3653,7 +3876,7 @@ AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000572 "6/11/9: Edited at OBI works AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000572 "Bjoern Peters"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000572 "wikipedia http://en.wikipedia.org/wiki/Documenting"@en) AnnotationAssertion(rdfs:label obo:IAO_0000572 "documenting"@en) -SubClassOf(obo:IAO_0000572 obo:OBI_0000011) +SubClassOf(obo:IAO_0000572 obo:COB_0000035) SubClassOf(obo:IAO_0000572 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000030)) SubClassOf(obo:IAO_0000572 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000310)) @@ -3682,7 +3905,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000574 "Person:Bjoern Peters"@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000574 "Person:Melanie Courtot"@en) AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000574 "assigning a CRID") AnnotationAssertion(rdfs:label obo:IAO_0000574 "assigning a centrally registered identifier"@en) -SubClassOf(obo:IAO_0000574 obo:OBI_0000011) +SubClassOf(obo:IAO_0000574 obo:COB_0000035) SubClassOf(obo:IAO_0000574 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000577)) SubClassOf(obo:IAO_0000574 ObjectSomeValuesFrom(obo:RO_0000057 obo:IAO_0000579)) @@ -3694,7 +3917,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000575 "A planned process in which AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000575 "PERSON:Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000575 "associating information with a CRID in the CRID registry") AnnotationAssertion(rdfs:label obo:IAO_0000575 "associating information with a centrally registered identifier in its registry"@en) -SubClassOf(obo:IAO_0000575 obo:OBI_0000011) +SubClassOf(obo:IAO_0000575 obo:COB_0000035) SubClassOf(obo:IAO_0000575 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000030)) SubClassOf(obo:IAO_0000575 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000577)) SubClassOf(obo:IAO_0000575 ObjectSomeValuesFrom(obo:RO_0000057 obo:IAO_0000579)) @@ -3769,7 +3992,7 @@ AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000580 "PERSON: Bjoern Peters"@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000580 "PERSON: Melanie Courtot"@en) AnnotationAssertion(obo:IAO_0000118 obo:IAO_0000580 "looking up a CRID") AnnotationAssertion(rdfs:label obo:IAO_0000580 "looking up a centrally registered identifier"@en) -SubClassOf(obo:IAO_0000580 obo:OBI_0000011) +SubClassOf(obo:IAO_0000580 obo:COB_0000035) SubClassOf(obo:IAO_0000580 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000577)) SubClassOf(obo:IAO_0000580 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000030)) SubClassOf(obo:IAO_0000580 ObjectSomeValuesFrom(obo:RO_0000057 obo:IAO_0000579)) @@ -4471,10 +4694,19 @@ AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000650 ) AnnotationAssertion(rdfs:label obo:IAO_0000650 "database extract, transform, and load process"@en) AnnotationAssertion(foaf:page obo:IAO_0000650 ) -SubClassOf(obo:IAO_0000650 obo:OBI_0000011) +SubClassOf(obo:IAO_0000650 obo:COB_0000035) SubClassOf(obo:IAO_0000650 ObjectSomeValuesFrom(obo:OBI_0000293 obo:IAO_0000030)) SubClassOf(obo:IAO_0000650 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0000030)) +# Class: obo:IAO_0000651 (title section) + +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000651 "the section of the document where the title appears"@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000651 "This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000651 "Charles Tapley Hoyt"@en) +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000651 "https://github.com/information-artifact-ontology/IAO/issues/286"^^xsd:anyURI) +AnnotationAssertion(rdfs:label obo:IAO_0000651 "title section"@en) +SubClassOf(obo:IAO_0000651 obo:IAO_0000314) + # Class: obo:IAO_0000701 (descriptive data section) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000701 "descriptive data section"@en) @@ -4587,6 +4819,17 @@ AnnotationAssertion(obo:IAO_0000233 obo:IAO_0000708 "https://github.com/informat AnnotationAssertion(rdfs:label obo:IAO_0000708 "ORCID identifier"@en) SubClassOf(obo:IAO_0000708 obo:IAO_0000578) +# Class: obo:IAO_0001000 (data collection) + +AnnotationAssertion(obo:IAO_0000111 obo:IAO_0001000 "data collection"@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0001000 "A data entity that consists of multiple data entities."@en) +AnnotationAssertion(obo:IAO_0000117 obo:IAO_0001000 "Sebastian Duesing") +AnnotationAssertion(obo:IAO_0000118 obo:IAO_0001000 "data set"@en) +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0001000 "https://github.com/information-artifact-ontology/IAO/issues/283") +AnnotationAssertion(obo:IAO_0000233 obo:IAO_0001000 "https://github.com/obi-ontology/obi/issues/1877") +AnnotationAssertion(rdfs:label obo:IAO_0001000 "data collection"@en) +SubClassOf(obo:IAO_0001000 obo:IAO_0000027) + # Class: obo:IAO_0020000 (identifier) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0020000 "identifier"@en) @@ -4623,8 +4866,8 @@ AnnotationAssertion(obo:IAO_0000118 obo:IAO_0020010 "naming"@en) AnnotationAssertion(obo:IAO_0000233 obo:IAO_0020010 "https://github.com/information-artifact-ontology/IAO/issues/237"@en) AnnotationAssertion(dc:creator obo:IAO_0020010 "Mathias Brochhausen") AnnotationAssertion(rdfs:label obo:IAO_0020010 "identifier creating process"@en) -EquivalentClasses(obo:IAO_0020010 ObjectIntersectionOf(obo:OBI_0000011 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0020000))) -SubClassOf(obo:IAO_0020010 obo:OBI_0000011) +EquivalentClasses(obo:IAO_0020010 ObjectIntersectionOf(obo:COB_0000035 ObjectSomeValuesFrom(obo:OBI_0000299 obo:IAO_0020000))) +SubClassOf(obo:IAO_0020010 obo:COB_0000035) # Class: obo:IAO_0020015 (personal name) @@ -4875,42 +5118,34 @@ AnnotationAssertion(obo:IAO_0000111 obo:IAO_8000020 "EL++ ontology module"@en) AnnotationAssertion(rdfs:label obo:IAO_8000020 "EL++ ontology module"@en) SubClassOf(obo:IAO_8000020 obo:IAO_8000019) -# Class: obo:OBI_0000011 (planned process) - -AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000011 "planned process"@en) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000011 "A process that realizes a plan which is the concretization of a plan specification."@en) -AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000011 obo:obi.owl) -AnnotationAssertion(rdfs:label obo:OBI_0000011 "planned process"@en) -SubClassOf(obo:OBI_0000011 obo:BFO_0000015) - # Class: obo:OBI_0000066 (investigation) AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000066 "investigation"@en) AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000066 "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)."@en) AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000066 obo:obi.owl) AnnotationAssertion(rdfs:label obo:OBI_0000066 "investigation"@en) -SubClassOf(obo:OBI_0000066 obo:OBI_0000011) +SubClassOf(obo:OBI_0000066 obo:COB_0000035) # Class: obo:OBI_0000471 (study design execution) AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000471 "study design execution") -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000471 "a planned process that carries out a study design") +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000471 "a planned process that carries out a study design"@en) AnnotationAssertion(obo:IAO_0000412 obo:OBI_0000471 obo:obi.owl) AnnotationAssertion(rdfs:label obo:OBI_0000471 "study design execution") -SubClassOf(obo:OBI_0000471 obo:OBI_0000011) +SubClassOf(obo:OBI_0000471 obo:COB_0000035) # Class: obo:OBI_0200000 (data transformation) AnnotationAssertion(obo:IAO_0000111 obo:OBI_0200000 "data transformation"@en) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200000 "A planned process that produces output data from input data."@en) +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0200000 "A completely executed planned process that produces output data from input data."@en) AnnotationAssertion(obo:IAO_0000412 obo:OBI_0200000 obo:obi.owl) AnnotationAssertion(rdfs:label obo:OBI_0200000 "data transformation"@en) -SubClassOf(obo:OBI_0200000 obo:OBI_0000011) +SubClassOf(obo:OBI_0200000 obo:COB_0000035) # Class: obo:OBI_0500000 (study design) AnnotationAssertion(obo:IAO_0000111 obo:OBI_0500000 "study design"@en) -AnnotationAssertion(obo:IAO_0000115 obo:OBI_0500000 "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.") +AnnotationAssertion(obo:IAO_0000115 obo:OBI_0500000 "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution."@en) AnnotationAssertion(obo:IAO_0000412 obo:OBI_0500000 obo:obi.owl) AnnotationAssertion(rdfs:label obo:OBI_0500000 "study design"@en) SubClassOf(obo:OBI_0500000 obo:IAO_0000104) @@ -4958,6 +5193,7 @@ SubClassOf(obo:PATO_0001241 obo:BFO_0000019) # Class: obo:UO_0000001 (length unit) AnnotationAssertion(obo:IAO_0000111 obo:UO_0000001 "length unit") +AnnotationAssertion(obo:IAO_0000115 obo:UO_0000001 "A unit which is a standard measure of the distance between two points.") AnnotationAssertion(obo:IAO_0000412 obo:UO_0000001 obo:uo.owl) AnnotationAssertion(rdfs:label obo:UO_0000001 "length unit") SubClassOf(obo:UO_0000001 obo:IAO_0000003) @@ -4965,6 +5201,7 @@ SubClassOf(obo:UO_0000001 obo:IAO_0000003) # Class: obo:UO_0000002 (mass unit) AnnotationAssertion(obo:IAO_0000111 obo:UO_0000002 "mass unit") +AnnotationAssertion(obo:IAO_0000115 obo:UO_0000002 "A unit which is a standard measure of the amount of matter/energy of a physical object.") AnnotationAssertion(obo:IAO_0000412 obo:UO_0000002 obo:uo.owl) AnnotationAssertion(rdfs:label obo:UO_0000002 "mass unit") SubClassOf(obo:UO_0000002 obo:IAO_0000003) @@ -4972,6 +5209,7 @@ SubClassOf(obo:UO_0000002 obo:IAO_0000003) # Class: obo:UO_0000003 (time unit) AnnotationAssertion(obo:IAO_0000111 obo:UO_0000003 "time unit") +AnnotationAssertion(obo:IAO_0000115 obo:UO_0000003 "A unit which is a standard measure of the dimension in which events occur in sequence.") AnnotationAssertion(obo:IAO_0000412 obo:UO_0000003 obo:uo.owl) AnnotationAssertion(rdfs:label obo:UO_0000003 "time unit") SubClassOf(obo:UO_0000003 obo:IAO_0000003) @@ -4990,8 +5228,11 @@ ClassAssertion(obo:IAO_0000078 obo:IAO_0000002) # Individual: obo:IAO_0000103 (failed exploratory term) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000103 "failed exploratory term"@en) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000103 "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000103 "The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000103 "Terms created as placeholders with the expectation of being permanent should instead be deprecated using the \"placeholder removed\" (obo:IAO_0000226) justification."@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000103 "Person:Alan Ruttenberg"@en) +AnnotationAssertion(dc:contributor obo:IAO_0000103 ) +AnnotationAssertion(dc:contributor obo:IAO_0000103 ) AnnotationAssertion(rdfs:label obo:IAO_0000103 "failed exploratory term"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000103) ClassAssertion(owl:Thing obo:IAO_0000103) @@ -5006,7 +5247,7 @@ ClassAssertion(obo:IAO_0000078 obo:IAO_0000120) # Individual: obo:IAO_0000121 (organizational term) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000121 "organizational term"@en) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000121 "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000121 "The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release."@en) AnnotationAssertion(rdfs:label obo:IAO_0000121 "organizational term"@en) ClassAssertion(obo:IAO_0000078 obo:IAO_0000121) @@ -5050,6 +5291,10 @@ AnnotationAssertion(owl:deprecated obo:IAO_0000224 "true"^^xsd:boolean) # Individual: obo:IAO_0000226 (placeholder removed) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000226 "placeholder removed"@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000226 "The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000226 "This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider."@en) +AnnotationAssertion(dc:contributor obo:IAO_0000226 ) +AnnotationAssertion(dc:contributor obo:IAO_0000226 ) AnnotationAssertion(rdfs:label obo:IAO_0000226 "placeholder removed"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000226) ClassAssertion(owl:Thing obo:IAO_0000226) @@ -5057,21 +5302,30 @@ ClassAssertion(owl:Thing obo:IAO_0000226) # Individual: obo:IAO_0000227 (terms merged) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000227 "terms merged"@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000227 "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000227 "The term has been combined with one or more other terms to create a more encompassing (merged) term."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000227 "The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(dc:contributor obo:IAO_0000227 ) +AnnotationAssertion(dc:contributor obo:IAO_0000227 ) AnnotationAssertion(rdfs:label obo:IAO_0000227 "terms merged"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000227) # Individual: obo:IAO_0000228 (term imported) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000228 "term imported"@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000228 "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000228 "The term has been replaced by a term imported from another ontology."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000228 "This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001."@en) +AnnotationAssertion(dc:contributor obo:IAO_0000228 ) +AnnotationAssertion(dc:contributor obo:IAO_0000228 ) AnnotationAssertion(rdfs:label obo:IAO_0000228 "term imported"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000228) # Individual: obo:IAO_0000229 (term split) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000229 "term split"@en) -AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000229 "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000229 "The term has been split into two or more new terms."@en) +AnnotationAssertion(obo:IAO_0000116 obo:IAO_0000229 "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001."@en) +AnnotationAssertion(dc:contributor obo:IAO_0000229 ) +AnnotationAssertion(dc:contributor obo:IAO_0000229 ) AnnotationAssertion(rdfs:label obo:IAO_0000229 "term split"@en) ClassAssertion(obo:IAO_0000225 obo:IAO_0000229) @@ -5130,20 +5384,32 @@ ClassAssertion(obo:IAO_0000078 obo:IAO_0000428) # Individual: obo:OMO_0001000 (out of scope) AnnotationAssertion(obo:IAO_0000115 obo:OMO_0001000 "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) -AnnotationAssertion(obo:IAO_0000116 obo:OMO_0001000 "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OMO_0001000 "This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype."@en) AnnotationAssertion(obo:IAO_0000117 obo:OMO_0001000 ) AnnotationAssertion(obo:IAO_0000233 obo:OMO_0001000 "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") AnnotationAssertion(obo:IAO_0000234 obo:OMO_0001000 "https://orcid.org/0000-0001-5208-3432") +AnnotationAssertion(dc:contributor obo:OMO_0001000 ) +AnnotationAssertion(dc:contributor obo:OMO_0001000 ) AnnotationAssertion(rdfs:label obo:OMO_0001000 "out of scope") ClassAssertion(obo:IAO_0000225 obo:OMO_0001000) +# Individual: obo:OMO_0001002 (domain entity does not exist) + +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0001002 "The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OMO_0001002 "This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). "@en) +AnnotationAssertion(obo:IAO_0000117 obo:OMO_0001002 ) +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0001002 "https://github.com/information-artifact-ontology/ontology-metadata/issues/136") +AnnotationAssertion(obo:IAO_0000234 obo:OMO_0001002 "https://orcid.org/0000-0002-4142-7153") +AnnotationAssertion(rdfs:label obo:OMO_0001002 "domain entity does not exist") +ClassAssertion(obo:IAO_0000225 obo:OMO_0001002) + DifferentIndividuals(obo:IAO_0000120 obo:IAO_0000121 obo:IAO_0000122 obo:IAO_0000123 obo:IAO_0000124 obo:IAO_0000125 obo:IAO_0000423 obo:IAO_0000428) DifferentIndividuals(obo:IAO_0000226 obo:IAO_0000227 obo:IAO_0000228 obo:IAO_0000229) SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000050 obo:BFO_0000066) obo:BFO_0000066) SubObjectPropertyOf(ObjectPropertyChain(obo:BFO_0000066 obo:BFO_0000050) obo:BFO_0000066) -DLSafeRule(Body(ClassAtom(obo:BFO_0000016 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000091 Variable() Variable()))) -DLSafeRule(Body(ClassAtom(obo:BFO_0000019 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000086 Variable() Variable()))) -DLSafeRule(Body(ClassAtom(obo:BFO_0000023 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000087 Variable() Variable()))) -DLSafeRule(Body(ClassAtom(obo:BFO_0000034 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000085 Variable() Variable()))) +DLSafeRule(Body(ClassAtom(obo:BFO_0000016 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000091 Variable() Variable()))) +DLSafeRule(Body(ClassAtom(obo:BFO_0000019 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000086 Variable() Variable()))) +DLSafeRule(Body(ClassAtom(obo:BFO_0000023 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000087 Variable() Variable()))) +DLSafeRule(Body(ClassAtom(obo:BFO_0000034 Variable()) ObjectPropertyAtom(obo:RO_0000053 Variable() Variable()))Head(ObjectPropertyAtom(obo:RO_0000085 Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl index dc25c43..596eab3 100644 --- a/src/ontology/imports/ido_import.owl +++ b/src/ontology/imports/ido_import.owl @@ -7,14 +7,15 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2025-07-02") +Annotation(owl:versionInfo "2026-06-07") Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -33,6 +34,7 @@ AnnotationAssertion( "Lindsay Cowell") AnnotationAssertion(rdfs:label "infectious disorder"@en) SubClassOf( ) +SubClassOf( ) # Class: (infection) diff --git a/src/ontology/imports/obi_import.owl b/src/ontology/imports/obi_import.owl index c3a76db..be42ea0 100644 --- a/src/ontology/imports/obi_import.owl +++ b/src/ontology/imports/obi_import.owl @@ -7,15 +7,15 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2025-07-02") + +Annotation( ) +Annotation(owl:versionInfo "2026-06-10") -Declaration(Class()) -Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -40,12 +40,12 @@ Declaration(AnnotationProperty()) AnnotationAssertion( "is specified output of") AnnotationAssertion( ) -AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) +AnnotationAssertion( "A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion( "Alan Ruttenberg"@en) AnnotationAssertion( "PERSON:Bjoern Peters") AnnotationAssertion(rdfs:label "is specified output of"@en) SubObjectPropertyOf( ) -ObjectPropertyRange( ) +ObjectPropertyRange( ) # Object Property: (is member of organization) @@ -78,21 +78,6 @@ AnnotationAssertion(rdfs:label "has # Classes ############################ -# Class: (planned process) - -AnnotationAssertion( "planned process") -AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") -AnnotationAssertion( ) -AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) -AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") -AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process.") -AnnotationAssertion( "Bjoern Peters") -AnnotationAssertion( "branch derived") -AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") -AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) -AnnotationAssertion(rdfs:label "planned process"@en) - # Class: (disease stage) AnnotationAssertion( "disease stage") @@ -102,30 +87,12 @@ AnnotationAssertion( "PERSON: Bjoern peters") AnnotationAssertion(rdfs:label "disease stage"@en) -# Class: (organism) - -AnnotationAssertion( "organism"@en) -AnnotationAssertion( "animal"@en) -AnnotationAssertion( "fungus"@en) -AnnotationAssertion( "plant"@en) -AnnotationAssertion( "virus"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) -AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") -AnnotationAssertion( "13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI.") -AnnotationAssertion( "GROUP: OBI Biomaterial Branch") -AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) -AnnotationAssertion(rdfs:label "organism"@en) -SubClassOf( ) - # Class: (data transformation) AnnotationAssertion( "data transformation"@en) AnnotationAssertion( "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.") AnnotationAssertion( ) -AnnotationAssertion( "A planned process that produces output data from input data."@en) +AnnotationAssertion( "A completely executed planned process that produces output data from input data."@en) AnnotationAssertion( "Elisabetta Manduchi"@en) AnnotationAssertion( "Helen Parkinson"@en) AnnotationAssertion( "James Malone"@en) @@ -138,7 +105,18 @@ AnnotationAssertion( "data processing"@en) AnnotationAssertion( "Branch editors"@en) AnnotationAssertion(rdfs:label "data transformation"@en) -SubClassOf( ) +SubClassOf( ) + +# Class: (material component separation) + +AnnotationAssertion( "material component separation"@en) +AnnotationAssertion( "Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "a material processing in which components of an input material become segregated in space"@en) +AnnotationAssertion( "Bjoern Peters"@en) +AnnotationAssertion( "IEDB"@en) +AnnotationAssertion(rdfs:label "material component separation"@en) +SubClassOf( ) # Class: (dialysis) @@ -149,7 +127,7 @@ AnnotationAssertion( "PERSON:Kevin Clancy"@en) AnnotationAssertion( "OBI branch derived"@en) AnnotationAssertion(rdfs:label "dialysis"@en) -SubClassOf( ) +SubClassOf( ) ) \ No newline at end of file diff --git a/src/ontology/imports/omo_import.owl b/src/ontology/imports/omo_import.owl index 2afbecc..c14ac57 100644 --- a/src/ontology/imports/omo_import.owl +++ b/src/ontology/imports/omo_import.owl @@ -12,9 +12,9 @@ Prefix(oboInOwl:=) Ontology( - -Annotation(dc:source ) -Annotation(owl:versionInfo "2025-08-13") + +Annotation(dc:source ) +Annotation(owl:versionInfo "2026-06-07") Declaration(Class(obo:IAO_0000027)) Declaration(Class(obo:IAO_0000030)) @@ -113,6 +113,7 @@ Declaration(AnnotationProperty(obo:OMO_0003009)) Declaration(AnnotationProperty(obo:OMO_0003010)) Declaration(AnnotationProperty(obo:OMO_0003011)) Declaration(AnnotationProperty(obo:OMO_0003012)) +Declaration(AnnotationProperty(obo:OMO_0003014)) Declaration(AnnotationProperty(obo:OMO_0004000)) Declaration(AnnotationProperty(dc:contributor)) Declaration(AnnotationProperty(dc:coverage)) @@ -267,13 +268,14 @@ AnnotationAssertion(rdfs:label obo:IAO_0000232 "curator note"@en) # Annotation Property: obo:IAO_0000233 (term tracker item) AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000233 "term tracker item"@en) -AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000233 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) +AnnotationAssertion(obo:IAO_0000112 obo:IAO_0000233 "the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588"@en) AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000233 obo:IAO_0000125) -AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000233 "An IRI or similar locator for a request or discussion of an ontology term."@en) +AnnotationAssertion(obo:IAO_0000115 obo:IAO_0000233 "A URL for a request or discussion of an ontology term."@en) AnnotationAssertion(obo:IAO_0000117 obo:IAO_0000233 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) AnnotationAssertion(obo:IAO_0000119 obo:IAO_0000233 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) AnnotationAssertion(rdfs:comment obo:IAO_0000233 "The 'tracker item' can associate a tracker with a specific ontology term."@en) AnnotationAssertion(rdfs:label obo:IAO_0000233 "term tracker item"@en) +AnnotationPropertyRange(obo:IAO_0000233 xsd:anyURI) # Annotation Property: obo:IAO_0000234 (ontology term requester) @@ -526,7 +528,7 @@ AnnotationAssertion(rdfs:label obo:OMO_0002001 "preferred label for community") # Annotation Property: obo:OMO_0003000 (abbreviation) AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003000 "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)") -AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003000 "A synonym type for describing abbreviations or initalisms") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003000 "A synonym type for describing abbreviations or initialisms") AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003000 ) AnnotationAssertion(terms:contributor obo:OMO_0003000 ) AnnotationAssertion(terms:created obo:OMO_0003000 "2023-03-03"^^xsd:date) @@ -650,6 +652,15 @@ AnnotationAssertion(terms:created obo:OMO_0003012 "2023-11-01"^^xsd:date) AnnotationAssertion(rdfs:label obo:OMO_0003012 "acronym") SubAnnotationPropertyOf(obo:OMO_0003012 oboInOwl:SynonymTypeProperty) +# Annotation Property: obo:OMO_0003014 (has ontology hierarchical property) + +AnnotationAssertion(obo:IAO_0000112 obo:OMO_0003014 "The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: ` a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`.") +AnnotationAssertion(obo:IAO_0000115 obo:OMO_0003014 "Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf.") +AnnotationAssertion(obo:IAO_0000233 obo:OMO_0003014 ) +AnnotationAssertion(terms:contributor obo:OMO_0003014 ) +AnnotationAssertion(terms:created obo:OMO_0003014 "2025-09-17"^^xsd:date) +AnnotationAssertion(rdfs:label obo:OMO_0003014 "has ontology hierarchical property") + # Annotation Property: obo:OMO_0004000 (has symbol) AnnotationAssertion(obo:IAO_0000112 obo:OMO_0004000 "A serial number such as \"12324X\"; a stop sign; a written proper name such as \"OBI") @@ -710,10 +721,10 @@ SubAnnotationPropertyOf(oboInOwl:hasRelatedSynonym obo:IAO_0000118) # Classes ############################ -# Class: obo:IAO_0000027 (data item) +# Class: obo:IAO_0000027 (data entity) -AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000027 "data item"@en) -AnnotationAssertion(rdfs:label obo:IAO_0000027 "data item"@en) +AnnotationAssertion(obo:IAO_0000111 obo:IAO_0000027 "data entity"@en) +AnnotationAssertion(rdfs:label obo:IAO_0000027 "data entity"@en) SubClassOf(obo:IAO_0000027 obo:IAO_0000030) # Class: obo:IAO_0000030 (information content entity) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index d48f9ff..3858721 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2025-07-02") + +Annotation( ) +Annotation(owl:versionInfo "2026-06-07") Declaration(Class()) Declaration(Class()) @@ -27,8 +27,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(ObjectProperty()) @@ -111,6 +110,8 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -164,6 +165,44 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -173,6 +212,7 @@ Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -185,11 +225,13 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:comment)) Declaration(AnnotationProperty(rdfs:label)) ############################ @@ -329,6 +371,20 @@ AnnotationAssertion( "Add as annotation triples in the granting ontology"@en) AnnotationAssertion(rdfs:label "term replaced by"@en) +# Annotation Property: (has_broad_synonym) + +AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has broad synonym"@en) +AnnotationAssertion(rdfs:label "has_broad_synonym") + +# Annotation Property: (has exact synonym) + +AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has exact synonym"@en) +AnnotationAssertion(rdfs:label "has_exact_synonym") + ############################ # Object Properties @@ -674,7 +730,7 @@ FunctionalObjectProperty() # Object Property: (before or simultaneous with) -AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) AnnotationAssertion( "<="@en) AnnotationAssertion(rdfs:comment "Primitive instance level timing relation between events") AnnotationAssertion(rdfs:label "before or simultaneous with"@en) @@ -682,7 +738,7 @@ SubObjectPropertyOf( (before) -AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)"@en) AnnotationAssertion(rdfs:label "before"@en) SubObjectPropertyOf( ) @@ -690,7 +746,7 @@ TransitiveObjectProperty() # Object Property: (ends after) -AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)"@en) AnnotationAssertion(rdfs:label "ends after"@en) SubObjectPropertyOf( ) @@ -698,7 +754,7 @@ TransitiveObjectProperty() # Object Property: (immediately preceded by) -AnnotationAssertion( "David Osumi-Sutherland") +AnnotationAssertion( ) AnnotationAssertion( "starts_at_end_of") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) AnnotationAssertion(rdfs:label "immediately preceded by"@en) @@ -708,7 +764,6 @@ InverseObjectProperties( (immediately precedes) AnnotationAssertion( ) -AnnotationAssertion( "David Osumi-Sutherland") AnnotationAssertion( "ends_at_start_of") AnnotationAssertion( "meets") AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) @@ -827,7 +882,6 @@ ObjectPropertyRange( ) AnnotationAssertion( "inverse of starts with") AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "Allen") AnnotationAssertion(rdfs:label "starts"@en) SubObjectPropertyOf( ) @@ -840,7 +894,6 @@ AnnotationAssertion( ) AnnotationAssertion( "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "started by") AnnotationAssertion(rdfs:label "starts with"@en) SubObjectPropertyOf( ) @@ -852,7 +905,6 @@ TransitiveObjectProperty() AnnotationAssertion( ) AnnotationAssertion( "inverse of ends with") AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") AnnotationAssertion(rdfs:label "ends"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -863,7 +915,6 @@ InverseObjectProperties( ) AnnotationAssertion( "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") AnnotationAssertion( ) -AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "finished by") AnnotationAssertion(rdfs:label "ends with"@en) SubObjectPropertyOf( ) @@ -1144,6 +1195,28 @@ AnnotationAssertion(rdfs:label "imme SubObjectPropertyOf( ) SubObjectPropertyOf( ) +# Object Property: (provides input for) + +AnnotationAssertion( "p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c.") +AnnotationAssertion( ) +AnnotationAssertion( "directly provides input for") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "provides input for"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (transitively provides input for) + +AnnotationAssertion( ) +AnnotationAssertion( "transitive form of directly_provides_input_for") +AnnotationAssertion( ) +AnnotationAssertion( "This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'.") +AnnotationAssertion(rdfs:label "transitively provides input for"@en) +SubObjectPropertyOf( ) +TransitiveObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (causally upstream of or within) AnnotationAssertion( "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q.") @@ -1203,6 +1276,7 @@ AnnotationAssertion( ) Annotation( ) "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.") AnnotationAssertion( ) AnnotationAssertion( "executes activity in") +AnnotationAssertion( "enables activity in") AnnotationAssertion(rdfs:label "is active in") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1214,6 +1288,7 @@ AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") +AnnotationAssertion( "in pairwise interaction with") AnnotationAssertion(rdfs:label "interacts with") SymmetricObjectProperty() ObjectPropertyDomain( ) @@ -1244,6 +1319,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( "molecularly controls") AnnotationAssertion(rdfs:label "directly regulates activity of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1257,6 +1333,7 @@ For example, A and B may be gene products and binding of B by A negatively regul AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "directly inhibits") +AnnotationAssertion( "molecularly decreases activity of") AnnotationAssertion(rdfs:label "directly negatively regulates activity of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -1269,6 +1346,7 @@ For example, A and B may be gene products and binding of B by A positively regul AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "directly activates") +AnnotationAssertion( "molecularly increases activity of") AnnotationAssertion(rdfs:label "directly positively regulates activity of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -1509,6 +1587,7 @@ AnnotationAssertion( "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") AnnotationAssertion( "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.") AnnotationAssertion( "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") +AnnotationAssertion(Annotation( ) "triggered by process") AnnotationAssertion(rdfs:label "realized in response to"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -1523,6 +1602,7 @@ AnnotationAssertion( "This pdf file generically depends on this server.") AnnotationAssertion( "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*.") AnnotationAssertion( "[072-ISO]") +AnnotationAssertion( "g-depends on") AnnotationAssertion(rdfs:label "generically depends on") InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -1567,6 +1647,7 @@ AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) # Object Property: (regulates characteristic) @@ -1686,6 +1767,7 @@ SubClassOf( "GOC:pdt") "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs.") AnnotationAssertion( "This is the same as GO molecular function"@en) +AnnotationAssertion( "molecular function") AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.") AnnotationAssertion(rdfs:label "gene product or complex activity"@en) AnnotationAssertion(rdfs:label "molecular_function") @@ -1695,17 +1777,19 @@ SubClassOf( "GOC:pdt") "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.") AnnotationAssertion( "Wikipedia:Biological_process") +AnnotationAssertion( "biological process") +AnnotationAssertion( "physiological process") AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") AnnotationAssertion(rdfs:label "biological process"@en) AnnotationAssertion(rdfs:label "biological_process") SubClassOf( ) -DisjointClasses( ) # Class: (kinase activity) AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") AnnotationAssertion(Annotation(rdfs:label "FN3KRP phosphorylates PsiAm, RibAm") "Reactome:R-HSA-6788855") AnnotationAssertion(Annotation(rdfs:label "FN3K phosphorylates ketosamines") "Reactome:R-HSA-6788867") +AnnotationAssertion( "phosphokinase activity") AnnotationAssertion(rdfs:comment "Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.") AnnotationAssertion(rdfs:label "kinase activity") SubClassOf( ) @@ -1723,39 +1807,11 @@ AnnotationAssertion( "curation status specification"@en) EquivalentClasses( ObjectOneOf( )) -# Class: (planned process) - -AnnotationAssertion( "planned process") -AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") -AnnotationAssertion( ) -AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) -AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") -AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process.") -AnnotationAssertion( "Bjoern Peters") -AnnotationAssertion( "branch derived") -AnnotationAssertion( "6/11/9: Edited at workshop. Used to include: is initiated by an agent") -AnnotationAssertion( "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)"@en) -AnnotationAssertion(rdfs:label "planned process"@en) -SubClassOf( ) - -# Class: (organism) - -AnnotationAssertion( "organism"@en) -AnnotationAssertion( "animal"@en) -AnnotationAssertion( "fungus"@en) -AnnotationAssertion( "plant"@en) -AnnotationAssertion( "virus"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) -AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") -AnnotationAssertion( "13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI.") -AnnotationAssertion( "GROUP: OBI Biomaterial Branch") -AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) -AnnotationAssertion(rdfs:label "organism"@en) -SubClassOf( ) +# Class: (disease) + +AnnotationAssertion( "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism."@en) +AnnotationAssertion(rdfs:label "disease") +SubClassOf( ) # Class: (quality) @@ -1777,6 +1833,288 @@ SubClassOf( (Western Australian Mulga Shrublands Ecoregion) + +AnnotationAssertion( "Western Australia Ecoregion") +AnnotationAssertion( "WWF:AA1310") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1310") +AnnotationAssertion(rdfs:label "Western Australian Mulga Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Australasia Ecoregion) + +AnnotationAssertion( "https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands") +AnnotationAssertion(rdfs:label "Australasia Ecoregion"@en) + +# Individual: (Tirari-Sturt Stony Desert Ecoregion) + +AnnotationAssertion( "Southern central Australia Ecoregion"@en) +AnnotationAssertion( "WWF:AA1309") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1309") +AnnotationAssertion(rdfs:label "Tirari-Sturt Stony Desert Ecoregion") +ObjectPropertyAssertion( ) + +# Individual: (Simpson Desert Region) + +AnnotationAssertion( "Eastern central Australia Ecoregion") +AnnotationAssertion( "WWF:AA1308") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1308") +AnnotationAssertion(rdfs:label "Simpson Desert Region"@en) +ObjectPropertyAssertion( ) + +# Individual: (Pilbara Shrublands Ecoregion) + +AnnotationAssertion( "Western Australia Ecoregion") +AnnotationAssertion( "WWF:AA1307") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1307") +AnnotationAssertion(rdfs:label "Pilbara Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Carnarvon Xeric Shrublands Ecoregion) + +AnnotationAssertion( "Western coast of Australia Ecoregion") +AnnotationAssertion( "WWF:AA1301") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1301") +AnnotationAssertion(rdfs:label "Carnarvon Xeric Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Central Ranges Xeric Shrub Ecoregion) + +AnnotationAssertion( "Central Australia Ecoregion") +AnnotationAssertion( "WWF:AA1302") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1302") +AnnotationAssertion(rdfs:label "Central Ranges Xeric Shrub Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Gibson Desert Ecoregion) + +AnnotationAssertion( "Western central Australia") +AnnotationAssertion( "WWF:AA1303") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1303") +AnnotationAssertion(rdfs:label "Gibson Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (The Great Sandy-Tanami Desert Ecoregion) + +AnnotationAssertion( "Northwestern Australia") +AnnotationAssertion( "WWF:AA1304") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1304") +AnnotationAssertion(rdfs:label "The Great Sandy-Tanami Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Great Victoria Desert Ecoregion) + +AnnotationAssertion( "Southern Australia Ecoregion") +AnnotationAssertion( "WWF:AA1305") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1305") +AnnotationAssertion(rdfs:label "Great Victoria Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Nullarbor Plains Xeric Shrubland Ecoregion) + +AnnotationAssertion( "Southern Australia Ecoregion") +AnnotationAssertion( "WWF:AA1306") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/aa1306") +AnnotationAssertion(rdfs:label "Nullarbor Plains Xeric Shrubland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Afrotropical Ecoregion) + +AnnotationAssertion( "https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands") +AnnotationAssertion(rdfs:label "Afrotropical Ecoregion"@en) + +# Individual: (Succulent Karoo Ecoregion) + +AnnotationAssertion( "Southern Africa: Southern Namibia into South Africa") +AnnotationAssertion( "WWF:AT1322") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1322") +AnnotationAssertion(rdfs:label "Succulent Karoo Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Yemen and Saudi Arabia Ecoregion) + +AnnotationAssertion( "WWF:AT1321") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1321") +AnnotationAssertion( "Arabian Peninsula: Yemen and Saudi Arabia") +AnnotationAssertion(rdfs:label "Yemen and Saudi Arabia Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Yemen, Saudi Arabia, and Oman Ecoregion) + +AnnotationAssertion( "WWF:AT1320") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1320") +AnnotationAssertion( "Arabian Peninsula: Yemen, Saudi Arabia, and Oman") +AnnotationAssertion(rdfs:label "Yemen, Saudi Arabia, and Oman Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Somali Montane Xeric Woodland Ecoregion) + +AnnotationAssertion( "WWF:AT1319") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1319") +AnnotationAssertion( "Somali montane xeric woodlands ecoregion") +AnnotationAssertion(rdfs:label "Somali Montane Xeric Woodland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Socotran Archipelago Ecoregion) + +AnnotationAssertion( "Islands east of the Horn of Africa and south of Yemen Ecoregion") +AnnotationAssertion( "WWF:AT1318") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1318") +AnnotationAssertion(rdfs:label "Socotran Archipelago Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Red Sea Coastal Desert Ecoregion) + +AnnotationAssertion( "WWF:AT1317") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1317") +AnnotationAssertion(rdfs:label "Red Sea Coastal Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Namibian Savanna Woodland Ecoregion) + +AnnotationAssertion( "WWF:AT1316") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1316") +AnnotationAssertion(rdfs:label "Namibian Savanna Woodland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Namib Desert Ecoregion) + +AnnotationAssertion( "Africa: Namibia Ecoregion") +AnnotationAssertion( "WWF:AT1315") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1315") +AnnotationAssertion(rdfs:label "Namib Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Nama Karoo Ecoregion) + +AnnotationAssertion( "WWF:AT1314") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1314") +AnnotationAssertion(rdfs:label "Nama Karoo Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Masai Xeric Grasslands and Shrublands Ecoregion) + +AnnotationAssertion( "WWF:AT1313") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1313") +AnnotationAssertion(rdfs:label "Masai Xeric Grasslands and Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Madagascar Succulent Woodlands Ecoregion) + +AnnotationAssertion( "WWF:AT1312") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1312") +AnnotationAssertion(rdfs:label "Madagascar Succulent Woodlands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Madagascar Spiny Thickets Ecoregion) + +AnnotationAssertion( "WWF:AT1311") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1311") +AnnotationAssertion( "Madagascar spiny desert ecoregion") +AnnotationAssertion(rdfs:label "Madagascar Spiny Thickets Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Kaokoveld Desert Ecoregion) + +AnnotationAssertion( "WWF:AT1310") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1310") +AnnotationAssertion( "Africa: Coastal Namibia and Angola Ecoregion") +AnnotationAssertion(rdfs:label "Kaokoveld Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Kalahari Xeric Savanna Ecoregion) + +AnnotationAssertion( "WWF:AT1309") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1309") +AnnotationAssertion(rdfs:label "Kalahari Xeric Savanna Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Ile Europa and Bassas da India Ecoregion) + +AnnotationAssertion( "WWF:AT1308") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1308") +AnnotationAssertion( "Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion") +AnnotationAssertion(rdfs:label "Ile Europa and Bassas da India Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Hobyo Grassland and Shrubland Ecoregion) + +AnnotationAssertion( "Eastern Africa: Somalia") +AnnotationAssertion( "WWF:AT1307") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1307") +AnnotationAssertion(rdfs:label "Hobyo Grassland and Shrubland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Oman and United Arab Emirates Ecoregion) + +AnnotationAssertion( "WWF:AT1306") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1306") +AnnotationAssertion( "Arabian Peninsula: Oman and United Arab Emirates Ecoregion") +AnnotationAssertion(rdfs:label "Oman and United Arab Emirates Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Ethiopian Xeric Grasslands and Shrublands Ecoregion) + +AnnotationAssertion( "WWF:AT1305") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1305") +AnnotationAssertion(rdfs:label "Ethiopian Xeric Grasslands and Shrublands Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Eritrean Coastal Desert Ecoregion) + +AnnotationAssertion( "WWF:AT1304") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1304") +AnnotationAssertion(rdfs:label "Eritrean Coastal Desert Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (East Saharan Montane Xeric Woodland Ecoregion) + +AnnotationAssertion( "WWF:AT1303") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1303") +AnnotationAssertion( "North central Africa: Eastern Chad and small area of western Sudan") +AnnotationAssertion(rdfs:label "East Saharan Montane Xeric Woodland Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Oman, Yemen, and Saudi Arabia Ecoregion) + +AnnotationAssertion( "WWF:AT1302") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1302") +AnnotationAssertion( "Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion") +AnnotationAssertion(rdfs:label "Oman, Yemen, and Saudi Arabia Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Aldabra Island Xeric Scrub Ecoregion) + +AnnotationAssertion( "WWF:AT1301") +AnnotationAssertion( "https://www.worldwildlife.org/ecoregions/at1301") +AnnotationAssertion(rdfs:label "Aldabra Island Xeric Scrub Ecoregion"@en) +ObjectPropertyAssertion( ) + +# Individual: (Indo-Malay Ecoregion) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "Indo-Malay Ecoregion"@en) + +# Individual: (Thar Desert) + +AnnotationAssertion( ) +AnnotationAssertion( "WWF:IM1304") +AnnotationAssertion(rdfs:label "Thar Desert"@en) +ObjectPropertyAssertion( ) + +# Individual: (Northwestern Thorn Scrub Forests) + +AnnotationAssertion( ) +AnnotationAssertion( "WWF:IM1303") +AnnotationAssertion(rdfs:label "Northwestern Thorn Scrub Forests"@en) +ObjectPropertyAssertion( ) + +# Individual: (Solar radiation) + +AnnotationAssertion( "Stellar radiation emitted from Sol.") +AnnotationAssertion(rdfs:label "Solar radiation"@en) +ObjectPropertyAssertion( ) + # Individual: (example to be eventually removed) AnnotationAssertion( "example to be eventually removed"@en) @@ -1791,7 +2129,7 @@ AnnotationAssertion(rdfs:label "met # Individual: (organizational term) AnnotationAssertion( "organizational term"@en) -AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion( "The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release."@en) AnnotationAssertion(rdfs:label "organizational term"@en) # Individual: (ready for release) @@ -1874,6 +2212,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -1908,7 +2247,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) @@ -1919,17 +2258,17 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/mirror/iao.owl b/src/ontology/mirror/iao.owl index 2e2f9b4..14b867d 100644 --- a/src/ontology/mirror/iao.owl +++ b/src/ontology/mirror/iao.owl @@ -7,6 +7,7 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" @@ -15,7 +16,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Adam Goldstein Alan Ruttenberg @@ -23,6 +24,7 @@ Barry Smith Bjoern Peters Carlo Torniai + Charles Tapley Hoyt Chris Mungall Chris Stoeckert Christian A. Boelling @@ -60,7 +62,7 @@ IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 - 2022-11-07 + 2026-03-30 @@ -182,7 +184,7 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> @@ -230,6 +232,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + alternative label @@ -279,13 +282,14 @@ We also have the outstanding issue of how to aim different definitions to differ term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588 - An IRI or similar locator for a request or discussion of an ontology term. + A URL for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + @@ -638,11 +642,229 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + + 2025-06-02 + preferred label for community + + + + + + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) + A synonym type for describing abbreviations or initialisms + + + 2023-03-03 + abbreviation + + + + + + + + + A synonym type for describing ambiguous synonyms + + + 2023-03-03 + ambiguous synonym + + + + + + + + + A synonym type for describing dubious synonyms + + + 2023-03-03 + dubious synonym + + + + + + + + + EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) + A synonym type for describing layperson or colloquial synonyms + + + 2023-03-03 + layperson synonym + + + + + + + + + CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) + A synonym type for describing pluralization synonyms + + + 2023-03-03 + plural form + + + + + + + + + CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) + A synonym type for describing UK spelling variants + + + 2023-03-03 + UK spelling synonym + + + + + + + + + A synonym type for common misspellings + + + 2023-03-03 + misspelling + + + + + + + + + A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + + + 2023-03-03 + misnomer + + + + + + + + + MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. + A synonym type for names that have been used as primary labels in the past. + + + 2023-07-25 + previous name + + + + + + + + + The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College + A synonym type for the legal entity name + + + 2023-07-27 + legal name + + + + + + + + + CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label + The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + + + 2023-09-30 + INN + International Nonproprietary Name + + + + + + + + + nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis + A synonym type for describing Latin term synonyms. + + + 2023-10-12 + latin term + + + + + + + + + NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. + A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + + + 2023-11-01 + acronym + + + + + + + + + The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`. + Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf. + + + 2025-09-17 + has ontology hierarchical property + + + + + + + + A serial number such as "12324X"; a stop sign; a written proper name such as "OBI + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + + + 2024-03-25 + has symbol + + + + An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation + temporal interpretation @@ -695,6 +917,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + @@ -743,12 +971,36 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + + + + + + + + + + + @@ -774,6 +1026,19 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string + An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. + + + 2024-03-18 + has cross-reference + + + + @@ -855,6 +1120,23 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] + + + + + + + + + + + + + + One of my mental representations is directed towards the Pacific Ocean. + + A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality. + person: William Hogan + https://ceur-ws.org/Vol-1515/regular10.pdf + + In the definition source, the relation is called 'is_about'. To avoid confusion with the existing "is about" relation in IAO, we called it 'is directed towards' per Alan Ruttenberg's suggestion. + is directed towards + + + + @@ -1308,25 +1605,20 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - has_specified_input - has_specified_input + + + has specified input see is_input_of example_of_usage - The inverse property of is_specified_input_of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot - has_specified_input + has specified input @@ -1334,7 +1626,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - is_specified_input_of + is specified input of @@ -1342,23 +1634,18 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - has_specified_output - has_specified_output + + + has specified output - The inverse property of is_specified_output_of + The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot - has_specified_output + has specified output @@ -1367,15 +1654,14 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - is_specified_output_of - is_specified_output_of + + is specified output of - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters - is_specified_output_of + is specified output of @@ -1444,7 +1730,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -1455,10 +1741,17 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. + A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes. is concretized as @@ -1467,11 +1760,18 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + + + + + + + + A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. + A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant. concretizes @@ -1673,7 +1973,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in - http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in @@ -1852,7 +2152,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + @@ -1867,7 +2167,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + A planned process that has specified output a software product and that involves the creation of source code. Mathias Brochhausen William R. Hogan @@ -1907,7 +2207,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + @@ -1915,7 +2215,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + The planned process of finding the number of elements in a finite set of objects. Mathias Brochhausen http://en.wikipedia.org/wiki/Counting @@ -2001,7 +2301,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + @@ -2009,7 +2309,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - + creating a data set A planned process that has a data set as its specified output. William R. Hogan @@ -2232,6 +2532,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant @@ -2442,6 +2743,24 @@ Werner suggests a solution based on "Magnitudes" a proposal for which spatiotemporal region + + + + Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) + + + + + + Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) + + + + + + Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) + + @@ -2484,24 +2803,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - @@ -2521,6 +2822,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process @@ -2726,6 +3028,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -3023,6 +3326,7 @@ Werner suggests a solution based on "Magnitudes" a proposal for which the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. generically dependent continuant @@ -3481,6 +3785,29 @@ Werner suggests a solution based on "Magnitudes" a proposal for which + + + + + completely executed planned process + + completely executed planned process + + + + + + + + + planned process + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + + planned process + + + + @@ -3628,8 +3955,8 @@ interpreted by or directly executed by a processing unit. Superclass was 'digitial quality' person:Chris Stoeckert - group:OBI OBI_0000261 + group:OBI obsolete2_digital entity true @@ -3731,8 +4058,8 @@ Superclass was 'digitial quality' Superclass was 'digital entity' digital_entity person:Chris Stoeckert - group:OBI OBI_0000244 + group:OBI obsolete2_binary digital entity true @@ -3776,10 +4103,10 @@ Superclass was 'digital entity' - data item + data entity Data items include counts of things, analyte concentrations, and statistical summaries. - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. @@ -3795,7 +4122,8 @@ JAR: A data item is an approximately justified approximately true approximate be PERSON: Chris Stoeckert PERSON: Jonathan Rees data - data item + data item + data entity @@ -3942,12 +4270,12 @@ this case we explicitly refer to the singular form obsolete_study interpretation A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses - The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. Lawrence Hunter - PERSON: Jennifer Fostel PERSON: Alan Ruttenberg + PERSON: Jennifer Fostel PERSON: Melanie Courtot conclusion OBI_0000005 @@ -4057,8 +4385,8 @@ superclass was 'digital document' Replaced by defined version of figure person:Alan Ruttenberg person:Allyson Lister - group:OBI OBI_0000027 + group:OBI obsolete2_report figure true @@ -4184,12 +4512,12 @@ whole sentence is deleted. report element A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). - There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text 2009-03-16: needs some more work (clarify relations). 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion Replaced by textual entity and figure + There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text PERSON: Alan Ruttenberg PERSON: Allyson Lister PERSON: Melanie Courtot @@ -4211,8 +4539,8 @@ whole sentence is deleted. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity' person:Jennifer Fostel - group:OBI OBI_0000222 + group:OBI obsolete2_binary executable true @@ -4247,8 +4575,8 @@ superclass was 'digital entity' 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion person:Alan Ruttenberg person:Allyson Lister - group:OBI OBI_0000265 + group:OBI obsolete_report table true @@ -4271,6 +4599,7 @@ XML document; The instructions in a XSD file" PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 + data format specification @@ -4279,8 +4608,8 @@ XML document; The instructions in a XSD file" - - data set + + homogenous data collection Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. @@ -4288,9 +4617,9 @@ XML document; The instructions in a XSD file" 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert - OBI_0000042 + data set group:OBI - data set + homogenous data collection @@ -4374,8 +4703,8 @@ Request that IAO either clarify these or change definitions not to use them3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity' person:Jennifer Fostel - group:OBI OBI_0000195 + group:OBI obsolete2_digital document true @@ -5603,7 +5932,7 @@ GO gene ontology - + @@ -5627,7 +5956,7 @@ GO gene ontology - + A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. Person: Jie Zheng @@ -5657,7 +5986,7 @@ GO gene ontology - + @@ -5702,7 +6031,7 @@ points together with a line. - + @@ -5731,7 +6060,7 @@ points together with a line. - + @@ -5858,7 +6187,7 @@ points together with a line. - + @@ -6918,7 +7247,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - + @@ -6946,6 +7275,19 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta + + + + + the section of the document where the title appears + This term should not be confused with dc:title - this term represents the component of the document where the title appears, and not the value of the title itself. + Charles Tapley Hoyt + https://github.com/information-artifact-ontology/IAO/issues/286 + title section + + + + @@ -7090,6 +7432,21 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta + + + + + data collection + A data entity that consists of multiple data entities. + Sebastian Duesing + data set + https://github.com/information-artifact-ontology/IAO/issues/283 + https://github.com/obi-ontology/obi/issues/1877 + data collection + + + + @@ -7144,7 +7501,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - + @@ -7152,7 +7509,7 @@ Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Sta - + A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Justin Whorton Mathias Brochhausen @@ -7519,22 +7876,10 @@ No imports - - - - - planned process - A process that realizes a plan which is the concretization of a plan specification. - - planned process - - - - - + investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). @@ -7546,9 +7891,9 @@ No imports - + study design execution - a planned process that carries out a study design + a planned process that carries out a study design study design execution @@ -7558,9 +7903,9 @@ No imports - + data transformation - A planned process that produces output data from input data. + A completely executed planned process that produces output data from input data. data transformation @@ -7572,7 +7917,7 @@ No imports study design - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. + A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. study design @@ -7644,6 +7989,7 @@ No imports length unit + A unit which is a standard measure of the distance between two points. length unit @@ -7655,6 +8001,7 @@ No imports mass unit + A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit @@ -7666,6 +8013,7 @@ No imports time unit + A unit which is a standard measure of the dimension in which events occur in sequence. time unit @@ -7705,8 +8053,11 @@ No imports failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. + Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg + + failed exploratory term @@ -7728,7 +8079,7 @@ No imports organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release + The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. organizational term @@ -7797,6 +8148,10 @@ No imports placeholder removed + The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. + This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. + + placeholder removed @@ -7807,7 +8162,10 @@ No imports terms merged - An editor note should explain what were the merged terms and the reason for the merge. + The term has been combined with one or more other terms to create a more encompassing (merged) term. + The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. + + terms merged @@ -7818,7 +8176,10 @@ No imports term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + The term has been replaced by a term imported from another ontology. + This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. + + term imported @@ -7829,7 +8190,10 @@ No imports term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + The term has been split into two or more new terms. + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001. + + term split @@ -7916,15 +8280,31 @@ No imports The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 + + out of scope + + + + + The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. + This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). + + https://github.com/information-artifact-ontology/ontology-metadata/issues/136 + https://orcid.org/0000-0002-4142-7153 + domain entity does not exist + + + + - + - + @@ -7981,8 +8361,8 @@ No imports - - + + @@ -7992,7 +8372,7 @@ No imports - + @@ -8007,8 +8387,8 @@ No imports - - + + @@ -8024,8 +8404,8 @@ No imports - - + + @@ -8035,7 +8415,7 @@ No imports - + @@ -8050,8 +8430,8 @@ No imports - - + + @@ -8067,8 +8447,8 @@ No imports - - + + @@ -8078,7 +8458,7 @@ No imports - + @@ -8093,8 +8473,8 @@ No imports - - + + @@ -8110,8 +8490,8 @@ No imports - - + + @@ -8121,7 +8501,7 @@ No imports - + @@ -8136,8 +8516,8 @@ No imports - - + + diff --git a/src/ontology/mirror/obi.owl b/src/ontology/mirror/obi.owl index 3478afb..7054a46 100644 --- a/src/ontology/mirror/obi.owl +++ b/src/ontology/mirror/obi.owl @@ -7,15 +7,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -82,7 +79,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2025-05-01 + 2026-05-08 @@ -104,32 +101,10 @@ - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - + editor preferred label editor preferred label editor preferred term editor preferred term @@ -138,7 +113,7 @@ The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - + editor preferred label editor preferred label editor preferred term editor preferred term @@ -155,7 +130,6 @@ A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - example of usage @@ -192,8 +166,11 @@ definition textual definition + A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. + English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition. 2012-04-05: Barry Smith @@ -216,7 +193,6 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition definition textual definition @@ -232,7 +208,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note @@ -247,7 +222,6 @@ We also have the outstanding issue of how to aim different definitions to differ 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - term editor @@ -263,9 +237,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - alternative term @@ -279,7 +251,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source @@ -304,7 +275,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg - curator note @@ -314,13 +284,14 @@ We also have the outstanding issue of how to aim different definitions to differ term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588 - An IRI or similar locator for a request or discussion of an ontology term. + A URL for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + @@ -360,7 +331,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - imported from @@ -509,7 +479,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - elucidation @@ -522,7 +491,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language - has associated axiom(nl) @@ -535,7 +503,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax - has associated axiom(fol) @@ -600,7 +567,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label @@ -720,11 +686,24 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + + 2025-06-02 + preferred label for community + + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) - A synonym type for describing abbreviations or initalisms + A synonym type for describing abbreviations or initialisms 2023-03-03 @@ -899,6 +878,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`. + Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf. + + + 2025-09-17 + has ontology hierarchical property + + + + @@ -912,12 +904,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1051,12 +1037,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1185,6 +1165,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + @@ -1194,12 +1180,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1295,17 +1275,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - label + label + A human readable name for this class. label + label @@ -1316,12 +1293,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + realized in @@ -1456,13 +1394,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1471,15 +1403,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - preceded by - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + preceded by @@ -1488,50 +1415,43 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + precedes - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in + + + + executed by + + + + + + + + intended to realize + + + + + + + + has plan - + - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + intended plan process type @@ -1539,10 +1459,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has measurement unit label - + has measurement unit label @@ -1551,9 +1469,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is about + A (currently) primitive relation that relates an information artifact to an entity. - is about @@ -1563,9 +1480,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - denotes + + A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - denotes @@ -1575,9 +1492,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is quality measurement of + m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - is quality measurement of @@ -1586,9 +1502,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - denoted by + inverse of the relation 'denotes' - denoted by @@ -1597,10 +1512,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has coordinate unit label - has coordinate unit label @@ -1610,9 +1522,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is duration of + relates a process to a time-measurement-datum that represents the duration of the process - is duration of @@ -1654,11 +1565,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has specified input see is_input_of example_of_usage - The inverse property of is specified input of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters @@ -1690,11 +1601,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified input of @@ -1743,10 +1654,10 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - + has specified output - The inverse property of is specified output of + The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter @@ -1910,10 +1821,10 @@ instance level relation [GOC:cjm] - + is specified output of - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified output of @@ -2011,7 +1922,7 @@ level of radioactivity is_proxy_for level of toxicity - + achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' @@ -2130,7 +2041,7 @@ level of radioactivity is_proxy_for level of toxicity - + objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. @@ -2255,15 +2166,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + - @@ -2377,15 +2288,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2394,16 +2297,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - has characteristic @@ -2412,15 +2306,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in participates in @@ -2429,16 +2315,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -2447,11 +2324,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as @@ -2461,10 +2333,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes @@ -2474,15 +2342,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this catalysis function is a function of this enzyme + function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of @@ -2491,14 +2353,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this red color is a quality of this apple + quality of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of @@ -2507,14 +2364,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this investigator role is a role of this person + role of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of @@ -2523,13 +2375,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + has function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function + has function @@ -2538,12 +2386,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this apple has quality this red color + has quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality + has quality @@ -2552,13 +2397,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) + has role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role + has role @@ -2567,11 +2408,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - + has disposition a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition @@ -2580,8 +2419,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + inverse of has disposition + disposition of @@ -2590,47 +2430,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - derives from - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - + derives from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from derives from - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - location of @@ -2640,97 +2451,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in + located in - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately preceded by @@ -2739,11 +2472,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - David Osumi-Sutherland - ends_at_start_of - meets - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + immediately precedes @@ -2752,14 +2482,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + has component w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - + has component - @@ -2767,11 +2493,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + capable of A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - has function realized in - capable of + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + capable of @@ -2779,9 +2506,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - surrounded by - x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y + surrounded by + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x surrounded by @@ -2796,15 +2522,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + inverse of surrounded by + surrounds + + + + - - - move to BFO? - Allen - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporal relation + temporally related to + + temporally related to @@ -2812,61 +2544,50 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + starts inverse of starts with - Chris Mungall - Allen + starts - + - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input - + - - - - has member is a mereological relation between a collection and an item. - SIO - - has member + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + has output - + - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true + + inverse of enables + enabled by - + - - DEPRECATED bearer of - true + + + has member + has member is a mereological relation between a collection and an item. + + has member @@ -2888,17 +2609,47 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - - has measurement value - - has measurement value + + has quantity + + + + + Number of protons in an atomic nucleus + has atomic number + + + + + + + + + has number of atomic nuclei + + + + + + + + has inchi string + + + + + + + + + + @@ -2972,518 +2723,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - + process - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - @@ -3491,226 +2736,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - disposition - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - + realizable entity - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - - specifically dependent continuant - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - @@ -3718,183 +2754,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - role - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - @@ -3902,105 +2763,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - site - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - @@ -4008,439 +2772,40 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - function - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - material - MaterialEntity + material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - material entity - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - + immaterial entity - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - + - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history + + + Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. + electron - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - @@ -4449,7 +2814,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ insulin - A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. + A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the β cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. insulin @@ -4459,7 +2824,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + water An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms @@ -4471,7 +2836,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ATP An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. @@ -4491,7 +2856,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ biotin - An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. + An organic heterobicyclic compound that consists of 2-oxohexahydro-1<em>H</em>-thieno[3,4-<em>d</em>]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin @@ -4501,9 +2866,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cholesterol - A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. + A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3β-hydroxy group. cholesterol @@ -4513,7 +2878,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ammonia An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. @@ -4525,7 +2890,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phospholipid A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. @@ -4537,7 +2902,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + nitrite The nitrogen oxoanion formed by loss of a proton from nitrous acid. @@ -4549,9 +2914,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + carbon dioxide - A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. + A one-carbon compound with formula CO<small><sub>2</sub></small> in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. carbon dioxide @@ -4563,7 +2928,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ peptide - Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. + Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide @@ -4573,7 +2938,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + globulin type One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. @@ -4585,7 +2950,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatinine A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. @@ -4597,9 +2962,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + mycophenolic acid - A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. + A member of the class of 2-benzofurans that is 2-benzofuran-1(3<em>H</em>)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2<i>E</i>)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by <em>Penicillium brevi-compactum, P. stoloniferum, P. echinulatum</em> and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. mycophenolic acid @@ -4609,7 +2974,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatine A glycine derivative having methyl and amidino groups attached to the nitrogen. @@ -4621,7 +2986,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bilirubin IXalpha A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. @@ -4645,9 +3010,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + progesterone - A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. + A C<small><sub>21</sub></small>-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. progesterone @@ -4657,7 +3022,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogensulfite hydrogensulfite @@ -4668,7 +3033,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + homocysteine A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. @@ -4680,7 +3045,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + glucose An aldohexose used as a source of energy and metabolic intermediate. @@ -4692,9 +3057,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + testosterone - An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. + An androstanoid having 17β-hydroxy and 3-oxo groups, together with unsaturation at C-4‒C-5.. testosterone @@ -4704,9 +3069,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methemoglobin - A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. + A hemoprotein that is the ferric (Fe<small><sup>3+</small></sup>) form of hemoglobin. methemoglobin @@ -4716,7 +3081,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogencarbonate The carbon oxoanion resulting from the removal of a proton from carbonic acid. @@ -4728,9 +3093,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. + A 17α-hydroxy-C<small><sub>21</sub></small>-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. cortisol @@ -4740,7 +3105,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5'-adenylyl sulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. @@ -4752,7 +3117,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + triglyceride Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. @@ -4764,7 +3129,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chloride A halide anion formed when chlorine picks up an electron to form an an anion. @@ -4776,7 +3141,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3-hydroxybutyric acid A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. @@ -4788,7 +3153,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bile salt A sodium salt of the conjugate of any bile acid with either glycine or taurine. @@ -4797,23 +3162,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - - molecular entity - - - - - + cytochalasin cytochalasin @@ -4824,7 +3176,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + estradiol A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. @@ -4836,21 +3188,35 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-ethyl-N-nitrosourea - A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. + A member of the class of <em>N</em>-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. N-ethyl-N-nitrosourea + + + + + hormone + Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. + + hormone + + + + - + + proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + Nuclear particle of charge number +1, spin ½ and rest mass of 1.007276470(12) u. proton @@ -4860,7 +3226,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + iron cation iron cation @@ -4871,7 +3237,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. @@ -4880,10 +3246,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + nitrogen atom + + nitrogen atom + + + + - + amikacin An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. @@ -4895,7 +3272,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. @@ -4907,7 +3284,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + uric acid An oxopurine that is the final oxidation product of purine metabolism. @@ -4919,7 +3296,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lead(0) lead(0) @@ -4930,9 +3307,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + vancomycin - A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. + A complex glycopeptide from <em>Streptomyces orientalis</em>. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria <em>Staphylococcus aureus</em> and <em>Clostridium difficile</em>. vancomycin @@ -4944,7 +3321,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ rac-lactic acid - A racemate comprising equimolar amounts of (R)- and (S)-lactic acid. + A racemate comprising equimolar amounts of (<i>R</i>)- and (<i>S</i>)-lactic acid. rac-lactic acid @@ -4954,7 +3331,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. @@ -4966,9 +3343,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dehydroepiandrosterone - An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. + An androstanoid that is androst-5-ene substituted by a β-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. dehydroepiandrosterone @@ -4978,7 +3355,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3,3',5'-triiodothyronine 3,3',5'-triiodothyronine @@ -4989,7 +3366,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tobramycin A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. @@ -5001,7 +3378,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium(1+) A monoatomic monocation obtained from sodium. @@ -5013,7 +3390,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + potassium(1+) A monoatomic monocation obtained from potassium. @@ -5025,7 +3402,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydroxyl hydroxyl @@ -5036,20 +3413,29 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + deuterium atom - The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). + The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek δευτερον, second). deuterium atom + + + + + Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. + neutron + + + + - + thyroxine An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. @@ -5061,7 +3447,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ruthenium atom ruthenium atom @@ -5069,6 +3455,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + bile acid + Any member of a group of hydroxy-5β-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5β-configuration. + + bile acid + + + + @@ -5090,7 +3488,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadodiamide hydrate The hydrate of gadodiamide. @@ -5102,7 +3500,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadoteridol A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5114,9 +3512,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phenol red - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. phenol red @@ -5126,7 +3524,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium citrate dihydrate The dihydrate of trisodium citrate. @@ -5138,7 +3536,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methyl group An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom. @@ -5147,14 +3545,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - - atom - A chemical entity constituting the smallest component of an element having the chemical properties of the element. - - atom + + + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 + atomic nucleus @@ -5162,7 +3566,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + elemental oxygen elemental oxygen @@ -5173,7 +3577,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rare earth metal atom rare earth metal atom @@ -5184,7 +3588,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rhodium atom A cobalt group element atom of atomic number 45. @@ -5196,7 +3600,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium atom gadolinium atom @@ -5207,7 +3611,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + terbium atom terbium atom @@ -5220,7 +3624,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ nucleic acid - A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), <small>D</small>-ribose or 2-deoxy-<small>D</small>-ribose and phosphoric acid. nucleic acid @@ -5242,7 +3646,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + amino acid A carboxylic acid containing one or more amino groups. @@ -5254,7 +3658,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer @@ -5267,7 +3671,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hemoglobin hemoglobin @@ -5278,7 +3682,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + fatty acid Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. @@ -5290,7 +3694,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium molecular entity gadolinium molecular entity @@ -5301,7 +3705,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phosphate ion A phosphorus oxoanion that is the conjugate base of phosphoric acid. @@ -5310,10 +3714,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + A particle smaller than an atom. + subatomic particle + + + + - + gadodiamide A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5325,9 +3740,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + folic acids - A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. + A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more <small>L</small>-glutamic acid units. folic acids @@ -5337,7 +3752,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium phosphate sodium phosphate @@ -5348,7 +3763,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5367,7 +3782,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5376,7 +3791,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ phosphorus-33 atom - The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. + The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin <small><sup>1</small></sup>/<small><sub>2</sub></small>. phosphorus-33 atom @@ -5417,6 +3832,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cytochrome P450 + + cytochrome P450 + + + + @@ -5456,7 +3882,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium cation calcium cation @@ -5467,7 +3893,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium ion calcium ion @@ -5478,7 +3904,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + magnesium cation Any magnesium ion that is positively charged. @@ -5510,7 +3936,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ digoxigenin - A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. + A hydroxy steroid that consists of 5β-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3β-, 12β- and 14β-positions. It has been isolated from the plant species of the genus <em>Digitalis</em>. digoxigenin @@ -5520,7 +3946,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA(4-) A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). @@ -5532,7 +3958,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + deoxyribonucleotide A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen. @@ -5544,9 +3970,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + digoxin - A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. + A cardenolide glycoside that is digitoxin β-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, <em>Digitalis lanata</em>, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. digoxin @@ -5567,7 +3993,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. @@ -5579,7 +4005,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + low-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). @@ -5591,7 +4017,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + high-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). @@ -5603,15 +4029,37 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chromium-51 - A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. + A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of γ rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. chromium-51 + + + + + 2'-(4-ethoxyphenyl)-5-(4-methylpiperazin-1-yl)-2,5'-bibenzimidazole + + 2'-(4-ethoxyphenyl)-5-(4-methylpiperazin-1-yl)-2,5'-bibenzimidazole + + + + + + + + + resorufin + + resorufin + + + + @@ -5667,7 +4115,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. @@ -5679,7 +4127,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dimethyl sulfate The dimethyl ester of sulfuric acid. @@ -5691,7 +4139,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + diethyl pyrocarbonate The diethyl ester of dicarbonic acid. @@ -5703,7 +4151,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 1,1-dihydroxy-3-ethoxy-2-butanone A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. @@ -5715,9 +4163,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide - A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. + A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two <em>N</em>-substituents. N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide @@ -5727,9 +4175,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-methylisatoic anhydride - A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. + A 3,1-benzoxazin-1,4-dione having an <em>N</em>-methyl substituent. N-methylisatoic anhydride @@ -5739,9 +4187,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + (S)-1-(4-bromoacetamidobenzyl)EDTA - A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. + A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (<i>S</i>)-configuration. (S)-1-(4-bromoacetamidobenzyl)EDTA @@ -5751,7 +4199,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA methidiumpropylamide A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. @@ -5763,19 +4211,31 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bromophenol blue - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. bromophenol blue + + + + + 1-methyl-7-nitroisatoic anhydride + A 3,1-benzoxazin-1,4-dione having an <em>N</em>-methyl substituent and a nitro group at the 7-position. + + 1-methyl-7-nitroisatoic anhydride + + + + - + tacrolimus hydrate A hydrate that is the monohydrate form of tacrolimus. @@ -5787,7 +4247,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + oxygen radical An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. @@ -5799,7 +4259,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lipoprotein A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. @@ -5811,7 +4271,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + thyroid stimulating hormone thyroid stimulating hormone @@ -5822,7 +4282,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Luteinizing hormone Luteinizing hormone @@ -5833,7 +4293,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Follicle stimulating hormone Follicle stimulating hormone @@ -5844,9 +4304,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 25-hydroxyvitamin D2 - A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. + A hydroxycalciol that is vitamin D<small><sub>2</sub></small> in which the hydrogen at position 25 has been replaced by a hydroxy group. 25-hydroxyvitamin D2 @@ -5856,9 +4316,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tris - A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. + A primary amino compound that is <em>tert</em>-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7—9; p<em>K</em><small><sub>a</sub></small> = 8.3 at 20 °C; p<em>K</em><small><sub>a</sub></small> = 7.82 at 37 °C. tris @@ -5960,7 +4420,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5980,24 +4440,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - cell line cell + + + + + + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture - + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. cell line cell - - - - - - - - - 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. - @@ -6005,9 +4459,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mortal cell line cell A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. - mortal cell line cell @@ -6017,9 +4469,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immortal cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. - immortal cell line cell @@ -6028,7 +4478,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -6041,11 +4491,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cell line A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). - cell line @@ -6067,9 +4515,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immortal cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. - immortal cell line @@ -6098,9 +4544,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mortal cell line A cell line is able to support only a limited number of passages in vitro. - mortal cell line @@ -6109,11 +4553,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - cell + PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell @@ -6153,26 +4597,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - primary cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. - primary cultured cell - - - - - obsolete native cell - OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - - obsolete native cell - - - - @@ -6196,9 +4626,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. - cultured cell @@ -6208,9 +4636,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sperm A mature male germ cell that develops from a spermatid. - sperm @@ -6220,9 +4646,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - fibroblast + + + + + + + + + + + + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. - fibroblast @@ -6232,9 +4668,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - epithelial cell + + + + + + + + + + + + + A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. - epithelial cell @@ -6244,21 +4691,27 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mesothelial cell A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement. - mesothelial cell + + + + + A cell found predominately in the blood. + blood cell + + + + - T cell A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. - T cell @@ -6267,22 +4720,52 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - mast cell + + + + + + + + + + + + + A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. - mast cell + + + + + + + + + + + + + + + + + A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system. + oligodendrocyte + + + + - hepatocyte The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. - hepatocyte @@ -6291,10 +4774,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - erythrocyte + A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. - erythrocyte @@ -6303,10 +4784,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - platelet + A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. - platelet @@ -6315,10 +4794,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - macrophage + A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. - macrophage @@ -6328,21 +4805,28 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - B cell A lymphocyte of B lineage that is capable of B cell mediated immunity. - B cell + + + + + A cell that initiates an electrical signal and passes that signal to another cell. + electrically signaling cell + + + + - - dendritic cell + + A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). - dendritic cell @@ -6351,10 +4835,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + - neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. - neuron @@ -6364,9 +4847,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - lymphocyte A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - lymphocyte @@ -6376,9 +4857,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - megakaryocyte A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release. - megakaryocyte @@ -6388,9 +4867,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - reticulocyte + + + + + + + + + + + + An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. - reticulocyte @@ -6400,9 +4889,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - band form neutrophil A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. - band form neutrophil @@ -6412,9 +4899,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - nucleate erythrocyte An erythrocyte having a nucleus. - nucleate erythrocyte @@ -6423,11 +4908,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - monocyte Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. - monocyte @@ -6437,16 +4919,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + - experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. - experimentally modified cell in vitro @@ -6456,9 +4935,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - natural killer cell A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. - natural killer cell @@ -6468,9 +4945,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD4-positive, alpha-beta T cell + A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. - CD4-positive, alpha-beta T cell @@ -6480,21 +4956,39 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD8-positive, alpha-beta T cell A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. - CD8-positive, alpha-beta T cell + + + + + A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration. + radial glial cell + + + + - leukocyte + + + + + + + + + + + + An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. - leukocyte @@ -6503,10 +4997,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - basophil + + + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. - basophil @@ -6515,10 +5020,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + - eosinophil + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. - eosinophil @@ -6527,10 +5043,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + - neutrophil + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. - neutrophil @@ -6540,9 +5067,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immature neutrophil Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking. - immature neutrophil @@ -6551,10 +5076,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - plasma cell + A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. - plasma cell @@ -6564,9 +5087,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - alpha-beta T cell A T cell that expresses an alpha-beta T cell receptor complex. - alpha-beta T cell @@ -6576,9 +5097,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD8-positive, alpha-beta cytotoxic T cell A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. - CD8-positive, alpha-beta cytotoxic T cell @@ -6588,9 +5107,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mature NK T cell A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. - mature NK T cell @@ -6600,9 +5117,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - promyelocyte + + + + + + + + + + + + A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. - promyelocyte @@ -6611,11 +5138,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - mononuclear cell + + + + + + + + + + + + + A leukocyte with a single non-segmented nucleus in the mature form. - - mononuclear cell + mononuclear leukocyte @@ -6624,9 +5161,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - malignant cell A neoplastic cell that is capable of entering a surrounding tissue - malignant cell @@ -6636,9 +5171,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - metamyelocyte A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. - metamyelocyte @@ -6648,9 +5181,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - myelocyte A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. - myelocyte @@ -6660,21 +5191,49 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - neural cell + + + + + + + + + + + + A cell that is part of the nervous system. - neural cell + + + + + An epithelial cell of the respiratory tract epithelium. These cells have an endodermal origin. + respiratory tract epithelial cell + + + + + + + + + A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + neural crest cell + + + + - segmented neutrophil of bone marrow A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface. - segmented neutrophil of bone marrow @@ -6684,22 +5243,303 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - peripheral blood mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. - peripheral blood mononuclear cell + + + + + obsolete elementary charge + true + + + + + + + + + + + + + + + + A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. + atom + + + + + + + + + + + + + + + A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. + This molecular entity is different than ChEBI's 'molecular entity'. + We would like to have cardinality restrictions on the logic, but there are some technical limitations. + molecule + + + + + + + + + obsolete macromolecular entity + true + + + + + + + + + + obsolete subcellular structure + true + + + + + + + + + A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. + gross anatomical part + + + + + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + obsolete geographical location + true + + + + + + + + + + + + + + + + + completely executed planned process + + + + + + + + + A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. + nucleic acid chain + + + + + + + + + + obsolete immaterial anatomical entity + true + + + + + + + + + obsolete gene product + true + + + + + + + + + + obsolete action specification + true + + + + - complex of molecules - A complex of two or more molecular entities that are not covalently bound. - - complex of molecules + + + + + + + A complex of two or more molecules that are not covalently bound. + complex of molecules + + + + + + + + + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + planned process + + + + + + + + + failed planned process + + + + + + + + + + + + + + + + + + + + + + + A completely executed planned process that intends to output material entities from input material entities + material processing + + + + + + + + + obsolete cellular membrane + true + + + + + + + + + obsolete physical information carrier + true + + + + + + + + + characteristic + + + + + + + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + + + + + + + + + + + + A processed material entity which is designed to be capable of a process. + device @@ -6740,6 +5580,83 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + A material part of an astronomical body. + geophysical entity + + + + + + + + + An environmental system which includes both living and non-living components. + ecosystem + + + + + + + + + A process in which includes the components of an environmental system as participants. + environmental system process + + + + + + + + + food material by consumer group + + food material by consumer group + + + + + + + + + food material + Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience + + food material + + + + + + + + + animal feed + Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs. + + animal feed + + + + + + + + + food material for animals + Food product for animal covers foods intended for consumption by domesticated animals. + + food material for animals + + + + @@ -6806,6 +5723,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neural crest cell migration + The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo. + + neural crest cell migration + + + + + + + + + neuron migration + The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature. + + neuron migration + + + + @@ -6891,6 +5832,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hematopoietic progenitor cell differentiation + The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. + + hematopoietic progenitor cell differentiation + + + + @@ -6984,6 +5937,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + renal system process + An organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). + + renal system process + + + + + + + + + heart process + A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. + + heart process + + + + @@ -6999,7 +5976,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + glomerular filtration The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein. @@ -7014,7 +5991,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -7096,10 +6075,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - L-alanine:2-oxoglutarate aminotransferase activity - Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate. + L-alanine:2-oxoglutarate transaminase activity + Catalysis of the reaction: L-alanine + 2-oxoglutarate = pyruvate + L-glutamate. - L-alanine:2-oxoglutarate aminotransferase activity + L-alanine:2-oxoglutarate transaminase activity @@ -7120,10 +6099,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - L-aspartate:2-oxoglutarate aminotransferase activity + L-aspartate:2-oxoglutarate transaminase activity Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate. - L-aspartate:2-oxoglutarate aminotransferase activity + L-aspartate:2-oxoglutarate transaminase activity @@ -7156,10 +6135,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - glutamate dehydrogenase [NAD(P)+] activity - Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+. + L-glutamate dehydrogenase [NAD(P)+] activity + Catalysis of the reaction: L-glutamate + NAD(P)+ + H2O = 2-oxoglutarate + NH4+ + NAD(P)H + H+. - glutamate dehydrogenase [NAD(P)+] activity + L-glutamate dehydrogenase [NAD(P)+] activity @@ -7169,7 +6148,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ glutathione transferase activity - Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group. + Catalysis of the reaction: RX + glutathione = an S-substituted glutathione + a halide anion + H+. glutathione transferase activity @@ -7205,7 +6184,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ RNA nuclease activity - Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. + Catalysis of the cleavage of phosphodiester bonds in chains of RNA. RNA nuclease activity @@ -7227,6 +6206,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). @@ -7296,6 +6284,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of DNA repair + Any process that modulates the frequency, rate or extent of DNA repair. + + regulation of DNA repair + + + + @@ -7320,6 +6320,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + apoptotic process + A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. + + apoptotic process + + + + @@ -7344,6 +6356,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + plasma membrane organization + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + + plasma membrane organization + + + + @@ -7368,6 +6392,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + female pregnancy + The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. + + female pregnancy + + + + + + + + + embryo implantation + Attachment of the blastocyst to the uterine lining. + + embryo implantation + + + + @@ -7392,14 +6440,32 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + growth factor activity + The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation. + + growth factor activity + + + + - + + + + + + biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + biological process biological_process @@ -7453,6 +6519,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + glial cell migration + The orderly movement of a glial cell, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system. + + glial cell migration + + + + @@ -7465,6 +6543,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + response to toxic substance + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. + + response to toxic substance + + + + @@ -7549,6 +6639,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cell migration + The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. + + cell migration + + + + + + + + + oxidoreductase activity + Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. + + oxidoreductase activity + + + + @@ -7585,6 +6699,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cytolysis + The rupture of cell membranes and the loss of cytoplasm. + + cytolysis + + + + @@ -7669,6 +6795,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neuron differentiation + The process in which a relatively unspecialized cell acquires specialized features of a neuron. + + neuron differentiation + + + + + + + + + neuron projection development + The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). + + neuron projection development + + + + @@ -8190,7 +7340,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + @@ -8200,6 +7351,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ protein-containing complex A ribosome is a protein complex. A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + This is not covalently bonded, which conflicts with changes to the parent definition. protein complex protein-containing complex @@ -8339,6 +7491,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of growth + Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. + + regulation of growth + + + + @@ -8375,6 +7539,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hormone biosynthetic process + The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone biosynthetic process + + + + + + + + + hormone catabolic process + The chemical reactions and pathways resulting in the breakdown of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone catabolic process + + + + @@ -8439,6 +7627,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + drinking behavior + The specific behavior of an organism relating to the intake of liquids, especially water. + + drinking behavior + + + + + + + + + neuron projection + A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. + + neuron projection + + + + @@ -8475,6 +7687,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Any constituent part of a virion, a complete fully infectious extracellular virus particle. + virion component + + + + @@ -8511,6 +7733,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + DNA-templated DNA replication maintenance of fidelity + A DNA metabolic process that prevents or corrects errors to ensure that DNA is replicated accurately. Errors can be corrected either by intrinsic DNA polymerase proofreading activity or via mismatch repair. + + DNA-templated DNA replication maintenance of fidelity + + + + @@ -8523,6 +7757,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + synapse + The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. + + synapse + + + + + + + + + luciferin monooxygenase activity + Catalysis of the generalized reaction: luciferin + O2 = oxidized luciferin + CO2 + light. There may be additional substrates and reactants involved in the reaction. The reaction results in light emission as luciferin returns to the ground state after enzymatic oxidation. + + luciferin monooxygenase activity + + + + @@ -8535,6 +7793,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oligodendrocyte differentiation + The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system. + + oligodendrocyte differentiation + + + + + + + + + anatomical structure development + The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. + + anatomical structure development + + + + @@ -8607,6 +7889,55 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + embryonic process involved in female pregnancy + A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother. + + embryonic process involved in female pregnancy + + + + + + + + + estrous cycle phase + The progression of physiological phases, occurring in the endometrium during the estrous cycle that recur at regular intervals during the reproductive years. The estrous cycle is an ovulation cycle where the endometrium is resorbed if pregnancy does not occur. + + estrous cycle phase + + + + + + + + + regulation of feeding behavior + Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food. + + regulation of feeding behavior + + + + + + + + + + establishment of endothelial barrier + The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition. + + establishment of endothelial barrier + + + + @@ -8835,6 +8166,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of synapse maturation + Any process that modulates the extent of synapse maturation, the process that organizes a synapse so that it attains its fully functional state. + + regulation of synapse maturation + + + + @@ -8967,6 +8310,49 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + synaptic signaling + Cell-cell signaling to, from or within a synapse. + + synaptic signaling + + + + + + + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. + Overlaps with some cellular components from GO + cellular anatomical entity + + + + + + + + + neuron projection arborization + The process in which the anatomical structures of a neuron projection are generated and organized into branches. A neuron projection is any process extending from a neural cell, such as axons or dendrites. + + neuron projection arborization + + + + @@ -8991,6 +8377,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + negative regulation of cell wall organization or biogenesis + Any process that stops, prevents or reduces the frequency, rate or extent of cell wall organization or biogenesis. + + negative regulation of cell wall organization or biogenesis + + + + + + + + + mitotic DNA replication maintenance of fidelity + Any maintenance of fidelity that is involved in mitotic cell cycle DNA replication. + + mitotic DNA replication maintenance of fidelity + + + + @@ -9015,13 +8425,23 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Severity + The intensity or degree of a manifestation. + + Severity + + + + - conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. - conditional specification @@ -9031,9 +8451,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - measurement unit label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - measurement unit label @@ -9043,9 +8461,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - objective specification A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - objective specification @@ -9055,21 +8471,27 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - narrative object A narrative object is an information content entity that is a set of propositions. - narrative object + + + + + A directive information entity that describes an action the bearer will take. + action specification + + + + - datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - datum label @@ -9079,10 +8501,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. - software @@ -9092,10 +8512,12 @@ interpreted by or directly executed by a processing unit. + data entity data item An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - + An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + data entity data item @@ -9105,9 +8527,7 @@ interpreted by or directly executed by a processing unit. - symbol An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - symbol @@ -9116,10 +8536,10 @@ interpreted by or directly executed by a processing unit. - + information content entity A generically dependent continuant that is about some thing. - + Pier: 'data, information or knowledge'. OR 'representation' information content entity @@ -9136,9 +8556,7 @@ interpreted by or directly executed by a processing unit. - scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - scalar measurement datum @@ -9148,9 +8566,7 @@ interpreted by or directly executed by a processing unit. - directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. - directive information entity @@ -9160,9 +8576,7 @@ interpreted by or directly executed by a processing unit. - dot plot A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - dot plot @@ -9172,9 +8586,7 @@ interpreted by or directly executed by a processing unit. - graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - graph @@ -9184,9 +8596,7 @@ interpreted by or directly executed by a processing unit. - rule A rule is an executable which guides, defines, restricts actions. - rule @@ -9196,9 +8606,7 @@ interpreted by or directly executed by a processing unit. - algorithm A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - algorithm @@ -9230,7 +8638,6 @@ interpreted by or directly executed by a processing unit. PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 - curation status specification @@ -9240,9 +8647,7 @@ interpreted by or directly executed by a processing unit. - density plot A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. - density plot @@ -9252,9 +8657,7 @@ interpreted by or directly executed by a processing unit. - report A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - report @@ -9264,10 +8667,8 @@ interpreted by or directly executed by a processing unit. - data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - data format specification @@ -9277,10 +8678,8 @@ Example: The ISO document specifying what encompasses an XML document; The instr - data set A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - - data set + homogenous data collection @@ -9289,9 +8688,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - image @@ -9313,9 +8710,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - plan specification A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - plan specification @@ -9331,9 +8726,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - measurement datum @@ -9356,9 +8749,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - conclusion textual entity A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. - conclusion textual entity @@ -9368,9 +8759,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - material information bearer A material entity in which a concretization of an information content entity inheres. - material information bearer @@ -9380,10 +8769,8 @@ Example: The ISO document specifying what encompasses an XML document; The instr - histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. - histogram @@ -9393,11 +8780,9 @@ distribution in terms of occurrence frequencies of different event classes. - heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. - heatmap @@ -9407,11 +8792,9 @@ two-dimensional map. - dendrogram A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. - dendrogram @@ -9421,9 +8804,7 @@ clustering algorithm. - scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - scatter plot @@ -9460,9 +8841,7 @@ clustering algorithm. - textual entity A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - textual entity @@ -9472,9 +8851,7 @@ clustering algorithm. - table A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions - table @@ -9484,9 +8861,7 @@ clustering algorithm. - figure An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - figure @@ -9496,9 +8871,7 @@ clustering algorithm. - document A collection of information content entities intended to be understood together as a whole - document @@ -9508,9 +8881,7 @@ clustering algorithm. - publication A document that is the output of a publishing process. - publication @@ -9520,9 +8891,13 @@ clustering algorithm. - publication about an investigation + + + + + + A publication that is about an investigation - publication about an investigation @@ -9532,9 +8907,7 @@ clustering algorithm. - one dimensional cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region - one dimensional cartesian spatial coordinate datum @@ -9544,9 +8917,13 @@ clustering algorithm. - length measurement datum + + + + + + A scalar measurement datum that is the result of measurement of length quality - length measurement datum @@ -9579,9 +8956,7 @@ clustering algorithm. - mass measurement datum A scalar measurement datum that is the result of measurement of mass quality - mass measurement datum @@ -9591,9 +8966,7 @@ clustering algorithm. - time measurement datum A scalar measurement datum that is the result of measuring a temporal interval - time measurement datum @@ -9603,9 +8976,7 @@ clustering algorithm. - postal address A textual entity that is used as directive to deliver something to a person, or organization - postal address @@ -9615,8 +8986,6 @@ clustering algorithm. - email address - email address @@ -9625,10 +8994,8 @@ clustering algorithm. - - documenting + A planned process in which a document is created or added to by including the specified input in it. - documenting @@ -9638,10 +9005,8 @@ clustering algorithm. - line graph A line graph is a type of graph created by connecting a series of data points together with a line. - line graph @@ -9650,10 +9015,8 @@ points together with a line. - - assigning a centrally registered identifier + A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - assigning a centrally registered identifier @@ -9663,9 +9026,7 @@ points together with a line. - centrally registered identifier symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - centrally registered identifier symbol @@ -9675,9 +9036,7 @@ points together with a line. - centrally registered identifier registry A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. - centrally registered identifier registry @@ -9687,9 +9046,7 @@ points together with a line. - software application A software application is software that can be directly executed by some processing unit. - software application @@ -10021,6 +9378,17 @@ No imports + + + + + A process in which at least one of the participants is a molecule. + This is meant to capture processes that are more fundamental than macromolecular activities + physico-chemical process + + + + @@ -10415,7 +9783,7 @@ No imports - + Viruses Viruses @@ -10560,10 +9928,19 @@ No imports + + + + + cellular organism + + + + - + Treponema pallidum Treponema pallidum @@ -10585,8 +9962,9 @@ No imports - + Bacteria + bacteria eubacteria Bacteria @@ -10597,7 +9975,7 @@ No imports - + Archaea Archaea @@ -10611,6 +9989,7 @@ No imports Riboviria RNA viruses + RNA viruses and retroviruses RNA viruses and viroids Riboviria @@ -10644,9 +10023,8 @@ No imports - + Eukaryota - eucaryotes eukaryotes Eukaryota @@ -10659,6 +10037,7 @@ No imports Orthoherpesviridae + Herpesviridae Orthoherpesviridae @@ -10734,6 +10113,7 @@ No imports Metazoa + animals metazoans multicellular animals @@ -10753,6 +10133,17 @@ No imports + + + + + Pseudomonadati + + Pseudomonadati + + + + @@ -10828,7 +10219,7 @@ No imports Ascomycota - ascomycetes + ascomycete fungi sac fungi Ascomycota @@ -10853,6 +10244,7 @@ No imports Saccharomyces cerevisiae + Saccharomyces boulardii Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast @@ -10982,7 +10374,7 @@ No imports - + Orientia tsutsugamushi Orientia tsutsugamushi @@ -11051,6 +10443,7 @@ No imports Rodentia rodent + rodents Rodentia @@ -11060,7 +10453,7 @@ No imports - + biological attribute biological attribute @@ -11223,30 +10616,21 @@ No imports - - - - - - - - - - - - - planned process + + obsolete planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + obsolete planned process + true @@ -11529,7 +10913,7 @@ objectives is a planned process. - + drug role @@ -11549,7 +10933,7 @@ objectives is a planned process. - + @@ -11584,7 +10968,7 @@ objectives is a planned process. - + physical document a book is a physical document @@ -11615,24 +10999,16 @@ objectives is a planned process. - - - - - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + obsolete processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material + PERSON: Alan Ruttenberg + + + obsolete processed material + true @@ -11919,7 +11295,7 @@ objectives is a planned process. - + polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. @@ -11934,7 +11310,7 @@ objectives is a planned process. - + @@ -12041,7 +11417,21 @@ objectives is a planned process. - + + + + + + + + + + + + + + + @@ -12127,7 +11517,7 @@ objectives is a planned process. - + @@ -12190,7 +11580,7 @@ objectives is a planned process. - + culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 @@ -12332,38 +11722,21 @@ In regard to the statement that reagents are 'distinct' from the speci - - - - - - - - - - - - - - - - - - - - - material processing + + obsolete material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material - PERSON: Bjoern Peters + PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra - material transformation - OBI branch derived - material processing + OBI branch derived + + + obsolete material processing + true @@ -12478,7 +11851,7 @@ editor = PRS - + @@ -12867,7 +12240,7 @@ specimen can later be subject. - + @@ -13602,7 +12975,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13690,7 +13063,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13986,7 +13359,7 @@ for now. - + @@ -14028,10 +13401,16 @@ for now. + + + + + + plan The plan of researcher X to perform an experiment according to a protocol. - A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived @@ -14193,8 +13572,8 @@ for now. - - + + @@ -14273,7 +13652,7 @@ for now. - + @@ -14372,14 +13751,14 @@ for now. - + - + @@ -14442,7 +13821,7 @@ need to add mobile phase as role - + @@ -14515,7 +13894,6 @@ need to add mobile phase as role - @@ -14629,7 +14007,7 @@ Proposal is to obsolete. - + @@ -14791,7 +14169,7 @@ Proposal is to obsolete. - + @@ -15143,7 +14521,7 @@ Proposal is to obsolete. - + @@ -15207,7 +14585,7 @@ Proposal is to obsolete. - + @@ -15468,7 +14846,7 @@ Proposal is to obsolete. - + @@ -15687,7 +15065,7 @@ activity) - + @@ -15708,7 +15086,7 @@ activity) - + @@ -16081,7 +15459,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16243,7 +15621,6 @@ that has_part some material entity is a material entity. If we add as equivalent genotyping assay - High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. Philippe Rocca-Serra @@ -16258,7 +15635,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16327,7 +15704,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16627,7 +16004,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16737,7 +16114,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16747,7 +16124,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + manufacturing @@ -16950,7 +16327,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16963,7 +16340,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. @@ -17152,7 +16529,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR sample holder An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. @@ -17366,7 +16743,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR tube washing system An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. @@ -17382,7 +16759,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR console A component of an NMR instrument that controls the activities of the other components. @@ -17689,7 +17066,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR magnet A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. @@ -17748,7 +17125,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -17759,7 +17136,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -17772,33 +17149,20 @@ that has_part some material entity is a material entity. If we add as equivalent - - - - - - - - - - - - - - - - + + + - - + + - - + + clinical chemistry assay Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. - An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. + An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a specimen collected from an organism in order to determine a phenotype of that organism. Philippe Rocca-Serra chemical pathology detection of analyte in blood sample @@ -17841,7 +17205,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18201,7 +17565,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18433,7 +17797,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + autosampler An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. @@ -18802,13 +18166,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + scattered molecular aggregate @@ -19699,15 +19063,6 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - @@ -19775,26 +19130,55 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - + + + + hematology assay Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 - An assay that studies blood and blood producing organs using a variety of techniques and instruments + An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments Philippe Rocca-Serra blood analysis haematology @@ -20229,7 +19613,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20272,11 +19656,11 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + device setting @@ -20375,7 +19759,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20383,7 +19767,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20850,7 +20234,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + whole organism preparation @@ -21278,7 +20662,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21288,13 +20672,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + animal feeding @@ -21454,7 +20838,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21469,7 +20853,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21741,14 +21125,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + @@ -21811,7 +21195,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21879,7 +21263,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21905,7 +21289,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22057,7 +21441,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22081,7 +21465,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22211,7 +21595,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. @@ -22306,7 +21690,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + host role @@ -22526,7 +21910,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. @@ -22580,7 +21964,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -22605,7 +21989,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs @@ -22630,13 +22014,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - - - + cloning vector @@ -22783,7 +22165,6 @@ the role 'adjuvant role' inheres in some 'material entity' a - nucleic acid restriction enzyme digest A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site @@ -23255,6 +22636,7 @@ the role 'adjuvant role' inheres in some 'material entity' a + @@ -23489,11 +22871,11 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23565,7 +22947,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23598,7 +22980,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23689,14 +23071,14 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23765,7 +23147,6 @@ http://en.wikipedia.org/wiki/Survival_rate - amplified DNA Amplied DNA created by PCR @@ -23780,7 +23161,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23813,24 +23194,15 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - - - - - - - - - - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule - a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. + a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues placeholder for SO BP et al - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule + true @@ -23884,7 +23256,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + Berichrom(r) Antithrombin III (A) Kit For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution @@ -23921,7 +23293,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + fucoidan Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). @@ -23935,7 +23307,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24193,7 +23565,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24214,7 +23586,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + pill A dose of medicine or placebo in the form of a small pellet. @@ -24273,7 +23645,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24281,7 +23653,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + measurement device A ruler, a microarray scanner, a Geiger counter. @@ -24406,7 +23778,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + material maintenance A planned process with the objective to maintain some or all of the characteristics of an input material over time. @@ -24418,6 +23790,7 @@ http://en.wikipedia.org/wiki/Survival_rate + @@ -24446,7 +23819,7 @@ placeholder - + @@ -24474,7 +23847,7 @@ placeholder - + @@ -24495,7 +23868,7 @@ placeholder - + @@ -24577,23 +23950,14 @@ placeholder - - - - - - - - - - - - - primary structure of RNA molecule + + obsolete primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters - primary structure of RNA molecule + + obsolete primary structure of RNA molecule + true @@ -25144,7 +24508,7 @@ placeholder - + @@ -25467,7 +24831,7 @@ Person: Chris Stoeckert - + @@ -25478,7 +24842,7 @@ Person: Chris Stoeckert - + @@ -25884,7 +25248,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26031,7 +25395,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26055,7 +25419,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - + @@ -26773,8 +26137,8 @@ Updated both textual and logical definition. Both input and output material of f - + labeled specimen A specimen that has been modified in order to be able to detect it in future experiments @@ -26794,7 +26158,7 @@ Updated both textual and logical definition. Both input and output material of f - + infectious agent is a material entity bearing the disposition to infect an organism @@ -26903,7 +26267,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26955,7 +26319,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26963,7 +26327,7 @@ Updated both textual and logical definition. Both input and output material of f - + material separation device flow cytometer @@ -27045,7 +26409,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27122,7 +26486,7 @@ Updated both textual and logical definition. Both input and output material of f - + training process e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility @@ -27225,7 +26589,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27238,7 +26602,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27351,7 +26715,7 @@ Biochimie. 2010 Feb 18. - + service provider role @@ -27521,14 +26885,14 @@ Biochimie. 2010 Feb 18. - + - + processed specimen @@ -27593,7 +26957,7 @@ Biochimie. 2010 Feb 18. - + @@ -27813,7 +27177,7 @@ Biochimie. 2010 Feb 18. - + @@ -27844,7 +27208,7 @@ Biochimie. 2010 Feb 18. - + @@ -27852,7 +27216,7 @@ Biochimie. 2010 Feb 18. - + container A device that can be used to restrict the location of material entities over time @@ -27866,50 +27230,21 @@ Biochimie. 2010 Feb 18. - - - - - - - - - - - - - - - - - - - - - - - - - device + + obsolete device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. - device + + + obsolete device + true @@ -27989,11 +27324,11 @@ In the examples above, a reagent is an operational component of a device, but th - + - + @@ -28004,7 +27339,7 @@ In the examples above, a reagent is an operational component of a device, but th sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + A data item that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data @@ -28111,7 +27446,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28531,7 +27866,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28853,7 +28188,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -28945,7 +28280,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. @@ -29332,7 +28667,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -29349,7 +28684,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30083,7 +29418,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30091,7 +29426,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) @@ -30109,7 +29444,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30117,7 +29452,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + perturbation device A homogenizer is a perturbation device. @@ -30137,7 +29472,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30153,7 +29488,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + environmental control device A growth chamber is an environmental control device. @@ -30446,7 +29781,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30532,7 +29867,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30629,7 +29964,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30731,7 +30066,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30751,7 +30086,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30797,7 +30132,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30823,7 +30158,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30883,7 +30218,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31032,7 +30367,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31052,7 +30387,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31283,7 +30618,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31355,7 +30690,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31457,7 +30792,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31477,7 +30812,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31651,7 +30986,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31719,7 +31054,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31864,7 +31199,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31918,7 +31253,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31978,7 +31313,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32046,7 +31381,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32066,7 +31401,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32126,7 +31461,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32365,7 +31700,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32418,7 +31753,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + individual organism identifier @@ -32577,7 +31912,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32676,7 +32011,7 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - + genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. @@ -32819,7 +32154,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -32830,7 +32165,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -33150,7 +32485,7 @@ All subtype will be defined by textual definition now. - + @@ -33166,11 +32501,11 @@ All subtype will be defined by textual definition now. - + - + service @@ -33320,15 +32655,6 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - @@ -33468,13 +32794,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + @@ -33486,7 +32812,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms @@ -37726,7 +37052,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -38335,7 +37661,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -40990,32 +40316,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - + genetic characteristics information @@ -43395,7 +42696,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -43424,7 +42725,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44305,7 +43606,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44361,7 +43662,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -46020,10 +45321,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + @@ -46044,30 +45345,20 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - + + + - - + + + + + - - - - - - - - - - - - - - - - + + @@ -46727,7 +46018,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + material processing service @@ -47182,7 +46473,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + DNA sequence data @@ -49290,7 +48581,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + purified material A mixture of peptide molecules that has been run through an HPLC column to remove 65 @@ -57712,7 +57003,7 @@ is realized in a specimen collection process. - + @@ -58378,7 +57669,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59378,7 +58669,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59730,7 +59021,7 @@ PMID: 23587118. - + @@ -59816,11 +59107,11 @@ When harvesting blood from a human, isolating T cells, and then limited dilution - + - + reagent @@ -60824,7 +60115,7 @@ The following are NOT conclusions based on data: data themselves; results from p - + cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. @@ -61926,7 +61217,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. @@ -62006,7 +61297,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -62142,7 +61433,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay @@ -62298,7 +61589,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - + @@ -62520,7 +61811,7 @@ PMID: 23587118. - + freezing A planned process with the objective to bring some material entity to a temperature below its freezing point. @@ -62683,7 +61974,7 @@ PMID: 23587118. - + @@ -62718,7 +62009,7 @@ PMID: 23587118. - + @@ -62966,7 +62257,7 @@ PMID: 23587118. - + @@ -63205,7 +62496,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63213,7 +62504,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63276,7 +62567,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63287,7 +62578,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64575,6 +63866,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + @@ -64689,54 +64004,6 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - histone modification identification by ChIP-Seq assay - - An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. - Chris Stoeckert - Jie Zheng - histone modification ChIP-Seq - Penn group - histone modification identification by ChIP-Seq assay - - - - - - - - - @@ -64745,39 +64012,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -64785,20 +64023,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - + @@ -64815,7 +64040,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64825,43 +64050,32 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - + - + - transcription factor binding site identification by ChIP-chip assay + histone modification identification by ChIP-Seq assay - A transcription factor binding site assay that utilizes ChIP-chip technology. + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. Chris Stoeckert Jie Zheng - TF Binding ChIP-chip + histone modification ChIP-Seq Penn group - transcription factor binding site identification by ChIP-chip assay + histone modification identification by ChIP-Seq assay - + - + - + @@ -64873,7 +64087,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64881,7 +64095,132 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transcription factor binding site identification by ChIP-chip assay + + A transcription factor binding site assay that utilizes ChIP-chip technology. + Chris Stoeckert + Jie Zheng + TF Binding ChIP-chip + Penn group + transcription factor binding site identification by ChIP-chip assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -65665,7 +65004,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -65695,7 +65034,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -67343,11 +66682,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + @@ -68066,14 +67405,14 @@ https://www.doi.org/ - high performance liquid chromotography assay + high performance liquid chromatography assay On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. ImmPort HPLC PMID:9491555 - high performance liquid chromotography assay + high performance liquid chromatography assay @@ -70590,7 +69929,7 @@ https://www.doi.org/ - + microtome blade A device that is the part of a microtome used to slice specimens to a desired thickness. @@ -70705,7 +70044,7 @@ https://www.doi.org/ - + determination if assay will provide reliable results A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. @@ -71707,7 +71046,7 @@ https://www.doi.org/ - + delivery form for hormonal replacement therapy A processed material used for delivery of hormones in hormone replacement therapy. @@ -72310,7 +71649,7 @@ https://www.doi.org/ - + @@ -72321,7 +71660,7 @@ https://www.doi.org/ - + @@ -72884,11 +72223,11 @@ https://www.doi.org/ - + - + @@ -72909,11 +72248,11 @@ https://www.doi.org/ - + - + @@ -73264,7 +72603,7 @@ https://www.doi.org/ - + pipette A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. @@ -74913,7 +74252,7 @@ https://www.doi.org/ - + esophagus muscularis mucosa specimen A specimen that is derived from esophagus muscularis mucosa. @@ -75151,7 +74490,7 @@ https://www.doi.org/ - + coronary artery specimen A specimen that is derived from coronary artery. @@ -75480,7 +74819,7 @@ https://www.doi.org/ - + minor salivary gland specimen A specimen that is derived from minor salivary gland. @@ -75621,7 +74960,7 @@ https://www.doi.org/ - + sigmoid colon specimen A specimen that is derived from sigmoid colon. @@ -76336,7 +75675,7 @@ https://www.doi.org/ - + @@ -76358,7 +75697,7 @@ https://www.doi.org/ - + machine learning A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. @@ -78586,19 +77925,14 @@ https://www.doi.org/ - - - - - - - 1 - - - - - + + + + 1 + + + individual organism specimen A specimen composed of an individual organism to be studied in an investigation. @@ -78660,7 +77994,7 @@ https://www.doi.org/ - + @@ -78668,7 +78002,7 @@ https://www.doi.org/ - + @@ -78691,7 +78025,7 @@ https://www.doi.org/ - + @@ -78713,7 +78047,7 @@ https://www.doi.org/ - + @@ -81919,7 +81253,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + @@ -81927,7 +81261,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + molecular label @@ -82001,7 +81335,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + passage process A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. @@ -82125,7 +81459,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + cDNA library cDNA library lacks the non-coding and regulatory elements found in genomic DNA @@ -82893,7 +82227,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + personal protective device Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. PPE is equipment worn by a worker to minimize exposure to specific hazards. @@ -83079,7 +82413,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + apron A garment which is worn over other clothing and covers mainly the front of the body. @@ -83185,7 +82519,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + transparent partition A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. @@ -83333,7 +82667,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + specimen collection device A device used to collect a specimen. @@ -83402,7 +82736,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + cotton swab A device which is a cotton pad mounted on one or both ends of a stick. @@ -83466,7 +82800,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. @@ -83838,7 +83172,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + arthropod trap A device designed to catch arthropods. @@ -83897,7 +83231,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -83957,7 +83291,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + dipper for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. @@ -85421,11 +84755,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -85591,7 +84925,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + device for collection of resting adult arthropods A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. @@ -85607,7 +84941,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + well net for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. @@ -86312,8 +85646,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + @@ -86701,7 +86034,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -86709,7 +86042,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87016,7 +86349,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87037,7 +86370,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + hand-held sweep net A device that consists of a network of mesh and is designed to capture adult arthropods. @@ -87414,7 +86747,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + common name of organism @@ -87502,7 +86835,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87513,7 +86846,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -88421,7 +87754,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -90922,7 +90255,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre leukapheresis - A blood harvesting process in which white blood cells are separated from a blood specimen. + A blood specimen collection in which white blood cells are separated from a blood specimen. Hector Guzman-Orozco https://en.wikipedia.org/wiki/Leukapheresis leukapheresis @@ -91529,7 +90862,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood assay datum - A data item that is the specified output of a blood assay. + A data entity that is the specified output of a blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91582,7 +90915,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre feces assay datum - A data item that is the specified output of a feces assay. + A data entity that is the specified output of a feces assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91635,7 +90968,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre urine assay datum - A data item that is the specified output of a urine assay. + A data entity that is the specified output of a urine assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91688,7 +91021,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre induced sputum assay datum - A data item that is the specified output of a induced sputum assay. + A data entity that is the specified output of a induced sputum assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91760,7 +91093,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre cerebrospinal fluid assay datum - A data item that is the specified output of a cerebrospinal fluid assay. + A data entity that is the specified output of a cerebrospinal fluid assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91944,7 +91277,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre umbilical cord blood assay datum - A data item that is the specified output of an umbilical cord blood assay. + A data entity that is the specified output of an umbilical cord blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -92822,7 +92155,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + mosquito membrane feeding device A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. @@ -93723,7 +93056,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -93731,7 +93064,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -94577,7 +93910,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre milk assay datum - A data item that is the specified output of a milk assay. + A data entity that is the specified output of a milk assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1515 @@ -94652,7 +93985,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf @@ -95568,7 +94901,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre antigen specific antibodies assay datum - A data item that is the specified output of an antigen specific antibodies assay. + A data entity that is the specified output of an antigen specific antibodies assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 @@ -96267,7 +95600,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -97825,7 +97158,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -98314,7 +97647,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100728,7 +100061,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100736,7 +100069,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100759,7 +100092,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100850,7 +100183,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100858,7 +100191,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100881,7 +100214,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100972,7 +100305,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100980,7 +100313,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -101003,7 +100336,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -102898,22 +102231,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - + + + + + + + + + + albumin-free serum A blood serum specimen that contains no albumin. @@ -102928,14 +102256,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -102948,7 +102276,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasting @@ -102988,7 +102316,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasted @@ -103266,15 +102594,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - @@ -103357,7 +102676,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - lavage fluid specimen The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. @@ -103791,7 +103109,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103833,7 +103151,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103874,7 +103192,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103942,7 +103260,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103966,7 +103284,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104022,7 +103340,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104033,7 +103351,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104080,7 +103398,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104091,7 +103409,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104138,7 +103456,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104149,7 +103467,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104196,7 +103514,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104207,7 +103525,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104254,7 +103572,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104265,7 +103583,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104312,7 +103630,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104323,7 +103641,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104370,7 +103688,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104381,7 +103699,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104428,7 +103746,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104439,7 +103757,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104486,7 +103804,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104497,7 +103815,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104550,7 +103868,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104561,7 +103879,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104614,7 +103932,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104625,7 +103943,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104770,7 +104088,7611 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + + + + + + + + + + + + cell based DNA damage assay + + A cytometry assay that measures DNA damage in cells. + Jennifer Fostel + cell based DNA damage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell count assay + + A cytometry assay to determine the number of natural killer cells in a specimen + Jennifer Fostel + natural killer cell count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell percentage assay + + A cytometry assay that measures the percentage of natural killer cells in a specimen. + Jennifer Fostel + natural killer cell percentage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sperm count assay + + A cytometry assay to count the number of mature sperm in a specimen. + Jennifer Fostel + sperm count assay + + + + + + + + + survey administration assay + + An assay that obtains data from one or more participants by using a survey or questionnaire + Jennifer Fostel + survey administration assay + + + + + + + + + maximum data transformation + + A data transformation that has as its output the greatest value in the input data set. + Sebastian Duesing + maximum data transformation + + + + + + + + + minimum data transformation + + A data transformation that has as its output the least value in the input data set. + Sebastian Duesing + minimum data transformation + + + + + + + + + + + + + + + + + + + + + + + + + clinical history collection assay + A clinician asking a patient about the patient's smoking status. + + A clinical assay that produces a data item indicating whether an organism has ever had a particular disease, lifestyle factor, immune exposure, or medical procedure. + Sebastian Duesing + HCC + clinical history collection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + disease severity assay + Measuring bone mineral density to determine the severity of osteoporosis. + + An assay that measures the severity of a disease in an organism. + Sebastian Duesing + HCC + disease severity assay + + + + + + + + + + + + + + + genetic characteristic assay + Determining a patient's HLA type. + + An assay that produces information about a genetic characteristic of an organism. + Sebastian Duesing + HCC + genetic characteristic assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood type assay + Identifying a person's ABO blood type. + + An assay that classifies an organism's blood within one or more blood group classification systems by identifying antigens present in the blood. + Sebastian Duesing + https://medlineplus.gov/ency/article/003345.htm + blood type assay + + + + + + + + + manual muscle testing 8 score + + A clinical data item that quantifies the muscle function of a person based on the person's ability to hold a series of eight body positions that target different muscle groups. + Sebastian Duesing + MMT-8 + https://www.niehs.nih.gov/sites/default/files/research/resources/assets/docs/mmt8_grading_and_testing_procedures_for_the_abbreviated_8_muscle_groups_508.pdf + manual muscle testing 8 score + + + + + + + + + childhood myositis assessment scale score + + A clinical data item that quantifies the degree of muscle function in a child with myositis based on performance of 14 tasks associated with muscular strength and endurance. + Sebastian Duesing + CMAS + https://pubmed.ncbi.nlm.nih.gov/10524696/ + childhood myositis assessment scale score + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + capillary electrophoresis mass spectrometry assay + + A mass spectrometry assay where a sample mixture is first separated by capillary electrophoresis before being analysed by mass spectrometry. + Sebastian Duesing + CE-MS + Thomas Payne + https://en.wikipedia.org/wiki/Capillary_electrophoresis–mass_spectrometry + https://github.com/obi-ontology/obi/issues/1904 + Thomas Payne + capillary electrophoresis mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite outgrowth assay + + A cell differentiation assay that detects neurite outgrowth and/or branching + The UBERON term for neurite is Neuron projection (GO:0043005; A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.). Multiplexed fluorescent imaging can be used to detect nuclei in neuronal cell bodies using Hoechst dye and neurites using anti-beta III-tubulin antibody staining. Commonly measured are neurite length, number and/or number of branch points (arborization). + Jennifer Fostel + neurite outgrowth assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuronal differentiation assay + + A cell differentiation assay that measures differentiation of neurons. + Jennifer Fostel + neuronal differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligodendrocyte differentiation assay + + A cell differentiation assay that measures differentiation of oligodendrocytes. + Jennifer Fostel + oligodendrocyte differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + regulation of synapse maturation assay + + A cell differentiation assay that measures synapse formation and maturation using antibodies to protein found in synaptic puncta. + Synaptic puncta is this context is a small (0.5 to 2 um) distinct localized cluster of proteins involved in synaptic transmission. + Jennifer Fostel + regulation of synapse maturation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ames assay + + A cell based DNA damage assay that uses several constructed bacterial strains to detect mutations. + The bacterial strains were originally constructed by Bruce Ames. Each carries a mutation in a gene involved in histidine synthesis. The cell requires histidine for growth but cannot produce it. The assay measures the creation of mutations that result in a return of function so that the cells can grow on a histidine-free medium. + Jennifer Fostel + Ames assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + micronucleus assay + + A cell based DNA damage assay in eukaryotic cells that detects cytoplasmic micronuclei. + The GO term "micronucleus" (GO:0031040) applies to protozoa but does not pertain to this case. Here micronucleus is a chromosome or fragment of a chromosome bounded by nuclear membrane that did not segregate properly at mitosis. + Jennifer Fostel + micronucleus assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PIG-a assay + + A cell based DNA damage assay in eukaryotic cells that detects loss of function through mutation of the X-linked (single-copy) Pig-a gene. + The Pig-A gene encodes a product involved in biosynthesis of cell surface anchor glycosylphosphatidylinositol (GPI). + Jennifer Fostel + PIG-a assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin + + A cell viability assay using the NAD(P)H-aided conversion of resazurin to resorufin by metabolically active cells. + Resazurin is the active ingredient in alamar blue; has a blue color and is non-fluorescent. Resorufin has pink color and is fluorescent. Detection of resorufin can be by absorbance or fluorescence. + Jennifer Fostel + Alamar Blue viability assay + cell viability assay based on detection of resorufin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay using caspase abundance to detect apoptosis + + A cell death assay that uses fluorescence imaging-based detection of caspases involved in apoptosis + Caspases 3 and 7 are frequently used as indicators of apoptosis. + Jennifer Fostel + cell death assay using caspase abundance to detect apoptosis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay + + A cell viability assay which measures the number or proportion of dead cells in a population. + Jennifer Fostel + cell death assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + A cell viability assay based on detection of resorufin that uses fluorescence to quantify resorufin + Resazurin (active ingredient in alamar blue and CellTiter blue reagents) has a blue color and is not fluorescent. Resorufin is pink and fluorescent. This assay uses the commercial reagent CellTiter Blue (Promega) containing resazurin and fluorescence to detect resorufin. + Jennifer Fostel + CellTiter Blue viability assay + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release + + A cell death assay that measures the release of intracellular LDH. + Jennifer Fostel + cell death assay detecting lactate dehydrogenase (LDH) release + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + A cell death assay detecting lactate dehydrogenase (LDH) release by absorbance of substrate + In this assay reagents are added so that LDH produces reduced nicotinamide adenine dinucleotide (NADH) when it catalyzes the oxidation of lactate to pyruvate, and the NADH converts a tetrazolium salt to a colored formazan product in the presence of an electron acceptor. This formazan product is detected by absorbance quality. + Jennifer Fostel + Cytotox 96 assay + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ovulation assessment in rodent assay + + A histological assay that measures the number of corpora lutea (UBERON:0002512) in the ovary of an organism; corpora lutea develop from the postovulatory follicle. + Jennifer Fostel + Corpus luteum count + ovulation assessment in rodent assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + macroscopic examination of material anatomical entity assay + + An assay that performs a macroscopic assessment of a material anatomical entity using the sense of sight. + Jennifer Fostel + macroscopic examination of material anatomical entity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pathological macroscopic examination of specimen assay + + A macroscopic examination of material anatomical entity assay performed on a post-mortem anatomical specimen. + one objective of this assay is to provide information about the character and extent of changes present and to inform on the cause of death. + Jennifer Fostel + Gross pathology assessment + pathological macroscopic examination of specimen assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle assay based on tissue morphology + + A histological assay that evaluates cells in the vaginal endometrium to assess the estrous cycle phase the subject was in at the time of specimen collection. + Jennifer Fostel + estrous cycle assay based on tissue morphology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo + + An organism development assay performed with a late embryo stage subject. + one objective of this assay is to assess anatomical structures and identify developmental phenotype + Jennifer Fostel + fetal examination + organism development assay in late embryo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pregnancy assessment based on tissue morphology assay + + A histological assay that measures the number of implantation sites in an organism. + An implantation site in this context is the site in the endometrium where the fertilized egg attaches and embeds itself to begin development + Jennifer Fostel + implantation site count + pregnancy assessment based on tissue morphology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay using vital dye + + A cell death assay that uses the Trypan blue vital dye to stain cells which have lost membrane integrity. + Living cells exclude Trypan blue + Jennifer Fostel + cell death assay using vital dye + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite length assay + + A cytometry assay that uses a distance measurement assay to determine the length of a neurite. + A neurite is a neuronal process greater than 10 um extending from a neuron. + Jennifer Fostel + neurite length assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite degree of arborization assay + + A cytometry assay that measures the degree of arborization, or branching, in neuronal processes + Jennifer Fostel + neurite branch point count + neurite degree of arborization assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite count assay + + A cytometry assay that measures the number of neurites in a cultured specimen. + A neurite is a neuronal process greater than 10 um extending from a neuron. + Jennifer Fostel + neurite count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron count assay + + A cytometry assay that measures the number of neurons in a sample + Jennifer Fostel + neuron count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell-body-associated presynaptic puncta count assay + + A regulation of synapse maturation assay that determines the number of synaptic puncta in the cell body compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. + Jennifer Fostel + cell-body-associated presynaptic puncta count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + dendrite-associated presynaptic puncta count assay + + A regulation of synapse maturation assay that determines the number of synaptic puncta in the dendritic compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. + Jennifer Fostel + dendrite-associated presynaptic puncta count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + synapse per neuron assay + + A regulation of synapse maturation assay that determines the number of synaptic puncta in a culture and normalizes it by the number of neurons in the culture. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. + Jennifer Fostel + synapse per neuron assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + absorbance quality detection assay + + An assay that measures the absorbance quality of the evaluant + the unit of this assay is absorbance unit (UO:0000269) + Jennifer Fostel + absorbance quality detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + hormone assay + + The analyte assay that measures the abundance of a hormone in a specimen. + Jennifer Fostel + hormone assay + + + + + + + + + chemiluminescent assay + + An analyte assay that detects a substance by measuring the release of light triggered by a chemical reaction. + SD + CLIA + HCC + HCC + chemiluminescent assay + + + + + + + + + electrochemiluminescence assay + + A chemiluminescent assay that detects a substance by measuring the release of light triggered by an electrochemical reaction. + SD + ECL + Meso Scale Discovery ECL + HCC + HCC + electrochemiluminescence assay + + + + + + + + + + + + + + + + + + + + + + proteomics by mass spectrometry assay + + A mass spectrometry assay that identifies and measures proteins. + SD + HCC + HCC + proteomics by mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + metabolomics by mass spectrometry assay + + A mass spectrometry assay that identifies and measures metabolites. + SD + HCC + HCC + metabolomics by mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + cellular indexing of transcriptomes and epitopes by sequencing + + An assay performed on single cells that simultaneously measures transcript expression via single-cell RNA sequencing and profiles surface proteins via sequencing of DNA-barcodes attached to antibodies recognizing particular surface proteins from individual cells. + SD + CITE-Seq + HCC + HCC + cellular indexing of transcriptomes and epitopes by sequencing + + + + + + + + + immune receptor repertoire profiling assay + + An assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors or T cell receptors within an input sample. + SD + HCC + HCC + immune receptor repertoire profiling assay + + + + + + + + + + + + + + + + + + + + antibody-dependent complement deposition assay + + An assay measuring antibody-dependent complement-dependent cytotoxicity. + SD + ADCD + HCC + HCC + antibody-dependent complement deposition assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial flagellin detection in plasma assay + + An analyte assay measuring bacterial flagellin in a plasma sample. + SD + HCC + HCC + bacterial flagellin detection in plasma assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial flagellin detection in feces assay + + An analyte assay measuring bacterial flagellin in a feces sample. + SD + HCC + HCC + bacterial flagellin detection in feces assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial lipopolysaccharide detection in plasma assay + + An analyte assay measuring bacterial lipopolysaccharide in a plasma sample. + SD + LPS + HCC + HCC + bacterial lipopolysaccharide detection in plasma assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial lipopolysaccharide detection in feces assay + + An analyte assay measuring bacterial lipopolysaccharide in a feces sample. + SD + LPS + HCC + HCC + bacterial lipopolysaccharide detection in feces assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + adenosine deaminase activity assay + + An analyte assay measuring adenosine deaminase activity in a sample. + SD + ADA + HCC + HCC + adenosine deaminase activity assay + + + + + + + + + pathogen neutralization assay + + An assay that measures neutralization of a pathogen. + SD + HCC + pathogen neutralization assay + + + + + + + + + bacterial neutralization assay + + A pathogen neutralization assay measuring neutralization of bacteria. + SD + HCC + bacterial neutralization assay + + + + + + + + + viral plaque assay + + An analyte assay measuring the number of discrete viral plaques. + SD + PMID:Ê25407402 + HCC + viral plaque assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + analyte detection by flow based bead assay + + An analyte assay that uses beads to measure the concentration of an analyte with a flow cytometer. + SD + HCC + HCC + analyte detection by flow based bead assay + + + + + + + + + bacterial lipopolysaccharide + + A molecule that is a component of the outermost membrane of the cell envelope of gram-negative bacteria and which consists of three parts: an outer core polysaccharide termed the O-antigen, an inner core oligosaccharide, and Lipid A, all covalently linked. + RV + SD + https://en.wikipedia.org/wiki/Lipopolysaccharide + Temporary term created for HCC & intended to be replaced with a term from a different ontology once one can be NTRed. + bacterial lipopolysaccharide + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine clarity assay + + A histological assay with urine evaluant that measures opacity of the urine + Jennifer Fostel + urine opacity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine color assay + + A histological assay with urine evaluant that measures color. + Jennifer Fostel + urine color assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine histological assay + + A histological assay with urine sediment as evaluant. + Frequently this assay detects the presence of cells, casts, crystals, bacteria and parasites. + Jennifer Fostel + urine histological assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + color detection assay + + An assay that measures the color of the evaluant + generally detected by sight, as a color indicator. + Jennifer Fostel + color detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + opacity determination assay + + An assay that measures the opacity of the evaluant + Jennifer Fostel + opacity determination assay + + + + + + + + + electrocardiograph + + An instrument for recording the changes of electrical potential occurring during the heartbeat used especially in diagnosing abnormalities of heart action. + Jennifer Fostel + https://www.merriam-webster.com/dictionary/electrocardiograph + electrocardiograph + + + + + + + + + biotelemeter + + A measurement device that also transmits the measurement information from a biological material to a distant station. + Jennifer Fostel + biotelemeter + + + + + + + + + multi-electrode array plate + + A measurement device consisting of grid of tightly spaced microscopic electrodes that can detect the electrical signals of cells in close proximity. + Multielectrode arrays can be embedded in the bottom of a well and cells can be cultured over the electrodes for passive, noninvasive monitoring of electrical activity. + Jennifer Fostel + multi-electrode array plate + + + + + + + + + Transepithelial Electrical Resistance (TEER) device + + A measurement device that measures monolayer barrier integrity via measurement of membrane potential and electrical resistance across a cell monolayer in culture. + Jennifer Fostel + Transepithelial Electrical Resistance (TEER) device + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle count assay + + An estrous cycle assay based on tissue morphology that determines the number of estrous cycles observed in a defined time. + Jennifer Fostel + estrous cycle count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle duration assay + + An estrous cycle assay based on tissue morphology that determines the average length of a full estrous cycle observed in a defined time. + Jennifer Fostel + estrous cycle duration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo based on examination of surface structure + + An organism development assay in late embryo that evaluates only the external surface structure of the organism + Jennifer Fostel + external fetal exam + organism development assay in late embryo based on examination of surface structure + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo based on examination of skeletal system + + An organism development assay in late embryo that evaluates the skeletal system of the organism + Jennifer Fostel + skeletal fetal exam + organism development assay in late embryo based on examination of skeletal system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo based on examination of anatomical system + + An organism development assay in late embryo that evaluates the anatomical system of the organism + Jennifer Fostel + visceral fetal exam + organism development assay in late embryo based on examination of anatomical system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + distance measurement assay + + An assay that measures the space between two entities. + Distance is a measure of the amount of space between two points. + Jennifer Fostel + distance measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + length measurement assay + + An assay that measures the distance between two points. + Typically length is a property of an object, the distance from end to end often in the largest dimension. + Jennifer Fostel + length measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + crown rump length + + A length measurement assay that measures the length of a neonate or fetus from crown of head to base of torso (rump) + Jennifer Fostel + crown rump length + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + path length assay + the distance traveled by a rodent in a maze + + An assay that measures the distance traveled in a defined period of time. + The total distance traveled by an entity in a given time; the sum of all segments in the path traveled if it is not straight. + Jennifer Fostel + path length assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell migration assay + + A distance measurement assay in which the migration of cells in culture is monitored by measuring the distance between the start position and the cell's location when observed. + This is the distance between the start and end points of cultured cells + Jennifer Fostel + cell migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligodendrocyte migration assay + + A cell migration assay that measures migration of an oligodendrocyte + Jennifer Fostel + oligodendrocyte migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + radial glial migration assay + + A cell migration assay that measures migration of a radial glia cell + Jennifer Fostel + radial glial migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron migration assay + + A cell migration assay that measures migration of a neuron + Jennifer Fostel + neuron migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neural crest cell migration assay + + A cell migration assay that measures migration of a neural crest cell + Jennifer Fostel + neural crest cell migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + acidity quality assay + + An assay that measures the acidity of a specimen on the pH scale. + The measurement of pH is the negative logarithm to base ten of the hydrogen ion activity in a solution, this measures the degree of acidity or alkalinity. + Jennifer Fostel + acidity quality assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specific gravity assay + + An assay that measures the specific gravity of a sample. + Specific gravity is the ratio of the density of the specimen to the ratio of water or other standard. + Jennifer Fostel + specific gravity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + speed measurement assay + + An assay to determine the speed of an evaluant. + Speed is a physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position (PATO). + Jennifer Fostel + speed measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + velocity measurement assay + + An assay to measure the velocity of an evaluant + Velocity is a physical quality inhering in a bearer by virtue of the bearer's rate of change of the position (PATO). + Jennifer Fostel + velocity measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + luminescence detection assay + + An assay that measures the luminescence of the evaluant + the unit of this assay is relative luminescence unit (UO:0000313) + Jennifer Fostel + luminescence detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay using luciferase to detect ATP in the cell + + A cell viability assay that uses an ATP bioluminescence assay to detect ATP in the living cell + one reagent is CellTiter Glo (Promega) which contains luciferase and luciferin. Luciferase uses ATP in the living cell to convert luciferin to oxyluciferin and light. + Jennifer Fostel + cell viability assay using luciferase to detect ATP in the cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + population count assay + + An assay that measures the number of elements in a portion of a population + Not a synonym of organism detection assay (OBI:0002738); "A population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + Jennifer Fostel + population count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + hemolysis assay + + A hematology assay that measures the fragility of red blood cells by observing spillage of hemoglobin from burst cells. + Jennifer Fostel + hemolysis assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mean firing rate + + An electrophysiology assay that measures action potential events in neurons during a time period. + Jennifer Fostel + neuron action potential rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron burst rate assay + + An electrophysiology assay that measures the number of action potential bursts in neurons during a time period. + A burst is temporal arrangement of action potentials that occur close together in time followed by a period of quiescence. + Jennifer Fostel + neuron burst rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron interburst interval assay + + An electrophysiology assay that measures the elapsed time between consecutive action potential bursts in neurons. + A burst is temporal arrangement of action potentials that occur close together in time followed by a period of quiescence, the interburst interval. + Jennifer Fostel + neuron interburst interval assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron burst duration assay + + An electrophysiology assay that measures the time elapsed between the first action potential in a neuron burst and the last in that burst. + Jennifer Fostel + neuron burst duration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + interspike interval within a burst + + An electrophysiology assay that measures the time elapsed between the peaks of consecutive action potential spikes in a neuron burst. + Jennifer Fostel + action potential interval assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + rate of action potentials in neuron burst assay + + An electrophysiology assay that measures the number of action potential spikes occurring within a neuron burst + singleton spikes in the same time period unrelated to a neuron burst are not included in the count. + Jennifer Fostel + rate of action potentials in neuron burst assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body mass assay + + A mass measurement assay with evaluant an individual organism. + Jennifer Fostel + body mass assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body mass change assay + + A body mass assay that measures the change in body mass for a subject over a period of time. + Jennifer Fostel + body mass change assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + terminal body weight assay + + A body weight assay with evaluant individual organism specimen with quality dead. + Jennifer Fostel + body weight assay at death + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tissue mass assay + + A mass measurement assay with evaluant tissue or bodily fluid specimen. + Jennifer Fostel + tissue mass assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tissue mass percent of body mass assay + + A mass measurement assay with evaluant tissue expressed as a percentage of the body weight of the organism from which the specimen was derived. + Jennifer Fostel + tissue mass percent of body mass assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + developmental marker age of attainment assessment + the age of the rat at testis descent, the age of a human child at first menses. + + An age determination assay which determines the age of the subject at the time of the change from a state where it did not have a developmental stage marker to one in which it does. + Jennifer Fostel + developmental marker age of attainment assessment + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytochrome P450 assay + + A protein assay that measures the abundance of cytochrome P450 in a specimen. + Jennifer Fostel + cytochrome P450 assay + + + + + + + + + + + + + + + + + + + + growth factor assay + + An analyte assay to measure the abundance of one or more growth factors in a volume of sample. + A growth factor is a signalling role of a chemical substance in which it stimulates a biological system to proliferate, divide, differentiate, migrate, and so forth. + Jennifer Fostel + growth factor assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Hoechst dye assay + + A fluorescence imaging-based cell morphology assay that uses Hoechst dye 33342 + Hoechst dye binds to DNA and can be used to visualize nuclei. Often used to quantify cells, identify position over time, identify the cell body and other assays. + Jennifer Fostel + Hoechst dye assay + + + + + + + + + + + + + + + + + + + + hypersensitivity assay + + An immune response assay to assess the hypersensitivity response in an organism or cell culture. + Jennifer Fostel + hypersensitivity assay + + + + + + + + + super-resolution microscopy assay + + A type of light microscopy assay where the images are taken with a resolution higher than the diffraction limit. + Lachlan Whitehead + Marek Cmero + super resolution microscopy assay + http://purl.obolibrary.org/obo/MI_2213 + super-resolution microscopy assay + + + + + + + + + + + + + + + multi-photon microscope + + A microscope that uses simultaneous absorption of multiple photons to excite fluorescent molecules. + PERSON: Lachlan Whitehead + PERSON: Marek Cmero + PERSON: Pradeep Rajasekhar + MPLSM + multiphoton laser scanning microscope + two-photon excitation microscope + doi:10.1364/AOP.7.000276 + multiphoton microscope + + + + + + + + + + + + + + + light sheet microscope + + A microscope that uses illumination and detection objectives to image a sample illuminated with a thin sheet of laser light. + PERSON: Lachlan Whitehead + PERSON: Marek Cmero + light-sheet microscope + lightsheet microscope + doi:10.1016/B978-0-12-420138-5.00011-2 + light sheet microscope + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1M7 RNA structure mapping assay + PMID: 29551268 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methyl-7-nitroisatoic anhydride as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 1M7 probe + 1M7 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + NAI RNA structure mapping assay + PMID: 37674078 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-methylnicotinic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using NAI probe + NAI RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + NAI-N3 RNA structure mapping assay + PMID: 29804836 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-(azidomethyl)nicotinic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using NAI-N3 probe + NAI-N3 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 2A3 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-aminopyridine-3-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 2A3 probe + 2A3 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + I5 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using indoline-5-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using I5 probe + I5 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 1M4 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methylimidazole-4-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 1M4 probe + 1M4 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 6A3 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 6-aminopyridine-3-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 6A3 probe + 6A3 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + B5 RNA structure mapping assay + PMID:33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using benzotriazole-5-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using B5 probe + B5 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + NIC RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using nicotinic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using NIC probe + NIC RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + BzCN RNA structure mapping assay + PMID: 33453165 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using benzoyl cyanide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using BzCN probe + BzCN RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 1M6 RNA structure mapping assay + PMID: 30341219 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methyl-6-nitroisatoic anhydride as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 1M6 probe + 1M6 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 5NIA RNA structure mapping assay + PMID: 36062555 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 5-nitroisatoic anhydride as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 5NIA probe + 5NIA RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell count assay + + An assay that measures the number of cells in a portion of a cell culture or tissue or bodily fluid + OBI:2100330 count bodily fluid cell count assay / OBI:2100345 bodily fluid cell count assay + Jennifer Fostel + cell count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + differential leukocyte count assay + + A hematology assay that measures the percentage of classes of leukocytes in a sample. + Jennifer Fostel + differential leukocyte count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + electrocardiogram assay + + An electrophysiology assay that measures heart activity using electrodes placed to detect electrical signals from the heart. + related to electrocardiography (MAXO:0010203): A procedure that displays the electrical activity of the heart. + Jennifer Fostel + electrocardiogram assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + telemeter sensor detection assay + + An assay which uses an implanted telemeter to measure physiological data in a living organism and transmit the measures via radio waves to a recording device. + different types of telemeters can measure blood pressure, gross activity, heart rate, ECG, glucose and other physiological parameters. + Jennifer Fostel + telemeter sensor detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MEA assay + + A multi-unit recording assay using a multi-electrode array (MEA) on the surface of a well on a cell culture plate. + When cells capable of electrical signaling are cultured in the well the MEA grid can detect electrical signaling by the cells. + Jennifer Fostel + multi-electrode array assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transepithelial / transendothelial electrical resistance (TEER) assay + An example would be a TEER assay to measure the integrity of a cell monolayer with apical surface exposed to air and basal surface in culture medium; this mimics the airway epithelium. + + An extracellular electrophysiology recording assay to measure the integrity of a cell monolayer + the assay measures electrical resistance by manually placing two chopstick-style electrodes on each side of a confluent cell layer. A low frequency current is applied and the resistance of the barrier is measured. + Jennifer Fostel + transepithelial / transendothelial electrical resistance (TEER) assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + number of active electrodes + + A multi-electrode array assay that measures the number of electrodes in a well where the mean rate of action potentials is at least 5 spikes per minute. + Jennifer Fostel + count of multi-electrode plate electrodes detecting action potential assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + number of bursting electrodes + + A multi-electrode array assay that measures the number of electrodes in a well where the burst rate is at least 0.5 bursts per minute. + A burst is temporal arrangement of action potentials that occur close together in time followed by a period of quiescence. + Jennifer Fostel + count of multi-electrode plate electrodes detecting neuron burst assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neural network spike rate assay + + An multi-electrode assay that measures the number of events when multiple electrodes simultaneously detect an action potential during a time period. + In a microelectrode array assay, the number of instances during a 15-minute recording when 5 or more electrodes in a well participate in an action potential burst at the same time. + Jennifer Fostel + neural network spike rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neural network spike duration assay + + A multi-electrode assay that measures the mean duration of events when multiple electrodes detect an action potential + In a microelectrode array (MEA) assay, the time interval before and after the network spike peak when half as many electrodes are spiking as at the peak of the network spike . + Jennifer Fostel + neural network spike duration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + network spike peak + + A multi-electrode array assay that measures the average number of electrodes detecting a network spike, measured at the peak of a network spike. + a network spike is defined in this context as an event when multiple electrodes detect an action potential + Jennifer Fostel + count of multi-electrode plate electrodes detecting spike peak assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mean interspike interval in network spike + + A multi-electrode assay that measures the average interval between network spikes, events where multiple electrodes simultaneously detect an action potential. + The time interval between the peaks of consecutive network spikes in a microelectrode array (MEA). A network spike is an event where multiple electrodes simultaneously detect an action potential. + Jennifer Fostel + mean interspike interval in network spike + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -104778,35 +111700,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - - - - - - - - - - - cell based DNA damage assay + bile acid concentration assay - A cytometry assay that measures DNA damage in cells. + An analyte assay that measures the abundance of bile acid in a volume of sample. + The major component of bile acids are cholic and chenodeoxycholic acid. Jennifer Fostel - cell based DNA damage assay + bile acid concentration assay - + - - + + @@ -104818,7 +111730,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104829,7 +111741,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104841,30 +111753,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - natural killer cell count assay - - A cytometry assay to determine the number of natural killer cells in a specimen - Jennifer Fostel - natural killer cell count assay - - - - - - - - @@ -104873,10 +111761,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -104884,17 +111772,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + @@ -104905,24 +111783,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - natural killer cell percentage assay + urea nitrogen assay - A cytometry assay that measures the percentage of natural killer cells in a specimen. + An analyte assay that measures the abundance of urea nitrogen. + urea nitrogen is the nitrogen component of urea found in a biological specimen Jennifer Fostel - natural killer cell percentage assay + urea nitrogen assay - + - - + + @@ -104934,7 +111813,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104945,7 +111824,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104957,35 +111836,80 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + + + + + + + + + - + - sperm count assay + urea nitrogen concentration assay - A cytometry assay to count the number of mature sperm in a specimen. + A urea nitrogen assay that measures the abundance of urea nitrogen in a specimen + urea nitrogen is the nitrogen component of urea found in a biological specimen Jennifer Fostel - sperm count assay + urea nitrogen concentration assay - + - - - survey administration assay - - An assay that obtains data from one or more participants by using a survey or questionnaire - Jennifer Fostel - survey administration assay + + + randomized clinical trial + + A clinical trial in which the participants are divided by chance into separate groups that compare different treatments or other interventions. Using chance to divide people into groups means that the groups will be similar and that the effects of the treatments they receive can be compared more fairly. At the time of the trial, it is not known which treatment is best. + Sebastian Duesing + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/randomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + randomized clinical trial + + + + + + + + + non-randomized clinical trial + + A clinical trial in which the participants are not assigned by chance to different treatment groups. Participants may choose which group they want to be in, or they may be assigned to the groups by the researchers. + Sebastian Duesing + nonrandomized clinical trial + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/nonrandomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + non-randomized clinical trial @@ -105032,7 +111956,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + Epstein Barr virus transformed B cell PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. @@ -105047,7 +111971,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + chimera An organism which contains cells or tissues with a different genotype @@ -105081,7 +112005,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -105155,31 +112078,22 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - organism - animal - fungus - plant - virus + + obsolete organism + animal + fungus + plant + virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism + WEB: http://en.wikipedia.org/wiki/Organism + + + obsolete organism + true @@ -105340,7 +112254,7 @@ This issue is outside the scope of OBI. - + @@ -105350,7 +112264,7 @@ This issue is outside the scope of OBI. - + xenograft @@ -105369,7 +112283,7 @@ This issue is outside the scope of OBI. - + @@ -105484,7 +112398,7 @@ Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39- - + screening library PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] @@ -105514,7 +112428,6 @@ change biomaterial to material in definition - synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme @@ -105533,7 +112446,7 @@ DS: Is this synthetic an oxymoron to the biomaterial? - + @@ -105653,7 +112566,21 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - + + + + + + + + + + + + + + + @@ -105685,7 +112612,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. - A planned process that produces output data from input data. + A completely executed planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone @@ -107840,7 +114767,7 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - + @@ -109676,28 +116603,23 @@ determinations of compounds. - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. @@ -109784,7 +116706,7 @@ determinations of compounds. - + @@ -109812,7 +116734,7 @@ determinations of compounds. - + @@ -109836,7 +116758,7 @@ determinations of compounds. - + @@ -109959,15 +116881,16 @@ determinations of compounds. - comet assay + DNA damage comet assay PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. - An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis + A cell based DNA damage assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis Philippe Rocca-Serra SCGE assay + comet assay single cell gel electrophoresis assay PMID:7686265 - comet assay + DNA damage comet assay @@ -110069,7 +116992,6 @@ determinations of compounds. - denatured polymer Is a polymer which has lost secondary or tertiary structure @@ -110094,7 +117016,7 @@ determinations of compounds. - + decapitated organism Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 @@ -110188,7 +117110,6 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - methylated polymer Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 @@ -110207,7 +117128,7 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 - + @@ -110215,8 +117136,8 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 + - genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 @@ -110402,7 +117323,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110423,7 +117344,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110456,7 +117377,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110489,11 +117410,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + - + @@ -110538,7 +117459,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110687,7 +117608,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + intentional overdosing @@ -110753,7 +117674,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110774,7 +117695,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110806,14 +117727,14 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + - + @@ -110876,7 +117797,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110904,7 +117825,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -110931,7 +117852,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + validation PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. @@ -111017,7 +117938,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -111235,7 +118156,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112165,7 +119086,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112199,7 +119120,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + particle delivery vessel FC 500 particle delivery vessel @@ -112285,7 +119206,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112307,7 +119228,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112549,7 +119470,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112640,7 +119561,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112711,7 +119632,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112830,7 +119751,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113199,7 +120120,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113374,7 +120295,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113449,7 +120370,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -114107,7 +121028,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114136,14 +121057,14 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114159,7 +121080,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114213,7 +121134,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114230,13 +121151,13 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114316,7 +121237,7 @@ Relates to the creation of a class 'selection rule' - + exposure of material to environment Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. @@ -114436,7 +121357,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114463,11 +121384,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + @@ -114479,7 +121400,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114675,7 +121596,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114698,7 +121619,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114892,7 +121813,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114914,7 +121835,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114977,7 +121898,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115074,7 +121995,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115096,7 +122017,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115152,7 +122073,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115226,7 +122147,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115266,7 +122187,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115287,17 +122208,17 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + - + @@ -115383,7 +122304,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115779,7 +122700,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115874,7 +122795,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115995,7 +122916,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116110,8 +123031,8 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ + - @@ -116139,7 +123060,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116167,7 +123088,7 @@ Isolation of proliferation factor of immature T-cell clone in concanavalin A-sti - + @@ -116235,7 +123156,7 @@ addition of has_role restriction - + @@ -116266,7 +123187,7 @@ old defintion: A mixture (collection) of cell components created by rupturing of - + @@ -116320,7 +123241,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - @@ -116350,7 +123270,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + assay bead Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. @@ -116675,7 +123595,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + Immunization in vivo @@ -116767,7 +123687,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116883,7 +123803,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116928,7 +123848,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116936,7 +123856,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + host of immune response A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. @@ -117204,7 +124124,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - lymph node cell specimen @@ -118000,19 +124919,20 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - blood harvesting + blood specimen collection - A material separation where blood is taken from an organism. + A specimen collection in which blood is collected from an organism. IEDB + blood harvesting IEDB - blood harvesting + blood specimen collection @@ -118200,7 +125120,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - splenocyte specimen @@ -122002,7 +128921,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + calcium cation assay An analyte assay that measures the abundance of calcium cation @@ -147892,18 +154811,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - phenotype - A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. - - phenotype - - - - @@ -147960,7 +154867,7 @@ realizes some 'host of immune response role' - + treatment A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process @@ -148010,7 +154917,7 @@ realizes some 'host of immune response role' health care provider role - A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. + A health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. health care provider role @@ -148044,7 +154951,7 @@ realizes some 'host of immune response role' - + parasite organism An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. @@ -148068,7 +154975,7 @@ realizes some 'host of immune response role' - + quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities @@ -148077,6 +154984,18 @@ realizes some 'host of immune response role' + + + + + speed + A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position. + + speed + + + + @@ -148089,6 +155008,19 @@ realizes some 'host of immune response role' + + + + + + color + A composite chromatic quality composed of hue, saturation and intensity parts. + + color + + + + @@ -148125,6 +155057,18 @@ realizes some 'host of immune response role' + + + + + distance + A quality that is the extent of space between two entities. + + distance + + + + @@ -148305,6 +155249,18 @@ realizes some 'host of immune response role' + + + + + opacity + An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. + + opacity + + + + @@ -148317,6 +155273,18 @@ realizes some 'host of immune response role' + + + + + mass density + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. + + mass density + + + + @@ -148404,7 +155372,7 @@ realizes some 'host of immune response role' - + physical object quality A quality which inheres in a continuant. @@ -148413,6 +155381,30 @@ realizes some 'host of immune response role' + + + + + full-spectrum EM radiation quality + An EM radiation quality that is independent of the EM wavelength range. + + full-spectrum EM radiation quality + + + + + + + + + absorption quality + A scalar EM radiation quality which obtains by the capacity of the bearer to retain radiation. + + absorption quality + + + + @@ -148749,6 +155741,18 @@ realizes some 'host of immune response role' + + + + + conductivity + A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium. + + conductivity + + + + @@ -148810,6 +155814,18 @@ realizes some 'host of immune response role' + + + + + electrical conductivity + A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity. + + electrical conductivity + + + + @@ -148834,6 +155850,18 @@ realizes some 'host of immune response role' + + + + + acidity + A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions). + + acidity + + + + @@ -148918,6 +155946,16 @@ realizes some 'host of immune response role' + + + + + A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. + electric charge + + + + @@ -148978,6 +156016,18 @@ realizes some 'host of immune response role' + + + + + velocity + A physical quality inhering in a bearer by virtue of the bearer's rate of change of the position. + + velocity + + + + @@ -149026,12 +156076,40 @@ realizes some 'host of immune response role' + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + collection of organisms + + + + + + + + + An anatomical entity that is or was part of a plant. + plant anatomical entity + + + + + protein antithrombin III is a protein + An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein @@ -149087,6 +156165,18 @@ realizes some 'host of immune response role' + + + + + adenosine deaminase + A protein that is a translation product of the human ADA gene or a 1:1 ortholog thereof. + + adenosine deaminase + + + + @@ -149279,6 +156369,16 @@ realizes some 'host of immune response role' + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + amino acid chain + + + + @@ -149412,6 +156512,30 @@ realizes some 'host of immune response role' + + + + + luciferase-like monooxygenase + A protein that is a translation product of the Escherichia coli K-12 yhbW gene or a 1:1 ortholog thereof. + + luciferase-like monooxygenase + + + + + + + + + bacterial protein + A protein that is encoded in the genome of some Bacteria <prokaryote>. + + bacterial protein + + + + @@ -149484,6 +156608,18 @@ realizes some 'host of immune response role' + + + + + modified histone + A histone that contains one or more amino acid modifications. + + modified histone + + + + @@ -149519,7 +156655,7 @@ realizes some 'host of immune response role' - + region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule @@ -149654,10 +156790,26 @@ realizes some 'host of immune response role' - - uterine cervix + + + + + + + + + + + + + + + + + + + Lower, narrow portion of the uterus where it joins with the top end of the vagina. - uterine cervix @@ -149666,10 +156818,8 @@ realizes some 'host of immune response role' - - pituitary gland + The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. - pituitary gland @@ -149678,10 +156828,14 @@ realizes some 'host of immune response role' - - peripheral nervous system + + + + + + + A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. - peripheral nervous system @@ -149690,10 +156844,26 @@ realizes some 'host of immune response role' - - lymph node + + + + + + + + + + + + + + + + + + + Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. - lymph node @@ -149702,22 +156872,50 @@ realizes some 'host of immune response role' - - urethra + + + + + + + The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. - urethra + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + anatomical structure + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + organ + + + + - life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. - life cycle stage @@ -149726,10 +156924,26 @@ realizes some 'host of immune response role' - - cloaca + + + + + + + + + + + + + + + + + + + Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. - cloaca @@ -149738,10 +156952,20 @@ realizes some 'host of immune response role' - - mouth + + + + + + + + + + + + + The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - mouth @@ -149751,9 +156975,7 @@ realizes some 'host of immune response role' - amniotic fluid Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. - amniotic fluid @@ -149763,9 +156985,13 @@ realizes some 'host of immune response role' - blood + + + + + + A fluid that is composed of blood plasma and erythrocytes. - blood @@ -149774,10 +157000,26 @@ realizes some 'host of immune response role' - - amnion + + + + + + + + + + + + + + + + + + + The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected. - amnion @@ -149786,10 +157028,14 @@ realizes some 'host of immune response role' - - breast + + + + + + + The upper ventral region of the torso of an organism. - breast @@ -149799,21 +157045,33 @@ realizes some 'host of immune response role' - cervical mucus A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. - cervical mucus + + + + + An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. + late embryo + + + + - - throat + + + + + + + In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. - throat @@ -149823,9 +157081,7 @@ realizes some 'host of immune response role' - renal medulla The inner portion of the kidney consisting of the renal pyramids. - renal medulla @@ -149835,9 +157091,7 @@ realizes some 'host of immune response role' - organism substance Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. - organism substance @@ -149846,22 +157100,57 @@ realizes some 'host of immune response role' + + + + + + + + + + - material anatomical entity + Anatomical entity that has mass. - material anatomical entity + + + + + + Anatomical entity that has no mass. + immaterial anatomical entity + + + + + + + + + + + + + + + Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. + anatomical system + + + + - - testis + + A gonad of a male animal. A gonad produces and releases sperm. - testis @@ -149870,10 +157159,8 @@ realizes some 'host of immune response role' - - anatomical cluster + Anatomical group whose component anatomical structures lie in close proximity to each other. - anatomical cluster @@ -149882,10 +157169,8 @@ realizes some 'host of immune response role' - - tissue + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. - tissue @@ -149894,10 +157179,14 @@ realizes some 'host of immune response role' - - multi-tissue structure + + + + + + + Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. - multi-tissue structure @@ -149907,9 +157196,13 @@ realizes some 'host of immune response role' - epithelium + + + + + + Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - epithelium @@ -149918,10 +157211,20 @@ realizes some 'host of immune response role' - - stomach + + + + + + + + + + + + + An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. - stomach @@ -149930,10 +157233,14 @@ realizes some 'host of immune response role' - - aorta + + + + + + + The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. - aorta @@ -149942,10 +157249,8 @@ realizes some 'host of immune response role' - - heart + A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. - heart @@ -149954,10 +157259,8 @@ realizes some 'host of immune response role' - - brain + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. - brain @@ -149966,10 +157269,14 @@ realizes some 'host of immune response role' - - cerebral cortex + + + + + + + The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. - cerebral cortex @@ -149978,10 +157285,8 @@ realizes some 'host of immune response role' - - eye + An organ that detects light. - eye @@ -149990,10 +157295,8 @@ realizes some 'host of immune response role' - - leg + The portion of the hindlimb that contains both the stylopod and zeugopod. - leg @@ -150002,10 +157305,8 @@ realizes some 'host of immune response role' - - ovary + The gonad of a female organism which contains germ cells. - ovary @@ -150014,10 +157315,20 @@ realizes some 'host of immune response role' - - uterus + + + + + + + + + + + + + The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. - uterus @@ -150026,10 +157337,20 @@ realizes some 'host of immune response role' - - vagina + + + + + + + + + + + + + A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. - vagina @@ -150039,9 +157360,20 @@ realizes some 'host of immune response role' - skin epidermis + + + + + + + + + + + + + The outer epithelial layer of the skin that is superficial to the dermis. - skin epidermis @@ -150050,10 +157382,9 @@ realizes some 'host of immune response role' - - respiratory system + + Functional system which consists of structures involved in respiration. - respiratory system @@ -150062,10 +157393,8 @@ realizes some 'host of immune response role' - - adipose tissue + Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. - adipose tissue @@ -150074,10 +157403,26 @@ realizes some 'host of immune response role' - - strand of hair + + + + + + + + + + + + + + + + + + + A filament, mostly protein, that grows from follicles found in the dermis[WP]. - strand of hair @@ -150086,22 +157431,54 @@ realizes some 'host of immune response role' - - rectum + + + + + + + + + + + + + + + + + + + The terminal portion of the intestinal tube, terminating with the anus. - rectum + + + + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + - pleural fluid Transudate contained in the pleural cavity. - pleural fluid @@ -150111,9 +157488,7 @@ realizes some 'host of immune response role' - urine Excretion that is the output of a kidney. - urine @@ -150123,9 +157498,7 @@ realizes some 'host of immune response role' - sweat Secretion produced by a sweat gland. - sweat @@ -150135,9 +157508,7 @@ realizes some 'host of immune response role' - synovial fluid Joint fluid is a transudate of plasma that is actively secreted by synovial cells. - synovial fluid @@ -150146,10 +157517,14 @@ realizes some 'host of immune response role' - - diaphragm + + + + + + + A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. - diaphragm @@ -150158,10 +157533,8 @@ realizes some 'host of immune response role' - - skeletal muscle tissue + Muscle tissue that consists primarily of skeletal muscle fibers. - skeletal muscle tissue @@ -150170,10 +157543,20 @@ realizes some 'host of immune response role' - - colon + + + + + + + + + + + + + A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. - colon @@ -150182,10 +157565,26 @@ realizes some 'host of immune response role' - - sigmoid colon + + + + + + + + + + + + + + + + + + + The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. - sigmoid colon @@ -150194,10 +157593,14 @@ realizes some 'host of immune response role' - - cortex of kidney + + + + + + + Outer cortical portion of the kidney, between the renal capsule and the renal medulla. - cortex of kidney @@ -150206,10 +157609,14 @@ realizes some 'host of immune response role' - - urinary bladder + + + + + + + Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. - urinary bladder @@ -150218,10 +157625,14 @@ realizes some 'host of immune response role' - - pancreas + + + + + + + An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. - pancreas @@ -150231,9 +157642,7 @@ realizes some 'host of immune response role' - peritoneal fluid Transudate contained in the peritoneal cavity. - peritoneal fluid @@ -150242,10 +157651,26 @@ realizes some 'host of immune response role' - - tibial nerve + + + + + + + + + + + + + + + + + + + The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]. - tibial nerve @@ -150255,21 +157680,39 @@ realizes some 'host of immune response role' - cerebrospinal fluid A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. - cerebrospinal fluid + + + + + + + + + + + + + + + + + Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. + skeletal system + + + + - - arm + The part of the forelimb extending from the shoulder to the autopod[cjm]. - arm @@ -150278,10 +157721,14 @@ realizes some 'host of immune response role' - - knee joint + + + + + + + The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. - knee joint @@ -150290,10 +157737,14 @@ realizes some 'host of immune response role' - - ankle joint + + + + + + + A joint that connects the hindlimb autopod and zeugopod skeletons. - ankle joint @@ -150303,9 +157754,7 @@ realizes some 'host of immune response role' - common carotid artery plus branches A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. - common carotid artery plus branches @@ -150314,10 +157763,20 @@ realizes some 'host of immune response role' - - digestive tract + + + + + + + + + + + + + A tube extending from the mouth to the anus. - digestive tract @@ -150326,10 +157785,14 @@ realizes some 'host of immune response role' - - upper respiratory tract + + + + + + + The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. - upper respiratory tract @@ -150338,10 +157801,14 @@ realizes some 'host of immune response role' - - lower respiratory tract + + + + + + + The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. - lower respiratory tract @@ -150350,10 +157817,14 @@ realizes some 'host of immune response role' - - cheek + + + + + + + A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. - cheek @@ -150362,10 +157833,8 @@ realizes some 'host of immune response role' - - facial muscle + A muscle innervated by a facial nerve. - facial muscle @@ -150375,9 +157844,13 @@ realizes some 'host of immune response role' - coronary artery + + + + + + An artery that supplies the myocardium. - coronary artery @@ -150386,10 +157859,14 @@ realizes some 'host of immune response role' - - artery + + + + + + + An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. - artery @@ -150398,10 +157875,14 @@ realizes some 'host of immune response role' - - vein + + + + + + + Any of the tubular branching vessels that carry blood from the capillaries toward the heart. - vein @@ -150410,10 +157891,14 @@ realizes some 'host of immune response role' - - tongue + + + + + + + A muscular organ in the floor of the mouth. - tongue @@ -150422,10 +157907,20 @@ realizes some 'host of immune response role' - - nasopharynx + + + + + + + + + + + + + The section of the pharynx that lies above the soft palate. - nasopharynx @@ -150434,10 +157929,20 @@ realizes some 'host of immune response role' - - oropharynx + + + + + + + + + + + + + The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. - oropharynx @@ -150447,9 +157952,19 @@ realizes some 'host of immune response role' - vitreous humor + + + + + + + + + + + + A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina. - vitreous humor @@ -150458,10 +157973,14 @@ realizes some 'host of immune response role' - - conjunctiva + + + + + + + The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball. - conjunctiva @@ -150470,10 +157989,32 @@ realizes some 'host of immune response role' - - nasal cavity mucosa + + + + + + + + + + + + + + + + + + + + + + + + + The mucous membrane that lines the nasal cavity[MP]. - nasal cavity mucosa @@ -150482,10 +158023,20 @@ realizes some 'host of immune response role' - - minor salivary gland + + + + + + + + + + + + + One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. - minor salivary gland @@ -150495,9 +158046,7 @@ realizes some 'host of immune response role' - saliva A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. - saliva @@ -150506,10 +158055,20 @@ realizes some 'host of immune response role' - - caudate nucleus + + + + + + + + + + + + + Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. - caudate nucleus @@ -150518,10 +158077,20 @@ realizes some 'host of immune response role' - - putamen + + + + + + + + + + + + + Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion. - putamen @@ -150531,9 +158100,19 @@ realizes some 'host of immune response role' - telencephalon + + + + + + + + + + + + Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. - telencephalon @@ -150543,9 +158122,7 @@ realizes some 'host of immune response role' - milk An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. - milk @@ -150555,9 +158132,7 @@ realizes some 'host of immune response role' - semen Organism substance that is composed of sperm cells suspended in seminal fluid. - semen @@ -150567,21 +158142,45 @@ realizes some 'host of immune response role' - bile Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. - bile + + + + + + + + + + + + + + + + + A vessel through which blood circulates in the body. + blood vessel + + + + - - placenta + + + + + + + Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. - placenta @@ -150591,9 +158190,7 @@ realizes some 'host of immune response role' - feces Portion of semisolid bodily waste discharged through the anus[MW,modified]. - feces @@ -150602,10 +158199,14 @@ realizes some 'host of immune response role' - - areola + + + + + + + Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. - areola @@ -150615,9 +158216,19 @@ realizes some 'host of immune response role' - cerebellum + + + + + + + + + + + + Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. - cerebellum @@ -150626,10 +158237,8 @@ realizes some 'host of immune response role' - - thyroid gland + A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. - thyroid gland @@ -150638,10 +158247,14 @@ realizes some 'host of immune response role' - - lung + + + + + + + Respiration organ that develops as an outpocketing of the esophagus. - lung @@ -150650,10 +158263,26 @@ realizes some 'host of immune response role' - - dermis + + + + + + + + + + + + + + + + + + + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. - dermis @@ -150662,10 +158291,26 @@ realizes some 'host of immune response role' - - hypodermis + + + + + + + + + + + + + + + + + + + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. - hypodermis @@ -150674,10 +158319,14 @@ realizes some 'host of immune response role' - - skin of body + + + + + + + The organ covering the body that consists of the dermis and epidermis. - skin of body @@ -150686,10 +158335,8 @@ realizes some 'host of immune response role' - - spleen + The organ that functions to filter blood and to store red corpuscles and platelets. - spleen @@ -150698,10 +158345,8 @@ realizes some 'host of immune response role' - - liver + An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. - liver @@ -150710,10 +158355,20 @@ realizes some 'host of immune response role' - - ileum + + + + + + + + + + + + + The portion of the small intestine that extends from the jejunum to the colon. - ileum @@ -150722,10 +158377,26 @@ realizes some 'host of immune response role' - - integument + + + + + + + + + + + + + + + + + + + The dermis, epidermis and hypodermis. - integument @@ -150735,9 +158406,19 @@ realizes some 'host of immune response role' - peritoneum + + + + + + + + + + + + A serous membrane that lines the peritoneal cavity[VHOG,modified]. - peritoneum @@ -150746,10 +158427,8 @@ realizes some 'host of immune response role' - - prostate gland + The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. - prostate gland @@ -150758,10 +158437,8 @@ realizes some 'host of immune response role' - - adrenal gland + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. - adrenal gland @@ -150771,21 +158448,55 @@ realizes some 'host of immune response role' - bone marrow + + + + + + + + + + + + The soft tissue that fills the cavities of bones. - bone marrow + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. + connective tissue + + + + + + + + + Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. + muscle tissue + + + + - - forelimb zeugopod + + + + + + + The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants. - forelimb zeugopod @@ -150794,10 +158505,8 @@ realizes some 'host of immune response role' - - manual digit + A digit that is part of a manus (hand). - manual digit @@ -150807,9 +158516,13 @@ realizes some 'host of immune response role' - lymph + + + + + + Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. - lymph @@ -150819,9 +158532,7 @@ realizes some 'host of immune response role' - pericardial fluid Transudate contained in the pericardial cavity.[FMA]. - pericardial fluid @@ -150830,10 +158541,8 @@ realizes some 'host of immune response role' - - tail + An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. - tail @@ -150842,10 +158551,14 @@ realizes some 'host of immune response role' - - lymphoid system + + + + + + + The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. - lymphoid system @@ -150854,22 +158567,68 @@ realizes some 'host of immune response role' - - esophagus mucosa + + + + + + + + + + + + + + + + + + + A mucosa that is part of a esophagus [Automatically generated definition]. - esophagus mucosa + + + + + + + + + + + A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID]. + corpus luteum + + + + + + + + + An organ that functions as a secretory or excretory organ. + gland + + + + - - left cerebral hemisphere + + + + + + + A cerebral hemisphere that is in the left side of a brain. - left cerebral hemisphere @@ -150878,22 +158637,40 @@ realizes some 'host of immune response role' - - right cerebral hemisphere + + + + + + + A cerebral hemisphere that is in the right side of a brain. - right cerebral hemisphere + + + + + Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. + surface structure + + + + - - trachea + + + + + + + The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. - trachea @@ -150902,10 +158679,20 @@ realizes some 'host of immune response role' - - cranium + + + + + + + + + + + + + Upper portion of the skull that excludes the mandible (when present in the organism). - cranium @@ -150914,10 +158701,14 @@ realizes some 'host of immune response role' - - omentum + + + + + + + A fold of peritoneum originating at the stomach and supporting the viscera. - omentum @@ -150926,10 +158717,20 @@ realizes some 'host of immune response role' - - esophagus muscularis mucosa + + + + + + + + + + + + + A muscularis mucosa that is part of a esophagus. - esophagus muscularis mucosa @@ -150938,10 +158739,38 @@ realizes some 'host of immune response role' - - mucosa of nasopharynx + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a nasopharynx [Automatically generated definition]. - mucosa of nasopharynx @@ -150950,10 +158779,44 @@ realizes some 'host of immune response role' - - mucosa of oropharynx + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a oropharynx [Automatically generated definition]. - mucosa of oropharynx @@ -150962,10 +158825,26 @@ realizes some 'host of immune response role' - - middle nasal concha + + + + + + + + + + + + + + + + + + + The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. - middle nasal concha @@ -150975,9 +158854,7 @@ realizes some 'host of immune response role' - bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. - bodily fluid @@ -150987,9 +158864,7 @@ realizes some 'host of immune response role' - respiratory system fluid/secretion A portion of organism substance that secreted_by a respiratory system. - respiratory system fluid/secretion @@ -150999,9 +158874,7 @@ realizes some 'host of immune response role' - atrium auricular region A small conical pouch projections located on the upper anterior portion of each atrium of the heart. - atrium auricular region @@ -151011,8 +158884,6 @@ realizes some 'host of immune response role' - digestive system secreted substance - digestive system secreted substance @@ -151022,9 +158893,13 @@ realizes some 'host of immune response role' - chorionic villus + + + + + + One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. - chorionic villus @@ -151034,9 +158909,13 @@ realizes some 'host of immune response role' - meconium + + + + + + A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. - meconium @@ -151046,9 +158925,7 @@ realizes some 'host of immune response role' - sputum Matter ejected from the lungs, bronchi, and trachea, through the mouth. - sputum @@ -151058,9 +158935,7 @@ realizes some 'host of immune response role' - tibial artery The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. - tibial artery @@ -151069,10 +158944,8 @@ realizes some 'host of immune response role' - - esophagogastric junction + The junction between the esophagus and the stomach epithelium. - esophagogastric junction @@ -151081,22 +158954,62 @@ realizes some 'host of immune response role' - - tendon of biceps brachii + + + + + + + + + + + + + A tendon that attaches_to a biceps brachii. - tendon of biceps brachii + + + + + A body of a multi-cellular organism that is no longer living. + carcass + + + + + + + + + An organism containing a developing embryo, fetus, or unborn offspring within the body. + gravid organism + + + + - omental fat pad + + + + + + + + + + + + Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon. - omental fat pad @@ -151105,10 +159018,14 @@ realizes some 'host of immune response role' - - brachioradialis + + + + + + + Brachioradialis is a muscle of the forearm that acts to flex the forearm at the elbow. It is also capable of both pronation and supination, depending on the position of the forearm. It is attached to the distal styloid process of the radius by way of the brachioradialis tendon, and to the lateral supracondylar ridge of the humerus. - brachioradialis @@ -151118,9 +159035,13 @@ realizes some 'host of immune response role' - umbilical cord blood + + + + + + Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. - umbilical cord blood @@ -151130,9 +159051,7 @@ realizes some 'host of immune response role' - arterial blood A blood that is part of a artery. - arterial blood @@ -151142,9 +159061,7 @@ realizes some 'host of immune response role' - venous blood A blood that is part of a vein. - venous blood @@ -151154,9 +159071,7 @@ realizes some 'host of immune response role' - capillary blood A blood that is part of a capillary. - capillary blood @@ -151165,10 +159080,26 @@ realizes some 'host of immune response role' - - suprapubic skin + + + + + + + + + + + + + + + + + + + Area of skin in the hypoastric region of the abdomen. - suprapubic skin @@ -151177,10 +159108,14 @@ realizes some 'host of immune response role' - - anterior nasal wall + + + + + + + Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule. - anterior nasal wall @@ -151190,9 +159125,7 @@ realizes some 'host of immune response role' - placental blood Blood located in the placenta. - placental blood @@ -151264,6 +159197,17 @@ realizes some 'host of immune response role' + + + + + speed/velocity unit + + speed/velocity unit + + + + @@ -151319,13 +159263,35 @@ realizes some 'host of immune response role' + + + + + phenotype + A phenotypic effect related to http://www.w3.org/2002/07/owl#Thing. + + phenotype + + + + + + + + + increased number of material anatomical entity in the urine + The presence of an increased number of material anatomical entity in the urine. + + increased number of material anatomical entity in the urine + + + + - - vaccine + Material entity that is manufactured to realize the vaccine function. - vaccine @@ -151335,9 +159301,7 @@ realizes some 'host of immune response role' - vaccination - A process of administering a vaccine in vivo to a recipient (e.g., human) with the intent to invoke a protective or therapeutic adaptive immune response. - + Process of administering a vaccine in vivo to a recipient (e.g., a human), with the intent to invoke a protective or therapeutic adaptive immune response. vaccination @@ -151390,8 +159354,11 @@ realizes some 'host of immune response role' failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. + Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg + + failed exploratory term @@ -151415,7 +159382,7 @@ realizes some 'host of immune response role' organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release + The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. PERSON:Alan Ruttenberg organizational term @@ -151488,6 +159455,10 @@ realizes some 'host of immune response role' placeholder removed + The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. + This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. + + placeholder removed @@ -151498,7 +159469,10 @@ realizes some 'host of immune response role' terms merged - An editor note should explain what were the merged terms and the reason for the merge. + The term has been combined with one or more other terms to create a more encompassing (merged) term. + The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. + + terms merged @@ -151509,7 +159483,10 @@ realizes some 'host of immune response role' term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + The term has been replaced by a term imported from another ontology. + This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. + + term imported @@ -151520,7 +159497,10 @@ realizes some 'host of immune response role' term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + The term has been split into two or more new terms. + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001. + + term split @@ -154934,10 +162914,12 @@ realizes some 'host of immune response role' The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 + + out of scope @@ -155625,12 +163607,6 @@ realizes some 'host of immune response role' microgram per liter - - - - - - @@ -155642,25 +163618,6 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - Person:Alan Ruttenberg - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - - - - - - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - geographic location A reference to a place on the Earth, by its name or by its geographical location. @@ -155678,48 +163635,16 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + @@ -155742,195 +163667,6 @@ realizes some 'host of immune response role' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/mirror/ro.owl b/src/ontology/mirror/ro.owl index a3d3910..fff2d40 100644 --- a/src/ontology/mirror/ro.owl +++ b/src/ontology/mirror/ro.owl @@ -9,7 +9,6 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" - xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" @@ -17,15 +16,14 @@ xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. OBO Relations Ontology - 2025-03-05 + 2025-12-17 https://github.com/oborel/obo-relations/ @@ -42,12 +40,6 @@ - - - - - - @@ -289,17 +281,6 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - @@ -1196,54 +1177,18 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1286,12 +1231,6 @@ Where we have an annotation assertion - - - - - - @@ -1322,30 +1261,6 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - @@ -1366,12 +1281,6 @@ Where we have an annotation assertion - - - - - - @@ -1476,30 +1385,6 @@ Where we have an annotation assertion - - - - - - - - - - - - - - - - - - - - - - - - @@ -1682,7 +1567,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - accidentally included in BFO 1.2 proposal - should have been BFO_0000062 obsolete preceded by @@ -1788,6 +1672,24 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y + lacks_part + + + + + + + + http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) + lacks_plasma_membrane_part + + + + @@ -2356,9 +2258,14 @@ A continuant cannot have an occurrent as part: use 'participates in'. + + + + + relation between an anatomical structure and a neuron projection bundle that has synaptic terminals in the structure. http://www.ncbi.nlm.nih.gov/pubmed/22402613 - innervated_by + innervated by @@ -2736,7 +2643,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + <= Primitive instance level timing relation between events @@ -2753,7 +2660,6 @@ Examples include: the relationship between two channels collected simultaneously x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - David Osumi-Sutherland t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with @@ -2766,7 +2672,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) before @@ -2779,7 +2685,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which ends @@ -2810,7 +2716,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -2827,7 +2733,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by @@ -2840,7 +2746,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. during which starts @@ -2857,7 +2763,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + starts before @@ -2873,7 +2779,6 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland ends_at_start_of meets @@ -2890,7 +2795,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) @@ -2905,7 +2810,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + d during @@ -2923,7 +2828,7 @@ Examples include: the relationship between two channels collected simultaneously - David Osumi-Sutherland + o overlaps @@ -3580,13 +3485,29 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - + - + - + + + + + + + + + + + + + + + + + @@ -3609,6 +3530,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + @@ -3617,6 +3542,18 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. + + + + + + + + + + + + x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. @@ -4271,7 +4208,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of starts with - Chris Mungall Allen starts @@ -4289,7 +4225,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall started by starts with @@ -4361,7 +4296,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of ends with - Chris Mungall ends @@ -4377,7 +4311,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - Chris Mungall finished by ends with @@ -5017,7 +4950,7 @@ If you need an axiom that says 'has_participant min 2 object', you sho - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where @@ -6247,8 +6180,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. @@ -6821,6 +6754,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A relation that holds between a disease or an organism and a phenotype @@ -8257,8 +8191,8 @@ the a supports either the existence of b, or the truth value of b. - - + + participates in a biotic-biotic interaction with @@ -8531,8 +8465,10 @@ the a supports either the existence of b, or the truth value of b. + c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. May be ceded to OBI + indicates is marker for @@ -8870,6 +8806,67 @@ the a supports either the existence of b, or the truth value of b. + + + + + + + According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle). + x is an ectomycorrhizal host of y if and only if x is a plant (Plantae) whose roots form an intercellular interface (aka Hartig net) with fungus (Fungi) y. This interface consists of highly branched hyphae forming a latticework between epidermal and cortical root cells. + + + + An ectomycorrhiza is a form of symbiotic relationship that occurs between a fungal symbiont, or mycobiont, and the roots of various plant species. The mycobiont is often from the phyla Basidiomycota and Ascomycota, and more rarely from the Zygomycota. Ectomycorrhizae form on the roots of around 2% of plant species, usually woody plants, including species from the birch, dipterocarp, myrtle, beech, willow, pine and rose families. Research on ectomycorrhizae is increasingly important in areas such as ecosystem management and restoration, forestry, and agriculture. Unlike other mycorrhizal relationships, such as arbuscular mycorrhiza and ericoid mycorrhiza, ectomycorrhizal fungi do not penetrate their host's cell wall. Instead they form an entirely intercellular interfaces known as the Hartig net, consisting of highly branched hyphae forming a latticework between epidermal and cortical root cells. + ectomycorrhizal host of + + + + + + + + + According to Linde & Selmes 2012, an individual of species Quercus robur (French oak) is an ectomycorrhizal host of an individual of Tuber melanosporum (black truffle). + inverse of ectomycorrhizal host of + + has ectomycorrhizal host + + + + + + + + + + + + According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae). + x is an arbuscular mycorrhizal host of y if and only if x is a vascular plant (Plantae) whose cortical cells of the roots are penetrated by fungus (Fungi) y and form arbuscules. + + + + An arbuscular mycorrhiza (AM) (plural mycorrhizae) is a type of mycorrhiza in which the symbiont fungus (Arbuscular mycorrhizal fungi, or AMF) penetrates the cortical cells of the roots of a vascular plant forming arbuscules. Arbuscular mycorrhiza is a type of endomycorrhiza along with ericoid mycorrhiza and orchid mycorrhiza (not to be confused with ectomycorrhiza). They are characterized by the formation of unique tree-like structures, the arbuscules. In addition, globular storage structures called vesicles are often encountered. Arbuscular mycorrhizae are formed by fungi in the subphylum Glomeromycotina and some fungi from the Mucoromycotina. These subphyla, along with the Mortierellomycotina, form the phylum Mucoromycota, a sister clade of the more well-known and diverse dikaryan fungi. AM fungi help plants to capture nutrients such as phosphorus, sulfur, nitrogen and micronutrients from the soil. It is believed that the development of the arbuscular mycorrhizal symbiosis played a crucial role in the initial colonisation of land by plants and in the evolution of the vascular plants. It has been said that it is quicker to list the plants that do not form endomycorrhizae than those that do. This symbiosis is a highly evolved mutualistic relationship found between fungi and plants, the most prevalent plant symbiosis known, and AMF is found in 80% of vascular plant families in existence today. + arbuscular mycorrhizal host of + + + + + + + + + According to Medina et al. 2003, an individual of a plant species Medicago sativa (commonly known as alfalfa or lucerne) is an arbuscular mycorrhizal host of an individual of a fungal species Funneliformis mosseae (formerly Glomus mosseae). + inverse of arbuscular mycorrhizal host of + + + has arbuscular mycorrhizal host + + + + @@ -9762,8 +9759,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. creates habitat for @@ -9775,8 +9772,8 @@ Environmental exposures include those imposed by natural environments, experimen - - + + An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. ecologically co-occurs with @@ -9808,7 +9805,7 @@ Environmental exposures include those imposed by natural environments, experimen - + Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. @@ -9899,7 +9896,7 @@ Environmental exposures include those imposed by natural environments, experimen - + sardine has consumer some homo sapiens 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. @@ -10855,6 +10852,24 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + + The information in a blueprint specifies the dimensions of a building. + The information in a recipe specifies what interredients to use and the steps needed to prepare a meal. + The information in a software program specifies the order of computations. + A relation between information and an entity such that the information serves as a rule or guide if the entity is an occurrent, or the information serves as a model if the entity is a continuant. + + 2025-06-16T17:08:04Z + prescribes + specifies + information specifies + https://www.ontologyrepository.com/CommonCoreOntologies/prescribes + + + + @@ -10910,6 +10925,17 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + inverse of 'has symptom' + + 2025-06-16T17:42:05Z + symptom of + + + + @@ -10942,6 +10968,29 @@ For example, protein A (transcription factor) indirectly increases by expression + + + + Inverse of information specifies. + + 2025-06-16T17:13:17Z + specified by information + + + + + + + + + Inverse relation of 'is marker for'. + + 2025-07-14T20:57:25Z + has marker + + + + @@ -11316,6 +11365,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + Given individuals f, i, x, and y, where f is a 'molecular function', i is an 'information biomacromolecule', and x and y are instances of different types of gene products, if f 'enabled by' i within an OWL model of a biological pathway, and i 'has substitutable entity' both x and y, then either x or y are valid enablers of function f within the modeled biological context. + Relates one individual to another which is capable of standing in for the first individual in its other relations to other individuals. + + + has substitutable entity + + + + @@ -11437,86 +11499,321 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - + - - This relation groups relations between diseases and any other kind of entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - - 2018-09-26T00:00:32Z - disease relationship + + + A cancer biomarker provides_clinical_information_for some cancer, which is to say that the presence of or features of the biomarker is clinically informative for the presence of or features of the cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' provides clinical information about 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: This does not imply that 'b' and 'd' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and 'd'. + +Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + provides clinical information for - + - - - p has anatomical participant c iff p has participant c, and c is an anatomical entity - - 2018-09-26T01:08:58Z - results in changes to anatomical or cellular structure + + + A below-normal level of creatine in cerebrospinal fluid is diagnostic_for guanidinoacetate methyltransferase deficiency, which is to say that such levels indicate that the patient has the indicated clinical issue. + An above-normal level of succinylacetone in urine is diagnostic_for type 1 tyrosinemia, while an above-normal level of 4-hydroxyphenylpyruvate is diagnostic_for either type 2 or type 3 tyrosinemia. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the presence or occurrence of 'd' or determine its subtype. + https://orcid.org/0000-0001-5809-9523 + + Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + diagnostic for - + - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - TODO: Add homeomorphy axiom - - - - - ECO:0000041 - SO:similar_to - sameness - similar to - correspondence - resemblance - in similarity relationship with - + + + Hemoglobin A1c (HbA1c) level in blood monitors_status_of diabetes since HbA1c levels reflect a three-month average of blood glucose levels, and can thus be used to monitor the disease progression. + A relationship between a serially-measured biomarker 'b' and a disease or condition of clinical interest 'd', where 'b' is used to infer the status of 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The status of 'd' refers to disease progression/remission or treatment response. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors status of - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - BGEE:curator - - - - - correspondence - - - + - - - - - - Similarity that results from common evolutionary origin. - - - homologous to - This broad definition encompasses all the working definitions proposed so far in the literature. - in homology relationship with - + + + The level of urinary glycosaminoglycans indicates_response_to enzyme replacement therapy for patients with mucopolysaccharidosis type 1. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to show that a biological response to 'e' has occurred. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates response to - - - - Similarity that results from common evolutionary origin. - - + + + + + + + + The incidence of squamous cell differentiation (indicated, for example, by keratinization) in non-small cell lung cancer patients predicts_effect_of the drug pemetrexed, where the prediction is that such patients will have a poor outcome with use of the drug. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to identify individuals who are likely to experience a favorable or unfavorable effect from exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. In the context of predictive biomarkers, 'e' is typically a medical product such as a drug. + +Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (RO:0020331), and 'predicts effect of' (this relation) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + predicts effect of + + + + + + + + + A high number of tumor cells expressing the nuclear protein Ki-67 is prognostic_for an aggressive cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the likelihood of a clinical event, disease recurrence or progression in patients who have 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The relations 'indicates risk of developing' (RO:0020333), 'prognostic for' (this relation), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + prognostic for + + + + + + + + + As an indicator of kidney issues, reduced creatinine clearance capability assesses_toxicity_of certain drugs (such as antibiotics or chemotherapy agents) to the kidneys. + A relationship between a biomarker 'b' and an exposure agent 'e', where 'b' is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect of exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + assesses toxicity of + + + + + + + + + The presence of a certain BRCA1 mutation indicates_risk_of_developing breast cancer in those who don't currently have the cancer. + A relationship between a biomarker 'b' and a disease or condition of clinical interest 'd', where the presence or occurrence of 'b' is used to infer the potential for developing 'd' in an individual that currently does not have 'd'. + https://orcid.org/0000-0001-5809-9523 + + Usage note: The relations 'indicates risk of developing' (this relation), 'prognostic for' (RO:0020331), and 'predicts effect of' (RO:0020330) are each used to relate biomarkers to possible future clinical outcomes: + - 'indicates risk of developing' pertains to cases where the biomarker indicates a potential clinical issue in a patient that does not currently exhibit the issue; + - 'prognostic for' is used for cases where the biomarker indicates the likelihood of a specified clinical event (including disease recurrence or progression) in a patient that has or had the clinical issue of interest; + - 'predicts effect of' is used to indicate the likely outcome of an intervention/treatment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates risk of developing + + + + + + + + + An image biomarker showing tumor size indicates_clinical_effect_of some radiotherapy. + A relationship between a biomarker 'b' and an exposure agent 'e', where the effect of exposure to 'e' is correlated with the presence or occurrence of 'b', and the observation of 'b' is used to infer exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Usage note: This does not imply that 'b' and exposure to 'e' are in a direct causal relationship, as it may be the case that there is a third entity 'a' that stands in a direct causal relationship with 'b' and exposure to 'e'. + +Basis: This relation is an umbrella for a set of relations that are based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + indicates clinical effect of + + + + + + + + + The level of prostate-specific antigen (PSA) monitors_effect_of therapies applied for the treatment of prostate cancers. + A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of a biological effect of 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors effect of + + + + + + + + + The concentration of tobacco specific nitrosamines in urine monitors_exposure_to tobacco/tobacco smoke. + A relationship between a serially-measured biomarker 'b' and an exposure agent 'e', where 'b' is used to provide evidence of exposure to 'e'. + https://orcid.org/0000-0001-5809-9523 + + Clarification: An 'exposure agent' can be either a medical product or some substance (e.g., pesticide) , physical factor (e.g., radiation), or organism (e.g., virus) that originates from the environment. + +Usage note: The relations 'monitors status of' (RO:0020328), 'monitors exposure to' (this relation), and 'monitors effect of' (RO:0020335) are each used for serially-measured biomarkers: + - 'monitors status of' pertains to cases where the biomarker is used to assess the progression/remission of a disease or condition of clinical interest; + - 'monitors exposure to' pertains to cases where the biomarker is used to assess the occurrence of or amount of exposure to some exposure agent; + - 'monitors effect of' pertains to cases where the biomarker is used to assess any possible biological effect arising from exposure to some exposure agent. + + Basis: This relation is based on the 'BEST' classification of and definition for 'biomarker', as given by the FDA-NIH Biomarker Working Group: A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions. The BEST classification includes diagnostic, prognostic, susceptibility/risk, monitoring, predictive, safety, and pharmacodynamic/response biomarkers. See PMID:29405771 for details. Note that any given biomarker can be of a different type in different contexts. + monitors exposure to + + + + + + + + + A polyubiquitin has_constituent_monomer some ubiquitin. + An amino acid chain has_constituent_monomer at least two amino acid residues. + A relation that holds between a polymer and its constituent monomers. P has_constituent_monomer 'm' if and only if P has_component multiple instances of 'm' and each instance of 'm' is covalently attached to another instance of 'm'. + + Usage note: The constituent monomers need not be covalently attached in an end-to-end manner; that is, polymers with internal connections (e.g., polyubiquitin) can use this relation, as can circular polymers (e.g., plasmids) and multi-branched polymers (e.g., glycans). This relation, as non-transitive, allows the number of instances of 'm' to be indicated. + has constituent monomer + + + + + + + + + + Charged tRNA (i.e., aminoacyl-tRNA) is a tRNA that is covalently_bound_to some amino acid. + A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of covalent interactions. + + Such entities will colocalize at all times of the interaction. + covalently bound to + + + + + + + + + + Holo-calmodulin is a calmodulin that is non-covalently_bound_to calcium. + A relation that holds between two distinct chemical entities that are held in close proximity to each other specifically via the force of non-covalent interactions. + + Such entities will colocalize at all times of the interaction. + non-covalently bound to + + + + + + + + This relation groups relations between diseases and any other kind of entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. + + 2018-09-26T00:00:32Z + disease relationship + + + + + + + + + p has anatomical participant c iff p has participant c, and c is an anatomical entity + + 2018-09-26T01:08:58Z + results in changes to anatomical or cellular structure + + + + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + TODO: Add homeomorphy axiom + + + + + ECO:0000041 + SO:similar_to + sameness + similar to + correspondence + resemblance + in similarity relationship with + + + + + + Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. + + BGEE:curator + + + + + correspondence + + + + + + + + + + + + + Similarity that results from common evolutionary origin. + + + homologous to + This broad definition encompasses all the working definitions proposed so far in the literature. + in homology relationship with + + + + + + Similarity that results from common evolutionary origin. + + @@ -11529,7 +11826,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that results from independent evolution. - + homoplasous to analogy @@ -11553,7 +11850,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - + ECO:0000075 homocracous to @@ -11579,7 +11876,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves different underlying mechanisms or structures. - + analogy Convergence usually implies a notion of adaptation. @@ -11602,7 +11899,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves homologous underlying mechanisms or structures. - + parallel evolution Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. @@ -11625,7 +11922,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by similarity with regard to selected structural parameters. - + ECO:0000071 MI:2163 @@ -11652,7 +11949,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by common descent. - + homology ECO:0000080 @@ -11687,7 +11984,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - + ECO:0000067 biological homologous to @@ -11713,7 +12010,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - + atavism rudiment @@ -11737,7 +12034,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected by similarity in content and organization between chromosomes. - + MeSH:Synteny SO:0000860 @@ -11764,7 +12061,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a duplication event. - + SO:0000854 SO:0000859 @@ -11792,7 +12089,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves sets of syntenic blocks. - + syntenic paralogous to duplicon @@ -11817,7 +12114,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Syntenic homology that involves chromosomes of different species. - + syntenic orthologous to in syntenic orthology relationship with @@ -11839,7 +12136,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - + fractional homology partial homologous to @@ -11868,7 +12165,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - + MeSH:Structural_Homology,_Protein protein structural homologous to @@ -11892,7 +12189,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves a pseudogenic feature and its functional ancestor. - + pseudogene SO:non_functional_homolog_of @@ -11916,7 +12213,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves genes that diverged after a speciation event. - + ECO:00000060 SO:0000855 @@ -11946,7 +12243,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - + xenologous to The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). @@ -11970,7 +12267,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members sharing no other homologs in the lineages considered. - + 1 to 1 homologous to 1:1 homology @@ -11995,7 +12292,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - + 1 to 1 orthologous to 1:1 orthology @@ -12020,7 +12317,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a whole genome duplication event. - + ohnologous to homoeology @@ -12044,7 +12341,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - + in-paralogous to inparalogy @@ -12068,7 +12365,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that results from a duplication preceding a given speciation event. - + alloparalogy out-paralogous to @@ -12092,7 +12389,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - + pro-orthologous to in pro-orthology relationship with @@ -12115,7 +12412,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - + semi-orthologous to The converse of pro-orthologous. @@ -12139,7 +12436,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves structures arranged along the main body axis. - + serial homologous to homonomy @@ -12162,7 +12459,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - + heterochronous homologous to heterochrony @@ -12186,7 +12483,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - + juvenification pedomorphosis @@ -12210,7 +12507,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - + in peramorphosis relationship with @@ -12231,7 +12528,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - + in progenesis relationship with @@ -12253,7 +12550,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by a retardation of somatic development. - + juvenilization neotenous to @@ -12277,7 +12574,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Convergence that results from co-evolution usually involving an evolutionary arms race. - + mimicrous to in mimicry relationship with @@ -12300,7 +12597,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - + 1 to many orthologous to 1:many orthology @@ -12327,7 +12624,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves two members of a larger set of homologs. - + many to many homologous to many-to-many homology @@ -12351,7 +12648,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - + 1 to many homologous to one-to-many homology @@ -12376,7 +12673,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - + apomorphous to synapomorphy @@ -12399,7 +12696,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is based on distant shared ancestry. - + plesiomorphous to symplesiomorphy @@ -12424,7 +12721,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - + deep genetic homology deep homologous to @@ -12451,7 +12748,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - + hemiplasous to in hemiplasy relationship with @@ -12473,7 +12770,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - + gametologous to in gametology relationship with @@ -12495,7 +12792,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - + MeSH:Chromosome_Pairing chromosomal homologous to @@ -12519,7 +12816,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves two genes that experienced duplications more recent than the species split that created them. - + many to many orthologous to many-to-many orthology @@ -12548,7 +12845,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from the same species. - + within-species paralogous to in within-species paralogy relationship with @@ -12570,7 +12867,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that involves genes from different species. - + between-species paralogous to The genes have diverged before a speciation event. @@ -12593,7 +12890,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - + post-displacement in postdisplacement relationship with @@ -12615,7 +12912,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Peramorphosis that is produced by a delay in the offset of development. - + in hypermorphosis relationship with @@ -12637,7 +12934,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - + synologous to in synology relationship with @@ -12661,7 +12958,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Orthology that involves functional equivalent genes with retention of the ancestral function. - + ECO:0000080 isoorthologous to @@ -12684,7 +12981,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - + tandem paralogous to iterative paralogy @@ -12710,7 +13007,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - + apomorphic tendency cryptic homology @@ -12742,7 +13039,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - + generative homology syngenous to @@ -12768,7 +13065,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - + 1:1 paralogy apparent 1:1 orthology @@ -12795,7 +13092,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - + pseudoparalogous to These genes may come out as paralogs in a single-genome analysis. @@ -12819,7 +13116,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves functional equivalent genes with retention of the ancestral function. - + equivalogous to This may include examples of orthology, paralogy and xenology. @@ -12842,7 +13139,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of interacting molecules in different organisms. - + interologous to in interology relationship with @@ -12865,7 +13162,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Similarity that is characterized by interchangeability in function. - + functional similarity in functional equivalence relationship with @@ -12888,7 +13185,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves parts of the same organism. - + iterative homologous to in iterative homology relationship with @@ -12910,7 +13207,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - + duplicate xenology multiple xenology @@ -12934,7 +13231,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - + plerologous to This phenomenon is usually due to gene conversion process. @@ -12958,7 +13255,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Structural homology that involves structures with the same or similar relative positions. - + homotopous to Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. @@ -12983,7 +13280,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Biological homology that involves an ectopic structure and the normally positioned structure. - + heterotopy in homeosis relationship with @@ -13007,7 +13304,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Synology that results from allopolyploidy. - + homoeologous to On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. @@ -13031,7 +13328,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - + axis paramorphism in paramorphism relationship with @@ -13054,7 +13351,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - + regulogous to in regulogy relationship with @@ -13446,6 +13743,38 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + completely executed planned process + + + + @@ -13462,6 +13791,16 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu + + + + + A processed material entity which is designed to be capable of a process. + device + + + + @@ -13487,14 +13826,19 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu An environmental system which can sustain and allow the growth of an ecological population. - - EcoLexicon:habitat LTER:238 SWEETRealm:Habitat - A habitat's specificity to an ecological population differentiates it from other environment classes. See Buttigieg et al. (2016; https://doi.org/10.1186/s13326-016-0097-6) for an explanation of ENVO's treatement of habitats. 3,849 of such habitat classes are available here: https://github.com/EnvironmentOntology/envo-habitats + https://en.wikipedia.org/wiki/Habitat + A habitat's specificity to an ecological population differentiates it from other environment classes. habitat + + + + An environmental system which can sustain and allow the growth of an ecological population. + EnvO:EnvO + @@ -13600,7 +13944,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-3781009 Reactome:R-HSA-3788724 Reactome:R-HSA-3797226 - Reactome:R-HSA-400267 Reactome:R-HSA-4332236 Reactome:R-HSA-446877 Reactome:R-HSA-450358 @@ -13649,6 +13992,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-975118 Reactome:R-HSA-975147 Reactome:R-HSA-9758604 + Reactome:R-HSA-9766227 Reactome:R-HSA-9793444 Reactome:R-HSA-9793485 Reactome:R-HSA-9793679 @@ -13665,6 +14009,10 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9834070 Reactome:R-HSA-9861563 Reactome:R-HSA-9861640 + Reactome:R-HSA-9929350 + Reactome:R-HSA-9934753 + Reactome:R-HSA-9948301 + Reactome:R-HSA-9954721 ubiquitin conjugating enzyme activity ubiquitin ligase activity ubiquitin protein ligase activity @@ -14083,12 +14431,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-3797226 Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease) - - - - Reactome:R-HSA-400267 - BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins - @@ -14249,7 +14591,7 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-69598 - Ubiquitination of phosphorylated Cdc25A + Ubiquitination of phosphorylated CDC25A @@ -14377,6 +14719,12 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9758604 Ubiquitination of IKBKG by TRAF6 + + + + Reactome:R-HSA-9766227 + MDM2 mediates CDH1 ubiquitination + @@ -14473,6 +14821,30 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu Reactome:R-HSA-9861640 CTLH E3 ligase ubiquitinates PKM-1 + + + + Reactome:R-HSA-9929350 + Ubiquitination of CD274 by BTRC-SCF E3-ligase complex + + + + + Reactome:R-HSA-9934753 + CBLL1 ubiquitinates CDH1 + + + + + Reactome:R-HSA-9948301 + ZNF598 K63 polyubiquitinates RPS10 (eS10) and RPS20 (uS10) of the 40S ribosomal subunit + + + + + Reactome:R-HSA-9954721 + NEDD8-K699-CUL2:ELOB:ELOC:RBX1:KLHDC10 K48 polyubiquitinates alanine-tailed nascent peptide + @@ -14509,7 +14881,6 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z @@ -14638,44 +15009,22 @@ A chemical with no chiral centers can not have an enantiomer. A chemical with mu - + - - - planned process - Injecting mice with a vaccine in order to test its efficacy - - A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process - + - + - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material - + - + assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. @@ -14694,7 +15043,6 @@ objectives is a planned process. - container A device that can be used to restrict the location of material entities over time @@ -14705,56 +15053,6 @@ objectives is a planned process. - - - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device - - - - - - - - - organism - animal - fungus - plant - virus - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism - - - - @@ -14950,6 +15248,7 @@ This issue is outside the scope of OBI. CARO:0000003 EHDAA2:0003003 EMAPA:0 + FAO:0000001 FMA:305751 FMA:67135 GAID:781 @@ -14967,6 +15266,7 @@ This issue is outside the scope of OBI. connected biological structure UBERON:0000061 + @@ -15335,73 +15635,596 @@ This issue is outside the scope of OBI. - + - - example to be eventually removed - example to be eventually removed + + + + 2019-03-05T17:25:21Z + Western Australia Ecoregion + WWF:AA1310 + https://www.worldwildlife.org/ecoregions/aa1310 + Western Australian Mulga Shrublands Ecoregion - + - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete + + + 2019-03-05T17:51:32Z + https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands + Australasia Ecoregion - + - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term + + + + 2019-03-05T17:52:41Z + Southern central Australia Ecoregion + WWF:AA1309 + https://www.worldwildlife.org/ecoregions/aa1309 + Tirari-Sturt Stony Desert Ecoregion - + - - ready for release - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release + + + + 2019-03-05T17:54:35Z + Eastern central Australia Ecoregion + WWF:AA1308 + https://www.worldwildlife.org/ecoregions/aa1308 + Simpson Desert Region - + - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete + + + + 2019-03-05T17:56:13Z + Western Australia Ecoregion + WWF:AA1307 + https://www.worldwildlife.org/ecoregions/aa1307 + Pilbara Shrublands Ecoregion - + - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated + + + + 2019-03-05T18:10:52Z + Western coast of Australia Ecoregion + WWF:AA1301 + https://www.worldwildlife.org/ecoregions/aa1301 + Carnarvon Xeric Shrublands Ecoregion - + - - - pending final vetting - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + + + + 2019-03-05T18:12:28Z + Central Australia Ecoregion + WWF:AA1302 + https://www.worldwildlife.org/ecoregions/aa1302 + Central Ranges Xeric Shrub Ecoregion + + + + + + + + + + 2019-03-05T18:15:11Z + Western central Australia + WWF:AA1303 + https://www.worldwildlife.org/ecoregions/aa1303 + Gibson Desert Ecoregion + + + + + + + + + + 2019-03-05T18:17:15Z + Northwestern Australia + WWF:AA1304 + https://www.worldwildlife.org/ecoregions/aa1304 + The Great Sandy-Tanami Desert Ecoregion + + + + + + + + + + 2019-03-05T18:24:06Z + Southern Australia Ecoregion + WWF:AA1305 + https://www.worldwildlife.org/ecoregions/aa1305 + Great Victoria Desert Ecoregion + + + + + + + + + + 2019-03-05T18:26:16Z + Southern Australia Ecoregion + WWF:AA1306 + https://www.worldwildlife.org/ecoregions/aa1306 + Nullarbor Plains Xeric Shrubland Ecoregion + + + + + + + + + 2019-03-06T22:01:41Z + https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands + Afrotropical Ecoregion + + + + + + + + + + 2019-03-06T22:02:37Z + Southern Africa: Southern Namibia into South Africa + WWF:AT1322 + https://www.worldwildlife.org/ecoregions/at1322 + Succulent Karoo Ecoregion + + + + + + + + + + 2019-03-06T22:07:38Z + WWF:AT1321 + https://www.worldwildlife.org/ecoregions/at1321 + Arabian Peninsula: Yemen and Saudi Arabia + Yemen and Saudi Arabia Ecoregion + + + + + + + + + + 2019-03-06T22:11:38Z + WWF:AT1320 + https://www.worldwildlife.org/ecoregions/at1320 + Arabian Peninsula: Yemen, Saudi Arabia, and Oman + Yemen, Saudi Arabia, and Oman Ecoregion + + + + + + + + + + 2019-03-06T22:13:00Z + WWF:AT1319 + https://www.worldwildlife.org/ecoregions/at1319 + Somali montane xeric woodlands ecoregion + Somali Montane Xeric Woodland Ecoregion + + + + + + + + + 2019-03-06T22:15:07Z + Islands east of the Horn of Africa and south of Yemen Ecoregion + WWF:AT1318 + https://www.worldwildlife.org/ecoregions/at1318 + Socotran Archipelago Ecoregion + + + + + + + + + 2019-03-06T22:18:55Z + WWF:AT1317 + https://www.worldwildlife.org/ecoregions/at1317 + Red Sea Coastal Desert Ecoregion + + + + + + + + + 2019-03-06T22:20:56Z + WWF:AT1316 + https://www.worldwildlife.org/ecoregions/at1316 + Namibian Savanna Woodland Ecoregion + + + + + + + + + 2019-03-06T22:24:28Z + Africa: Namibia Ecoregion + WWF:AT1315 + https://www.worldwildlife.org/ecoregions/at1315 + Namib Desert Ecoregion + + + + + + + + + 2019-03-06T22:26:15Z + WWF:AT1314 + https://www.worldwildlife.org/ecoregions/at1314 + Nama Karoo Ecoregion + + + + + + + + + 2019-03-06T22:28:43Z + WWF:AT1313 + https://www.worldwildlife.org/ecoregions/at1313 + Masai Xeric Grasslands and Shrublands Ecoregion + + + + + + + + + 2019-03-06T22:30:23Z + WWF:AT1312 + https://www.worldwildlife.org/ecoregions/at1312 + Madagascar Succulent Woodlands Ecoregion + + + + + + + + + 2019-03-06T22:31:29Z + WWF:AT1311 + https://www.worldwildlife.org/ecoregions/at1311 + Madagascar spiny desert ecoregion + Madagascar Spiny Thickets Ecoregion + + + + + + + + + 2019-03-06T22:39:32Z + WWF:AT1310 + https://www.worldwildlife.org/ecoregions/at1310 + Africa: Coastal Namibia and Angola Ecoregion + Kaokoveld Desert Ecoregion + + + + + + + + + 2019-03-06T22:42:47Z + WWF:AT1309 + https://www.worldwildlife.org/ecoregions/at1309 + Kalahari Xeric Savanna Ecoregion + + + + + + + + + 2019-03-06T22:44:54Z + WWF:AT1308 + https://www.worldwildlife.org/ecoregions/at1308 + Southern Africa: Islands about half-way between southern Madagascar and southern Mozambique Ecoregion + Ile Europa and Bassas da India Ecoregion + + + + + + + + + 2019-03-06T22:46:58Z + Eastern Africa: Somalia + WWF:AT1307 + https://www.worldwildlife.org/ecoregions/at1307 + Hobyo Grassland and Shrubland Ecoregion + + + + + + + + + 2019-03-06T22:54:57Z + WWF:AT1306 + https://www.worldwildlife.org/ecoregions/at1306 + Arabian Peninsula: Oman and United Arab Emirates Ecoregion + Oman and United Arab Emirates Ecoregion + + + + + + + + + 2019-03-07T00:08:06Z + WWF:AT1305 + https://www.worldwildlife.org/ecoregions/at1305 + Ethiopian Xeric Grasslands and Shrublands Ecoregion + + + + + + + + + 2019-03-07T00:11:29Z + WWF:AT1304 + https://www.worldwildlife.org/ecoregions/at1304 + Eritrean Coastal Desert Ecoregion + + + + + + + + + 2019-03-07T00:13:33Z + WWF:AT1303 + https://www.worldwildlife.org/ecoregions/at1303 + North central Africa: Eastern Chad and small area of western Sudan + East Saharan Montane Xeric Woodland Ecoregion + + + + + + + + + 2019-03-07T00:16:12Z + WWF:AT1302 + https://www.worldwildlife.org/ecoregions/at1302 + Western Asia: Oman, Yemen, and Saudi Arabia Ecoregion + Oman, Yemen, and Saudi Arabia Ecoregion + + + + + + + + + 2019-03-07T00:18:09Z + WWF:AT1301 + https://www.worldwildlife.org/ecoregions/at1301 + Aldabra Island Xeric Scrub Ecoregion + + + + + + + + 2019-04-26T23:38:50Z + + Indo-Malay Ecoregion + + + + + + + + + 2019-04-26T23:40:13Z + + WWF:IM1304 + Southern Asia: Western India into Pakistan + Thar Desert + + + + + + + + + 2019-04-27T00:12:51Z + + WWF:IM1303 + Southern Asia: Eastern India and western Pakistan + Northwestern Thorn Scrub Forests + + + + + + + + A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. + envoAtmo + envoPolar + Arctic front + + + + + A polar front between the deep, cold Arctic air and the shallower, warmer polar air of northern latitudes on Earth. + + + + + + + + + A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. + envoAtmo + envoPolar + Antarctic front + + + + + A polar front between the deep, cold Antarctic air and the shallower, warmer polar air of southern latitudes on Earth. + + + + + + + + + + Stellar radiation emitted from Sol. + Solar radiation + + + + + + + + example to be eventually removed + example to be eventually removed + + + + + + + + metadata complete + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + organizational term + The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. + organizational term + + + + + + + + ready for release + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + metadata incomplete + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + uncurated + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + pending final vetting + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -15493,6 +16316,69 @@ binary, and takes no temporal argument. + + + + researcher + Nicole Vasilevsky + + + + + researcher + + + + + + Nicole Vasilevsky + + + + + + + + + researcher + Darren A. Natale + + + + + researcher + + + + + + Darren A. Natale + + + + + + + + + researcher ORCID ID = 0000-0001-5948-3092 + Marta Costa + + + + + researcher ORCID ID = 0000-0001-5948-3092 + + + + + + Marta Costa + + + + + @@ -15535,6 +16421,27 @@ binary, and takes no temporal argument. + + + + researcher + Katja S Schulz + + + + + researcher + + + + + + Katja S Schulz + + + + + @@ -15556,6 +16463,27 @@ binary, and takes no temporal argument. + + + + researcher + David P Hill + + + + + researcher + + + + + + David P Hill + + + + + @@ -15598,6 +16526,48 @@ binary, and takes no temporal argument. + + + + American epidemiologist and ontologist + Melissa Haendel + + + + + American epidemiologist and ontologist + + + + + + Melissa Haendel + + + + + + + + + researcher + Jennifer Deegan + + + + + researcher + + + + + + Jennifer Deegan + + + + + @@ -15619,6 +16589,48 @@ binary, and takes no temporal argument. + + + + researcher + Alexander D Diehl + + + + + researcher + + + + + + Alexander D Diehl + + + + + + + + + researcher + Matthew Brush + + + + + researcher + + + + + + Matthew Brush + + + + + @@ -15682,6 +16694,48 @@ binary, and takes no temporal argument. + + + + researcher + Tanya Z Berardini + + + + + researcher + + + + + + Tanya Z Berardini + + + + + + + + + researcher + Sabrina Toro + + + + + researcher + + + + + + Sabrina Toro + + + + + @@ -15703,6 +16757,27 @@ binary, and takes no temporal argument. + + + + Researcher ORCID=0000-0002-5260-9315 + Patrick Ray + + + + + Researcher ORCID=0000-0002-5260-9315 + + + + + + Patrick Ray + + + + + @@ -15955,6 +17030,27 @@ binary, and takes no temporal argument. + + + + researcher + Terrence F Meehan + + + + + researcher + + + + + + Terrence F Meehan + + + + + @@ -16015,6 +17111,33 @@ binary, and takes no temporal argument. Charles Tapley Hoyt + + + + + + + researcher + Vasundra Touré + + + + + researcher + + + + + + Vasundra Touré + + + + + + + + @@ -16045,7 +17168,8 @@ binary, and takes no temporal argument. failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. + Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg failed exploratory term @@ -16073,21 +17197,26 @@ binary, and takes no temporal argument. placeholder removed + The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. + This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. placeholder removed terms merged - An editor note should explain what were the merged terms and the reason for the merge. + The term has been combined with one or more other terms to create a more encompassing (merged) term. + The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + The term has been replaced by a term imported from another ontology. + This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. term imported term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + The term has been split into two or more new terms. + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001. term split @@ -16216,6 +17345,12 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Add as annotation triples in the granting ontology is allocated id range + + has ontology root term + Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. + Nicolas Matentzoglu + has ontology root term + may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. @@ -16378,7 +17513,7 @@ No imports The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. out of scope @@ -16394,66 +17529,84 @@ No imports domain entity does not exist + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + 2025-06-02 + preferred label for community + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms + 2023-03-03 abbreviation A synonym type for describing ambiguous synonyms + 2023-03-03 ambiguous synonym A synonym type for describing dubious synonyms + 2023-03-03 dubious synonym EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) A synonym type for describing layperson or colloquial synonyms + 2023-03-03 layperson synonym CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms + 2023-03-03 plural form CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) A synonym type for describing UK spelling variants + 2023-03-03 UK spelling synonym A synonym type for common misspellings + 2023-03-03 misspelling A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway + 2023-03-03 misnomer MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. A synonym type for names that have been used as primary labels in the past. + 2023-07-25 previous name The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College A synonym type for the legal entity name + 2023-07-27 legal name CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. + 2023-09-30 INN International Nonproprietary Name @@ -16461,18 +17614,21 @@ No imports nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis A synonym type for describing Latin term synonyms. + 2023-10-12 latin term NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. + 2023-11-01 acronym A serial number such as "12324X"; a stop sign; a written proper name such as "OBI An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + 2024-03-25 has symbol @@ -16597,15 +17753,15 @@ No imports - - - + + + @@ -16616,6 +17772,7 @@ No imports + if effector directly negatively regulates X, its parent MF directly negatively regulates X @@ -16623,9 +17780,9 @@ No imports - - - + + + @@ -16634,9 +17791,9 @@ No imports - - - + + + @@ -16650,9 +17807,9 @@ No imports - - - + + + @@ -16660,6 +17817,7 @@ No imports + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -16667,9 +17825,9 @@ No imports - - - + + + @@ -16678,9 +17836,9 @@ No imports - - - + + + @@ -16693,17 +17851,29 @@ No imports - - - - + + + - + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -16711,9 +17881,9 @@ No imports - - - + + + @@ -16721,24 +17891,13 @@ No imports - - - + + + + - - - - - - - - - - - - - + @@ -16748,13 +17907,24 @@ No imports - - - - + + + - + + + + + + + + + + + + + @@ -16766,9 +17936,9 @@ No imports - - - + + + @@ -16776,9 +17946,10 @@ No imports - - - + + + + @@ -16792,9 +17963,9 @@ No imports - - - + + + @@ -16809,9 +17980,9 @@ No imports - - - + + + @@ -16819,9 +17990,10 @@ No imports - - - + + + + @@ -16835,9 +18007,9 @@ No imports - - - + + + @@ -16852,9 +18024,9 @@ No imports - - - + + + @@ -16862,9 +18034,10 @@ No imports - - - + + + + @@ -16878,9 +18051,9 @@ No imports - - - + + + @@ -16895,9 +18068,9 @@ No imports - - - + + + @@ -16905,9 +18078,10 @@ No imports - - - + + + + @@ -16921,9 +18095,9 @@ No imports - - - + + + @@ -16931,9 +18105,6 @@ No imports - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg @@ -16941,9 +18112,9 @@ No imports - - - + + + @@ -16952,36 +18123,12 @@ No imports - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -16992,9 +18139,9 @@ No imports - - - + + + @@ -17002,18 +18149,16 @@ No imports - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - + + + + @@ -17022,25 +18167,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -17051,9 +18183,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17061,9 +18193,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP @@ -17071,8 +18200,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17081,9 +18210,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17091,10 +18220,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -17110,9 +18238,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17127,9 +18255,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17138,37 +18266,11 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -17179,9 +18281,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17189,8 +18291,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction @@ -17198,9 +18298,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17208,26 +18308,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17238,9 +18324,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17248,7 +18334,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct neg reg edge from input to regulatory subfunction @@ -17256,9 +18341,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17266,26 +18351,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17296,9 +18367,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17306,7 +18377,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - inferring direct positive reg edge from input to regulatory subfunction @@ -17314,9 +18384,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17324,26 +18394,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - + @@ -17354,9 +18410,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17364,7 +18420,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - effector input is compound function input + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg @@ -17372,9 +18430,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17383,12 +18441,36 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + @@ -17400,8 +18482,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -17409,17 +18491,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - Input of effector is input of its parent MF + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts - - - - + + + @@ -17428,12 +18511,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17444,9 +18540,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17454,17 +18550,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly regulates X, its parent MF directly regulates X + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP - - - - + + + @@ -17473,12 +18570,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17487,11 +18597,11 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - + + + + + @@ -17499,7 +18609,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly positively regulates X, its parent MF directly positively regulates X @@ -17507,9 +18616,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17517,13 +18626,38 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -17534,9 +18668,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17544,7 +18678,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - if effector directly negatively regulates X, its parent MF directly negatively regulates X + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction @@ -17552,9 +18687,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17563,12 +18698,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17579,9 +18727,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17589,7 +18737,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + inferring direct neg reg edge from input to regulatory subfunction @@ -17597,9 +18745,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17608,12 +18756,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17623,29 +18784,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + - - - - - - - - - - - - - + - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). + inferring direct positive reg edge from input to regulatory subfunction @@ -17653,9 +18803,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17664,12 +18814,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -17679,28 +18842,18 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + + - - - - - - - - - - - - - + + effector input is compound function input @@ -17708,9 +18861,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17719,9 +18872,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17735,9 +18888,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17745,6 +18898,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + Input of effector is input of its parent MF @@ -17752,9 +18906,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17763,9 +18917,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17779,9 +18933,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17789,6 +18943,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + if effector directly regulates X, its parent MF directly regulates X @@ -17796,9 +18951,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17807,9 +18962,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17823,9 +18978,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17833,6 +18988,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase + if effector directly positively regulates X, its parent MF directly positively regulates X @@ -17840,9 +18996,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17851,9 +19007,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -17867,9 +19023,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + diff --git a/src/ontology/ogms-edit.owl b/src/ontology/ogms-edit.owl index 4c88ef8..44a561d 100644 --- a/src/ontology/ogms-edit.owl +++ b/src/ontology/ogms-edit.owl @@ -15,6 +15,7 @@ Prefix(oboInOwl:=) Ontology( Import() +Import() Import() Import() Import() @@ -57,7 +58,6 @@ Declaration(Class(obo:BFO_0000031)) Declaration(Class(obo:BFO_0000040)) Declaration(Class(obo:IAO_0000027)) Declaration(Class(obo:IAO_0000030)) -Declaration(Class(obo:OBI_0000011)) Declaration(Class(obo:OBI_0000278)) Declaration(Class(obo:OGMS_0000014)) Declaration(Class(obo:OGMS_0000015)) @@ -604,7 +604,6 @@ SubClassOf(obo:OGMS_0000074 obo:BFO_0000031) # Class: obo:OGMS_0000077 (pathological formation) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000077 "TODO: Define, relate to disorder, and place in the OGMS hierarchy."@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000077 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000077 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000077 "creation date: 2009-07-13T02:14:59Z") @@ -622,7 +621,6 @@ SubClassOf(obo:OGMS_0000078 obo:BFO_0000040) # Class: obo:OGMS_0000079 (portion of pathological body substance) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000079 "TODO: Define, relate to disorder, and place in the OGMS hierarchy."@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000079 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000079 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000079 "creation date: 2009-07-13T02:15:17Z") @@ -649,7 +647,6 @@ SubClassOf(obo:OGMS_0000081 obo:OGMS_0000061) # Class: obo:OGMS_0000082 (pathological invasion) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000082 "TODO: Define."@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000082 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000082 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000082 "creation date: 2009-07-13T02:17:47Z") @@ -658,7 +655,6 @@ SubClassOf(obo:OGMS_0000082 obo:OGMS_0000061) # Class: obo:OGMS_0000083 (physical examination finding) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000083 "TODO: Define."@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000083 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000083 "creation date: 2009-11-24T04:51:11Z") AnnotationAssertion(rdfs:label obo:OGMS_0000083 "physical examination finding") @@ -719,6 +715,7 @@ SubClassOf(obo:OGMS_0000089 obo:BFO_0000040) AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000090 "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process"@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000090 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000090 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:OGMS_0000090 "medical intervention"@en) AnnotationAssertion(rdfs:label obo:OGMS_0000090 "treatment") SubClassOf(obo:OGMS_0000090 obo:OGMS_0000096) @@ -784,7 +781,7 @@ Sagar Jain") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000096 "creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18") AnnotationAssertion(rdfs:label obo:OGMS_0000096 "health care process") -SubClassOf(obo:OGMS_0000096 obo:OBI_0000011) +SubClassOf(obo:OGMS_0000096 obo:COB_0000035) # Class: obo:OGMS_0000097 (health care encounter) @@ -804,7 +801,6 @@ SubClassOf(obo:OGMS_0000098 obo:OGMS_0000096) # Class: obo:OGMS_0000099 (outpatient encounter) -AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000099 "TODO"@en) AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000099 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000099 "creation date: 2011-02-21T09:57:44Z") AnnotationAssertion(rdfs:label obo:OGMS_0000099 "outpatient encounter") @@ -846,7 +842,7 @@ AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000103 "Whether or not 'prophylaxi AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000103 "Albert Goldfain") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000103 "creation date: 2011-09-20T09:57:44Z") AnnotationAssertion(rdfs:label obo:OGMS_0000103 "disease prophylaxis") -SubClassOf(obo:OGMS_0000103 obo:OBI_0000011) +SubClassOf(obo:OGMS_0000103 obo:COB_0000035) # Class: obo:OGMS_0000104 (diagnostic process) @@ -885,7 +881,7 @@ AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000107 "A planned process that has AnnotationAssertion(dc:date obo:OGMS_0000107 "2017-04-18") AnnotationAssertion(dc:publisher obo:OGMS_0000107 "Sagar Jain") AnnotationAssertion(rdfs:label obo:OGMS_0000107 "ancillary health care process") -SubClassOf(obo:OGMS_0000107 obo:OBI_0000011) +SubClassOf(obo:OGMS_0000107 obo:COB_0000035) # Class: obo:OGMS_0000108 (health care process assay) @@ -915,6 +911,7 @@ SubClassOf(obo:OGMS_0000110 obo:OGMS_0000096) AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000111 "A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.") AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000111 "Creation date: 2018-11-27") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:OGMS_0000111 "preventive intervention"@en) AnnotationAssertion(rdfs:label obo:OGMS_0000111 "prophylactic treatment"@en) SubClassOf(obo:OGMS_0000111 obo:OGMS_0000090) diff --git a/src/ontology/ogms-odk.yaml b/src/ontology/ogms-odk.yaml index 68b582b..3662534 100644 --- a/src/ontology/ogms-odk.yaml +++ b/src/ontology/ogms-odk.yaml @@ -32,6 +32,7 @@ import_group: module_type: filter base_iris: - http://purl.obolibrary.org/obo/OBI_ + - http://purl.obolibrary.org/obo/COB_ - id: bfo module_type: slme slme_individuals: exclude @@ -43,6 +44,9 @@ import_group: - http://purl.obolibrary.org/obo/IDO_ - id: omo module_type: mirror + - id: cob + module_type: slme + slme_individuals: exclude use_custom_import_module: TRUE robot_java_args: '-Xmx8G' diff --git a/src/ontology/tmp/bfo-download.owl b/src/ontology/tmp/bfo-download.owl deleted file mode 100644 index b440ee5..0000000 --- a/src/ontology/tmp/bfo-download.owl +++ /dev/null @@ -1,1715 +0,0 @@ - - - - - BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation. - BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science. - BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms. - Alan Ruttenberg - Albert Goldfain - Barry Smith - Bill Duncan - Bjoern Peters - Chris Mungall - David Osumi-Sutherland - Fabian Neuhaus - Holger Stenzhorn - James A. Overton - Janna Hastings - Jie Zheng - Jonathan Bona - Larry Hunter - Leonard Jacuzzo - Ludger Jansen - Mark Ressler - Mathias Brochhausen - Mauricio Almeida - Melanie Courtot - Pierre Grenon - Randall Dipert - Ron Rudnicki - Selja Seppälä - Stefan Schulz - Thomas Bittner - Werner Ceusters - Yongqun "Oliver" He - - Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. - The BSD license on the BFO project site refers to code used to build BFO. - This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version. - - - - - - - - - - - - - - - - - - - - - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - - - - - - editor preferred term - - - - - - - - - example of usage - - - - - - - - - definition - - - - - - - - - editor note - - - - - - - - - term editor - - - - - - - - - alternative term - - - - - - - - - definition source - - - - - - - - - curator note - - - - - - - - - imported from - - - - - - - - - elucidation - - - - - - - - - has associated axiom(nl) - - - - - - - - - has associated axiom(fol) - - - - - - - - - has axiom label - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - continuant - Continuant - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - - - - - occurrent - Occurrent - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - - - - - - - - - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - site - - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of requited love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - diff --git a/src/ontology/tmp/external_import_terms.txt b/src/ontology/tmp/external_import_terms.txt index 4ee8d51..1ba3e78 100644 --- a/src/ontology/tmp/external_import_terms.txt +++ b/src/ontology/tmp/external_import_terms.txt @@ -6,6 +6,9 @@ http://purl.obolibrary.org/obo/BFO_0000054 http://purl.obolibrary.org/obo/BFO_0000055 http://purl.obolibrary.org/obo/BFO_0000066 http://purl.obolibrary.org/obo/BFO_0000067 +http://purl.obolibrary.org/obo/COB_0000022 +http://purl.obolibrary.org/obo/COB_0000035 +http://purl.obolibrary.org/obo/COB_0000110 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000114 @@ -25,13 +28,12 @@ http://purl.obolibrary.org/obo/IAO_0100001 http://purl.obolibrary.org/obo/IDO_0000504 http://purl.obolibrary.org/obo/IDO_0000586 http://purl.obolibrary.org/obo/IDO_0000630 -http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000278 http://purl.obolibrary.org/obo/OBI_0000312 http://purl.obolibrary.org/obo/OBI_0000846 http://purl.obolibrary.org/obo/OBI_0001688 -http://purl.obolibrary.org/obo/OBI_0100026 http://purl.obolibrary.org/obo/OBI_0200000 +http://purl.obolibrary.org/obo/OBI_0600014 http://purl.obolibrary.org/obo/OBI_0600052 http://purl.obolibrary.org/obo/RO_0000052 http://purl.obolibrary.org/obo/RO_0000053 diff --git a/src/ontology/tmp/external_import_terms.txt.tmp b/src/ontology/tmp/external_import_terms.txt.tmp index dfcdad2..f156467 100644 --- a/src/ontology/tmp/external_import_terms.txt.tmp +++ b/src/ontology/tmp/external_import_terms.txt.tmp @@ -11,22 +11,24 @@ http://purl.obolibrary.org/obo/RO_0000057 http://purl.obolibrary.org/obo/BFO_0000051 http://purl.obolibrary.org/obo/IDO_0000630 http://purl.obolibrary.org/obo/IAO_0000116 -http://purl.obolibrary.org/obo/OBI_0100026 +http://purl.obolibrary.org/obo/COB_0000110 http://purl.obolibrary.org/obo/RO_0002083 http://purl.obolibrary.org/obo/RO_0002234 http://purl.obolibrary.org/obo/IAO_0000136 +http://purl.obolibrary.org/obo/OBI_0600014 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/RO_0000056 http://purl.obolibrary.org/obo/OBI_0000312 http://purl.obolibrary.org/obo/IAO_0000115 http://purl.obolibrary.org/obo/BFO_0000055 +http://purl.obolibrary.org/obo/COB_0000022 +http://purl.obolibrary.org/obo/COB_0000035 http://purl.obolibrary.org/obo/RO_0002218 http://purl.obolibrary.org/obo/RO_0002353 http://purl.obolibrary.org/obo/IAO_0000600 http://www.w3.org/2002/07/owl#Thing http://purl.obolibrary.org/obo/IAO_0000114 http://purl.obolibrary.org/obo/OBI_0000278 -http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/RO_0002012 http://purl.obolibrary.org/obo/BFO_0000054 http://purl.obolibrary.org/obo/RO_0002081 diff --git a/src/ontology/tmp/iao-download.owl b/src/ontology/tmp/iao-download.owl deleted file mode 100644 index 0946a2c..0000000 --- a/src/ontology/tmp/iao-download.owl +++ /dev/null @@ -1,8157 +0,0 @@ - - - - - en - Adam Goldstein - Alan Ruttenberg - Albert Goldfain - Barry Smith - Bjoern Peters - Carlo Torniai - Chris Mungall - Chris Stoeckert - Christian A. Boelling - Clint Dowland - Darren Natale - David Osumi-Sutherland - Gwen Frishkoff - Holger Stenzhorn - James A. Overton - James Malone - Jennifer Fostel - Jie Zheng - Jonathan Rees - Larisa Soldatova - Lawrence Hunter - Mathias Brochhausen - Matt Brush - Melanie Courtot - Michel Dumontier - Paolo Ciccarese - Pat Hayes - Philippe Rocca-Serra - Randy Dipert - Ron Rudnicki - Satya Sahoo - Sivaram Arabandi - Werner Ceusters - William Duncan - William Hogan - Yongqun (Oliver) He - The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. - Information Artifact Ontology (IAO) - - An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO - IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 - IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 - - 2022-11-07 - - - - - - - - - - - - - - - - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - editor preferred term - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - has curation status - - - - - - - - definition - - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - - editor note - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - - - - - - - - alternative label - - A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. - OBO Operations committee - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - - - - - - - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition source - - - - - - - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - - - - - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - - curator note - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - ontology term requester - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - - - - - - is denotator type - Relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - - - - - - - - imported from - - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - imported from - - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - antisymmetric property - part_of antisymmetric property xsd:true - Use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - has ID digit count - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - - - - - - has ID range allocated - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - - - - - - has ID policy for - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - - - - - - has ID prefix - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - - - - - - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - - elucidation - - - - - - - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - - has associated axiom(nl) - - - - - - - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - - has associated axiom(fol) - - - - - - - - is allocated id range - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - Add as annotation triples in the granting ontology - is allocated id range - - - - - - - - retired from use as of - relates a class of CRID to the date after which further instances should not be made, according to the central authority - In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp - Alan Ruttenberg - retired from use as of - - - - - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - - - - - may be identical to - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - #40 - VFB - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - may be identical to - - - - - - - - scheduled for obsoletion on or after - Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. - Chris Mungall, Jie Zheng - https://github.com/geneontology/go-ontology/issues/15532 - https://github.com/information-artifact-ontology/ontology-metadata/issues/32 - GO ontology - scheduled for obsoletion on or after - - - - - - - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - - has axiom label - - - - - - - - term replaced by - - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - Add as annotation triples in the granting ontology - term replaced by - - - - - - - - This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. - OBO Operations call - - logical characteristic of object property - - - - - - - - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } - Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. - - - - defined by construct - - - - - - - - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - has broad synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - - - - - - - - - An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - has exact synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - - - - - - - - - An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 - has narrow synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 - - - - - - - - - An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 - has related synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - - - - has measurement unit label - - - - - - - - - The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. - -Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. - -c = pattern in the ink -b = paper + ink -r = friend - - c specifically denotes r =def -r is a portion of reality -& c is a particular quality -& c depends specifically on some independent continuant b -& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. - -Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. - -Case 1 -Memory trace as mark created when reading some description of some friend. The trace can denote. - -Case 2 -Pattern of ink arrayed on paper as mark when writing down a friend's name - -Case 3 -Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. - 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_specifically denotes - true - - - - - - - - - This document is about information artifacts and their representations - - A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - is about - - - - - - - - - - - An information artifact IA mentions an entity E exactly when it has a component/part that denotes E - 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) - 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition - PERSON: Jonathan Rees - Person: Alan Ruttenberg - mentions - - - - - - - - Inverse of the relation 'mentions' - - - 2022-01-28T07:20:08Z - mentioned by - - - - - - - - - - - - A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. - A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. -g denotes r =def -r is a portion of reality -there is some c that is a concretization of g -every c that is a concretization of g specifically denotes r - person:Alan Ruttenberg - Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan - - denotes - - - - - - - - - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - - obsolete_materially denotes - true - - - - - - - - - - - - m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg - is quality measurement of - - - - - - - - - - obsolete_describes - true - - - - - - - - - - obsolete_represents - true - - - - - - - - - - inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - - denoted by - - - - - - - - - - - - relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point - has coordinate unit label - - - - - - - - - - - - relates a process to a time-measurement-datum that represents the duration of the process - Person:Alan Ruttenberg - is duration of - - - - - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - - - - - - - - A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. - Person:Alan Ruttenberg - Person:Bjoern Peters - is quality specification of - - - - - - - - - inverse of the relation of is quality specification of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - Person:Bjoern Peters - quality is specified as - - - - - - - - - - - - - relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken - Alan Ruttenberg - has time stamp - - - - - - - - - - - - - - - - - - - - - relates a time stamped measurement datum to the measurement datum that was measured - Alan Ruttenberg - has measurement datum - - - - - - - - - - - - - - - has_specified_input - has_specified_input - see is_input_of example_of_usage - - The inverse property of is_specified_input_of - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot - - has_specified_input - - - - - - - - is_specified_input_of - - - - - - - - - - - - - - - has_specified_output - has_specified_output - - The inverse property of is_specified_output_of - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot - - has_specified_output - - - - - - - - - - - - - - - is_specified_output_of - is_specified_output_of - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - Alan Ruttenberg - PERSON:Bjoern Peters - - is_specified_output_of - - - - - - - - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple - a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. - characteristic of - - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - has characteristic - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - disposition of - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - location of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - located in - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true - - - - - - - - DEPRECATED bearer of - true - - - - - - - - - - - - - - - - - - - - - - has measurement value - - - - - - - - - - - has x coordinate value - - - - - - - - - - - has z coordinate value - - - - - - - - - - - has y coordinate value - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process that has specified output a software product and that involves the creation of source code. - Mathias Brochhausen - William R. Hogan - http://en.wikipedia.org/wiki/Software_development - A planned process resulting in a software product involving the creation of source code. - software development - - - - - - - - - - - - - - - - - - - - A measurement datum that is the output of counting. - Mathias Brochhausen - A measurement datum that is the output of counting. - count - - - - - - - - - - - - - - - - - - - - The planned process of finding the number of elements in a finite set of objects. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Counting - The planned process of finding the number of elements in a finite set of objects. - counting - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - software source code version control repository - A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. - William R. Hogan - Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based - source code repository - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - process of compiling software - A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. - William R. Hogan - It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). - Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. - compiling software - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - - - - - - - - - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - site - - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of requited love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - - - conditional specification - - A directive information entity that specifies what should happen if the trigger condition is fulfilled. - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000349 - conditional specification - - - - - - - - - measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - measurement unit label - - - - - - - - - objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 - objective specification - - - - - - - - - narrative object - Examples of narrative objects are reports, journal articles, and patents submission. - - A narrative object is an information content entity that is a set of propositions. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions - person:Chris Stoeckert - OBI_0000013 - group:OBI - narrative object - - - - - - - - - Pour the contents of flask 1 into flask 2 - - A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - - - - - - - obsolete_artifact - true - - - - - - - - - datum label - - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - - datum label - - - - - - - - - software - - Software is a plan specification composed of a series of instructions that can be -interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI - software - - - - - - - - - obsolete_digital entity - A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - -Superclass was 'digitial quality' - person:Chris Stoeckert - OBI_0000261 - group:OBI - - obsolete2_digital entity - true - - - - - - - - - - - - - - - - - - - - - - journal article - Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. - - A report that is published in a journal. - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - OBI_0000159 - group:OBI - journal article - - - - - - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - information carrier - - - - - - - - - model number - - A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers - Person: Alan Ruttenberg - model number - - - - - - - - - - obsolete_material_entity - true - - - - - - - - - binary digital entity - MS Word document, ZIP file, DICOM file, JPEG file - A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -Superclass was 'digital entity' - digital_entity - person:Chris Stoeckert - OBI_0000244 - group:OBI - - obsolete2_binary digital entity - true - - - - - - - - - The length of a ruler. - a unit of measure is the quality of some material entity compared to which another quality is some multiple of. - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_unit of measure - true - - - - - - - - - programming language - R, Perl, Java - - A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000058 - group:OBI - programming language - - - - - - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data - data item - - - - - - - - - symbol - a serial number such as "12324X" - a stop sign - a written proper name such as "OBI" - - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - 20091104, MC: this needs work and will most probably change - 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). - PERSON: James A. Overton - PERSON: Jonathan Rees - based on Oxford English Dictionary - symbol - - - - - - - - - numeral - - A symbol that denotes a number. - PERSON: Jonathan Rees - numeral - - - - - - - - - - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - - A generically dependent continuant that is about some thing. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 - information content entity - - - - - - - - - integer numeral - - A numeral that denotes an integer - PERSON: Jonathan Rees - integer numeral - - - - - - - - - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - - A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - scalar measurement datum - - - - - - - - - - - - - - - - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - directive information entity - - - - - - - - - time trigger - - PlanAndPlannedProcess Branch - time trigger - - - - - - - - - obsolete_study interpretation - - A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses - 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. - Lawrence Hunter - PERSON: Alan Ruttenberg - PERSON: Jennifer Fostel - PERSON: Melanie Courtot - conclusion - OBI_0000005 - - obsolete_study interpretation - true - - - - - - - - - dot plot - Dot plot of SSC-H and FSC-H. - - A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000123 - group:OBI - dot plot - - - - - - - - - graph - - A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - PERSON: Lawrence Hunter - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000240 - group:OBI - graph - - - - - - - - - text based digital entity - XML file, C++ source code file - A text based digital entity is a digital entity that is encoded so that it only contains text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital document' - digital_entity - person:Chris Stoeckert - OBI_0000132 - group:OBI - - obsolete2_text based digital entity - true - - - - - - - - - rule - example to be added - - A rule is an executable which guides, defines, restricts actions. - MSI - PRS - OBI_0500021 - PRS - rule - - - - - - - - - contour plot - Contour plot of SSC-H, FSC-H, and FL1-H. - - generically_dependent_continuants - person:Allyson Lister - person:Chris Stoeckert - OBI_0000246 - group:Flow Cytometry community - contour plot - - - - - - - - - report figure - - A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements - I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report - Replaced by defined version of figure - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000027 - group:OBI - - obsolete2_report figure - true - - - - - - - - - algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - algorithm - - - - - - - - - software interpreter - R program, Perl interpreter, Java virtual machine - - A software interpreter is a software application that executes some specified input software. - Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000199 - group:OBI - software interpreter - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - density plot - Density plot of SSC-H and FSC-H. - - A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000179 - group:Flow Cytometry community - density plot - - - - - - - - - report - Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. - - A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on -something that has completed." Should it be restricted to those things -that are completed? For example, a progress report is (usually) about -something that definitely has *not* been completed, or may include -(only) projections. I think the definition would not suffer if the -whole sentence is deleted. - 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion - disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI - OBI_0000099 - report - - - - - - - - - report element - - A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). - 2009-03-16: needs some more work (clarify relations). - 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - Replaced by textual entity and figure - There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text - PERSON: Alan Ruttenberg - PERSON: Allyson Lister - PERSON: Melanie Courtot - GROUP:OBI - OBI_0000001 - - obsolete_report element - true - - - - - - - - - binary executable - Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital entity' - person:Jennifer Fostel - OBI_0000222 - group:OBI - - obsolete2_binary executable - true - - - - - - - - - source code module - The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. - - A source code module is a directive information entity that specifies, using a programming language, some algorithm. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000039 - group:OBI - source code module - - - - - - - - - report table - - A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000265 - group:OBI - - obsolete_report table - true - - - - - - - - - data format specification - - A data format specification is the information content borne by the document published defining the specification. -Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file" - PERSON: Alan Ruttenberg - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000187 - data format specification - - - - - - - - - data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI - data set - - - - - - - - - image - - An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - person:Alan Ruttenberg - person:Allyson - person:Chris Stoeckert - OBI_0000030 - group:OBI - image - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - Clint Dowland - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them - plan specification - https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 - - - - - - - - - digital document - A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digial entity' - person:Jennifer Fostel - OBI_0000195 - group:OBI - - obsolete2_digital document - true - - - - - - - - - measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI - measurement datum - - - - - - - - - - _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - -Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. - - obsolete_identifier - true - - - - - - - - - version number - - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. - Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version - GROUP: IAO - version number - - - - - - - - - serial number - - A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) - GROUP: IAO - serial number - - - - - - - - - lot number - - A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. - GROUP: IAO - batch number - lot number - - - - - - - - - - A settings datum is a datum that denotes some configuration of an instrument. - 2/3/2009 Feedback from OBI - -This should be a "setting specification". There is a question of whether it is information about a realizable or not. - -Pro other specification are about realizables. -Cons sometimes specifies a quality which is not a realizable. - Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. - setting datum - - - - - - - - - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - Need to rework digital entity. Digital quality was suggested by Barry. - - obsolete_digital quality - true - - - - - - - - - conclusion textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - 2009/10/23 Alan Ruttenberg: We need to work on the definition still - Person:Alan Ruttenberg - conclusion textual entity - - - - - - - - - - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO - material information bearer - - - - - - - - - histogram - - A histogram is a report graph which is a statistical description of a -distribution in terms of occurrence frequencies of different event classes. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - histogram - - - - - - - - - heatmap - - A heatmap is a report graph which is a graphical representation of data -where the values taken by a variable(s) are shown as colors in a -two-dimensional map. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - heatmap - - - - - - - - - Venn diagram - - A Venn diagram is a report graph showing all hypothetically possible -logical relations between a finite collection of sets. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Venn_diagram - Venn diagram - - - - - - - - - obsolete_survival curve - - A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://www.graphpad.com/www/book/survive.htm - - obsolete_survival curve - true - - - - - - - - - dendrogram - Dendrograms are often used in computational biology to -illustrate the clustering of genes. - - A dendrogram is a report graph which is a tree diagram -frequently used to illustrate the arrangement of the clusters produced by a -clustering algorithm. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Dendrogram - dendrogram - - - - - - - - - scatter plot - Comparison of gene expression values in two samples can be displayed in a scatter plot - - A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - scattergraph - WEB: http://en.wikipedia.org/wiki/Scatterplot - scatter plot - - - - - - - - - - A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. - PERSON:Alan Ruttenberg - PERSON:Joanne Luciano - PERSON:Melanie Courtot - WEB: http://en.wiktionary.org/wiki/photograph - photograph - - - - - - - - - - - - - - - - - - - - - - - - - photographic print - - A photographic print is a material entity upon which a photograph generically depends. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - photographic print - - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - textual entity - Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities - - A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. - MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. - PERSON: Lawrence Hunter - text - textual entity - - - - - - - - - - - - - - - citation - Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. - - A textual entity intended to identify a particular publication. - PERSON: Lawrence Hunter - citation - - - - - - - - - author identification - L. Hunter - - A textual entity intended to identify a particular author - PERSON: Lawrence Hunter - author identification - - - - - - - - - institutional identification - University of Colorado Denver School of Medicine - - A textual entity intended to identify a particular institution - PERSON: Lawrence Hunter - institutional identification - - - - - - - - - - - - - - - caption - Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. - - A textual entity that describes a figure - PERSON: Lawrence Hunter - caption - - - - - - - - - document title - Textual characteristics of traditional and Open Access scientific journals are similar - - A textual entity that names a document - PERSON: Lawrence Hunter - document title - - - - - - - - - table - | T F ---+----- -T | T F -F | F F - - A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions - PERSON: Lawrence Hunter - table - - - - - - - - - table of abbreviations - IAO information artifact ontology -OBI ontology of biomedical investiations -GO gene ontology - - A table where the constituent texts are abbreviations and their expansions - PERSON: Lawrence Hunter - table of abbreviations - - - - - - - - - figure - Any picture, diagram or table - - An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - PERSON: Lawrence Hunter - figure - - - - - - - - - diagram - A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. - - A figure that expresses one or more propositions - PERSON: Lawrence Hunter - diagram - - - - - - - - - document - A journal article, patent application, laboratory notebook, or a book - - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter - document - - - - - - - - - - - - - - - - - - - - publication - journal article, newspaper story, book, etc. - - A document that is the output of a publishing process. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - PERSON: Lawrence Hunter - published document - - Revisit the term in Octorber 2020. Improve the defintion. - publication - - - - - - - - - - - - - - - publication about an investigation - Most scientific journal articles - - A publication that is about an investigation - PERSON: Lawrence Hunter - scientific publication - publication about an investigation - - - - - - - - - patent - US Patent 6,449,603 - - A document that has been accepted by a patent authority - PERSON: Lawrence Hunter - patent - - - - - - - - - - - - - - - document part - An abstract, introduction, method or results section. - - An information content entity that is part of a document. - PERSON: Lawrence Hunter - document part - - - - - - - - - - - - - - - abstract - The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. - - A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. - PERSON: Lawrence Hunter - precis - - abstract - - - - - - - - - - - - - - - introduction to a publication about an investigation - Section labelled 'introduction' of a typical scientific journal article - - A part of a publication about an investigation that is about the objective specification (why the investigation is being done) - PERSON: Lawrence Hunter - background - introduction - overview - - introduction to a publication about an investigation - - - - - - - - - - - - - - - methods section - The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. - - A part of a publication about an investigation that is about the study design of the investigation - PERSON: Lawrence Hunter - experimental - experimental methods - experimental procedures - experimental section - method - methodology - methods - - methods section - - - - - - - - - - - - - - - results section - The section labelled 'results' in a typical scientific journal article - - A part of a publication about an investigation that is about a study design execution - PERSON: Lawrence Hunter - results - results section - - - - - - - - - discussion section of a publication about an investigation - - A part of a publication about an investigation that is about the study interpretation of the investigation - PERSON: Lawrence Hunter - discussion - discussion section - discussions - - discussion section of a publication about an investigation - - - - - - - - - - - - - - - references section - The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" - - A part of a document that has citations as parts - PERSON: Lawrence Hunter - literature cited - reference - reference list - references - - references section - - - - - - - - - - - - - - - author list - Lawrence Hunter and Kevin Brettonel Cohen - - A part of a document that enumerates the authors of the document - PERSON: Lawrence Hunter - author list - - - - - - - - - - - - - - - institution list - The University of Colorado Denver School of Medicine and the University of Colorado Boulder. - - A part of a document that has parts that are institution identifications associated with the authors of the document - PERSON: Lawrence Hunter - institution list - - - - - - - - - author contributions section - LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. - - A part of a publication that is about the specific contributions of each author - PERSON: Lawrence Hunter - author contributions - authors' contribution - authors' contributions - authors' roles - contributions by the authors - contributorship - - author contributions section - - - - - - - - - acknowledgements section - The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript - - Part of a publication that is about the contributions of people or institutions other than the authors. - PERSON: Lawrence Hunter - acknowledgement - acknowledgements - acknowledgment - acknowledgments - - acknowledgements section - - - - - - - - - - - - - - - footnote - The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. - - A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. - PERSON: Lawrence Hunter - endnote - footnotes - - footnote - - - - - - - - - supplementary material to a document - - A part of a document that is segregated from the rest of the document due to its size - PERSON: Lawrence Hunter - additional file - additional files - additional information - appendix - electronic supplementary material - electronic supplementary materials - supplemental data - supplemental information - supplemental material - supplementary data - supplementary files - supplementary information - supplementary material - supplementary materials - supporting information - - supplementary material to a document - - - - - - - - - table of contents - - A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of contents - - - - - - - - - table of figures - - A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of figures - - - - - - - - - running title - - A shorter version of a document title - PERSON: Lawrence Hunter - running title - - - - - - - - - copyright section - This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. - - A document part that describes legal restrictions on making or distributing copies of the document - PERSON: Lawrence Hunter - copyright section - - - - - - - - - - - - - - - - - - 1 - - - - A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude - 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - Alan Ruttenberg - AR notes: We need to discuss whether it should include site. - cartesian spatial coordinate datum - http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region - Alan Ruttenberg - one dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region - Alan Ruttenberg - two dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region - Alan Ruttenberg - three dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of length quality - Alan Ruttenberg - length measurement datum - - - - - - - - - - - - - - - - - - denotator type - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of mass quality - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - mass measurement datum - - - - - - - - - hypothesis textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses an assertion that is intended to be tested. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - hypothesis textual entity - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measuring a temporal interval - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - time measurement datum - - - - - - - - - - A textual entity that is used as directive to deliver something to a person, or organization - 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 - postal address - - - - - - - - - email address - - Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 - Person:Alan Ruttenberg - Person:Chris Stoeckart - email address - - - - - - - - - author role - - A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - author role - - - - - - - - - - - - - - - - - - - - - - A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing - Person:Alan Ruttenberg - data item extraction from journal article - - - - - - - - - - A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. - Person: Jie Zheng - https://en.wikipedia.org/wiki/Publishing - - VEuPathDB - publishing process - - - - - - - - - - A document that is in preparation for submission to be published. - PERSON: Jie Zheng - EFO_0001795 in preparation - - VEuPathDB - document in preparation for publication - - - - - - - - - - - - - - - - - - - - - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - - A planned process in which a document is created or added to by including the specified input in it. - 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting - documenting - - - - - - - - - line graph - - A line graph is a type of graph created by connecting a series of data -points together with a line. - PERSON:Chris Stoeckert - PERSON:Melanie Courtot - line chart - GROUP:OBI - WEB: http://en.wikipedia.org/wiki/Line_chart - line graph - - - - - - - - - - - - - - - - - - - - - A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. - - A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. - Person:Alan Ruttenberg - Person:Bjoern Peters - Person:Melanie Courtot - assigning a CRID - assigning a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - - - - Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. - - A planned process in which a CRID registry associates an information content entity with a CRID symbol - PERSON:Alan Ruttenberg - associating information with a CRID in the CRID registry - associating information with a centrally registered identifier in its registry - - - - - - - - - a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. - MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. - - obsolete_establishing a CRID registry - true - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID symbol - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier symbol - - - - - - - - - - - - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. - 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). - Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. - Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier - - - - - - - - - PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. - - A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. - Justin Whorton - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID registry - Original proposal from Bjoern, discussions at IAO calls - https://github.com/information-artifact-ontology/IAO/issues/237 - centrally registered identifier registry - - - - - - - - - - - - - - - - - - - - - - - - - - - Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. - - A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - looking up a CRID - looking up a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - time stamped measurement datum - - - - - - - - - - - - - - - pmid:20604925 - time-lapse live cell microscopy - - A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. - Alan Ruttenberg - experimental time series - time sampled measurement data set - - - - - - - - - written name - "Bill Clinton" - "The Eiffel Tower" - "United States of America" - - A textual entity that denotes a particular in reality. - PERSON: Bill Hogan - https://github.com/information-artifact-ontology/IAO/issues/114 - The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. - written name - - - - - - - - - - A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software method - - - - - - - - - - A software module is software composed of a collection of software methods. - PERSON: Melanei Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software module - - - - - - - - - - A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software library - - - - - - - - - - A software application is software that can be directly executed by some processing unit. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software application - - - - - - - - - - A software script is software whose instructions can be executed using a software interpreter. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software script - - - - - - - - - abbreviation textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. - A textual entity listing abbreviations and their expansions that are used in a document. - PERSON: Bill Baumgartner - - abbreviation textual entity - - - - - - - - - - - - - - - abbreviations section - The section labelled 'abbreviations' in a typical scientific journal article. - A part of a document where abbreviations and their long-forms used within the document are listed. - PERSON: Bill Baumgartner - abbreviation and acronyms - abbreviation list - abbreviations - abbreviations and acronyms - abbreviations list - abbreviations used - definitions for abbreviations - list of abbreviations - list of abbreviations used - non-standard abbreviations - nonstandard abbreviations - nonstandard abbreviations and acronyms - - - abbreviations section - - - - - - - - - - - - - - - author information section - The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) - A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - author information - authors’ information - biographies - contributor information - - - author information section - - - - - - - - - author information textual entity - From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): - -IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. - A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - - author information textual entity - - - - - - - - - - - - - - - author summary section - The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) - A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. - PERSON: Bill Baumgartner - author summary - summary - synopsis - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) - - author summary section - - - - - - - - - author summary textual entity - From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): - - -The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. - A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - PERSON: Bill Baumgartner - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - - author summary textual entity - - - - - - - - - - - - - - - availability section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. - PERSON: Bill Baumgartner - availability - availability of data - data archiving - data availability - data availability statement - data sharing statement - - - availability section - - - - - - - - - availability textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -Project home page:http://krux.googlecode.com - A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. - PERSON: Bill Baumgartner - - availability textual entity - - - - - - - - - - - - - - - case report section - The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) - A part of a document about the medical history of a specific patient as it relates to the topic of the document. - PERSON: Bill Baumgartner - case presentation - case report - - case report section - - - - - - - - - case report textual entity - Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): - -The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. - A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. - PERSON: Bill Baumgartner - - case report textual entity - - - - - - - - - - - - - - - conclusion section - The section labelled 'conclusion' in a typical scientific journal article. - A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. - PERSON: Bill Baumgartner - concluding remarks - conclusion - conclusions - findings - summary - - conclusion section - - - - - - - - - - - - - - - conflict of interest section - The section labelled 'conflict of interest statement' in a typical scientific journal article. - A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. - PERSON: Bill Baumgartner - authors' disclosures of potential conflicts of interest - competing financial interests - competing interests - conflict of interest - conflict of interest statement - conflict of interests - conflicts of interest - declaration of competing interest - declaration of competing interests - declaration of interest - declaration of interests - disclosure of conflict of interest - disclosure of potential conflicts of interest - duality of interest - statement of interest - - - conflict of interest section - - - - - - - - - conflict of interest statement - SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] - A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. - PERSON: Bill Baumgartner - - conflict of interest textual entity - - - - - - - - - - - - - - - consent section - The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) - A part of a document about the consent process that was used to enroll patients in a study. - PERSON: Bill Baumgartner - consent - - consent section - - - - - - - - - consent textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. - A textual entity that documents the consenting process used to enroll patients in a study. - PERSON: Bill Baumgartner - - consent textual entity - - - - - - - - - - - - - - - ethical approval section - The section labelled 'ethical approval' in a typical scientific journal article. - A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. - PERSON: Bill Baumgartner - ethical approval - ethical requirements - ethics - ethics statement - - - ethical approval section - - - - - - - - - - - - - - - ethical approval textual entity - From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - -The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. - A textual entity that documents the ethical approval of some study design. - PERSON: Bill Baumgartner - - ethical approval textual entity - - - - - - - - - - - - - - - figures section - The section labelled 'figures' in a typical scientific journal article. - A part of a document that contains one or more figures. - PERSON: Bill Baumgartner - figures - - figures section - - - - - - - - - - - - - - - funding source declaration section - The section labelled 'funding' in a typical scientific journal article. - A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. - PERSON: Bill Baumgartner - financial support - funding - funding information - funding sources - funding statement - funding/support - grants - role of the funding source - source of funding - sources of funding - study funding - - - funding source declaration section - - - - - - - - - funding souce declaration textual entity - From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): - -This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. - A textual entity documenting the source of funding that supported some study. - PERSON: Bill Baumgartner - - funding source declaration textual entity - - - - - - - - - - - - - - - future directions section - The section labelled 'future directions' in a typical scientific journal article. - A part of a document detailing extensions of the described work that may be implemented at some future point in time. - PERSON: Bill Baumgartner - future challenges - future considerations - future developments - future directions - future outlook - future perspectives - future plans - future prospects - future research - future research directions - future studies - future work - outlook - - - future directions section - - - - - - - - - future directions textual entity - Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): - -In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. - A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. - PERSON: Bill Baumgartner - - future directions textual entity - - - - - - - - - - - - - - - genome announcement section - The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) - A document part announcing the publication of a novel draft genome sequence. - PERSON: Bill Baumgartner - genome announcement - - genome announcement section - - - - - - - - - genome announcement textual entity - Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): - -Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). - A textual entity that describes the generation and public release of a novel, draft genome sequence. - PERSON: Bill Baumgartner - - genome announcement textual entity - - - - - - - - - keyword textual entity - From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): - -Exon orthology; alternative splicing; exon duplication; intron-exon structure. - A textual entity listing keywords indicating the major theme(s) of a document. - PERSON: Bill Baumgartner - - keyword textual entity - - - - - - - - - - - - - - - keywords section - The section labelled 'keywords' in a typical scientific journal article. - A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. - PERSON: Bill Baumgartner - keywords - - keywords section - - - - - - - - - - - - - - - - - - - - - study limitations section - The section labelled 'limitations' in a typical scientific journal article. - A part of a document about biases or short comings related to the study design and execution. - PERSON: Bill Baumgartner - limitations - study limitations - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations section - - - - - - - - - study limitations textual entity - Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). - -Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. - A textual entity addressing a shortcoming or bias of a study design or execution. - PERSON: Bill Baumgartner - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations textual entity - - - - - - - - - materials section - The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) - A part of a document about the materials required to reproduce the content of the document. - PERSON: Bill Baumgartner - materials - - materials section - - - - - - - - - notes section - The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. - PERSON: Bill Baumgartner - notes - - notes section - - - - - - - - - - - - - - - patients section - The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) - A part of a document about the patients that participated in a study. - PERSON: Bill Baumgartner - - patients section - - - - - - - - - patients textual entity - Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): - -Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. - A textual entity expressing information regarding the patients used in a study. - PERSON: Bill Baumgartner - - patients textual entity - - - - - - - - - - - - - - - pre-publication history section - The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) - A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. - PERSON: Bill Baumgartner - notice of republication - pre-publication history - - pre-publication history section - - - - - - - - - pre-publication history textual entity - From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): - -The pre-publication history for this paper can be accessed here: -http://www.biomedcentral.com/1471-2253/13/33/prepub - A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. - PERSON: Bill Baumgartner - - pre-publication history textual entity - - - - - - - - - - - - - - - related work section - The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) - A part of a document about work in other publications that is relevant to the content of the document. - PERSON: Bill Baumgartner - related literature - related work - - related work section - - - - - - - - - related work textual entity - Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): - -Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). - - - A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. - PERSON: Bill Baumgartner - - related work textual entity - - - - - - - - - - - - - - - requirements section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. - PERSON: Bill Baumgartner - requirements - - requirements section - - - - - - - - - requirements textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -• Operating systems: Platform independent - -• Programming language: Matlab, R, Python - -• Other requirements: None - -• License: GNU GPL v3 - -• Any restrictions to use by non-academics: None - A textual entity that expresses the requirements necessary to use a resource, e.g. software. - PERSON: Bill Baumgartner - - requirements textual entity - - - - - - - - - statistical analysis textual entity - From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): - -Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. - A textual entity documenting statistical analysis tools and techniques employed. - PERSON: Bill Baumgartner - - statistical analysis textual entity - - - - - - - - - - - - - - - statistical analysis section - The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) - A part of the document used to describe the statistical methodologies employed in the work presented in the document. - PERSON: Bill Baumgartner - statistical analysis - - statistical analysis section - - - - - - - - - - - - - - - tables section - The section labelled 'tables' in a typical scientific journal article. - A part of a document that contains one or more tables. - PERSON: Bill Baumgartner - tables - - tables section - - - - - - - - - An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. - Mathias Brochhausen - postal code - - - - - - - - - A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. - Mathias Brochhausen - Postal delivery route - - - - - - - - - A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. - Mathias Brochhausen - ZIP code - zone improvement plan code - - - - - - - - - - - - - - - - - - - - - database extract, transform, and load process - A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. - Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second - Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. - PERSON:Alan Ruttenberg - ETL - WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load - - - database extract, transform, and load process - - - - - - - - - - descriptive data section - - A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made. - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.equator-network.org/reporting-guidelines/prisma/ - - ONE ontology - descriptive data section - - - - - - - - - additional results section - - A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.) - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.equator-network.org/reporting-guidelines/consort/ - https://www.equator-network.org/reporting-guidelines/prisma/ - https://www.equator-network.org/reporting-guidelines/strobe/ - - ONE ontology - additional results section - - - - - - - - - research participants section - - A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.). - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.equator-network.org/reporting-guidelines/consort/ - https://www.equator-network.org/reporting-guidelines/prisma/ - https://www.equator-network.org/reporting-guidelines/strobe-nut/ - - ONE ontology - research participants section - - - - - - - - - measurement methods section - - A methods section that describes details of data assessment methods (data measurement). - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.equator-network.org/reporting-guidelines/strobe/ - - ONE ontology - measurement methods section - - - - - - - - - research settings section - - A document part that describes the physical/social/cultural conditions around a research trial. - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.ncbi.nlm.nih.gov/books/NBK262175/ - - ONE ontology - research settings section - - - - - - - - - study bias section - - A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others. - PERSON: Chen Yang - PERSON: Jie Zheng - DOI: 10.1097/PRS.0b013e3181de24bc - - ONE ontology - study bias section - - - - - - - - - graphical abstract - - An abstract that is pictorial summary of the main findings described in the document. - PERSON: Jie Zheng - PERSON: Tim Beck - visual abstract - https://www.elsevier.com/authors/journal-authors/graphical-abstract - - Biomedical literature NLP project - graphical abstract - - - - - - - - - - A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor. - "You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/] - This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25) - http://orcid.org/0000-0002-1595-3213 - ORCID ID - ORCiD - Open Researcher and Contributor ID - Open Researcher and Contributor Identifier - https://orcid.org/ - https://github.com/information-artifact-ontology/IAO/issues/259 - ORCID identifier - - - - - - - - - - - - - - - - - - - - - - - - identifier - An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. - Justin Whorton - Mathias Brochhausen - proper name - https://github.com/information-artifact-ontology/IAO/issues/237 - Mathias Brochhausen - Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) - identifier - - - - - - - - - alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems - An information content entity that is a fundamental unit in a written language. - Justin Whorton - http://en.wikipedia.org/wiki/Grapheme - https://github.com/information-artifact-ontology/IAO/issues/237 - Mathias Brochhausen - Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there. - grapheme - - - - - - - - - - - - - - - - - - - - A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. - Justin Whorton - Mathias Brochhausen - dubbing process - naming - https://github.com/information-artifact-ontology/IAO/issues/237 - Mathias Brochhausen - identifier creating process - - - - - - - - - An identifier referring to an individual entity that is ascribed personhood by the user of the identifier. - Justin Whorton - Mathias Brochhausen - http://en.wikipedia.org/wiki/Personal_name - https://github.com/information-artifact-ontology/IAO/issues/237 - Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name) - Personal names to not include names of fictional characters, e.g. Sherlock Holmes. - Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB) - personal name - - - - - - - - - A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name - Justin Whorton - Mathias Brochhausen - first name - http://en.wikipedia.org/wiki/Given_name - https://github.com/information-artifact-ontology/IAO/issues/237 - given name - - - - - - - - - An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. - Justin Whorton - Mathias Brochhausen - last name - surname - http://en.wikipedia.org/wiki/Family_name - https://github.com/information-artifact-ontology/IAO/issues/237 - family name - - - - - - - - - - - - - - - An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. - Alan Ruttenberg - Justin Whorton - Mathias Brochhausen - code map - code system - codeset - coding system - controlled vocabulary - https://github.com/information-artifact-ontology/IAO/issues/237 - Alan Ruttenberg - Clint Dowland - Matt Diller - Sarah Bost - William R. Hogan - Code sets might include non-entities/things (e.g. missing thumbs). - Does not imply absence vs. presence of any taxonomy. - Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. - Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. - -When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). - For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). - For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. - Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. - The information content entities do not denote each other. - code set - - - - - - - - - ontology module - I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. - ontology file - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - ontology module - - - - - - - - - base ontology module - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - base ontology module - - - - - - - - - - editors ontology module - An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. - source ontology module - editors ontology module - - - - - - - - - main release ontology module - An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. - TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module - main release ontology module - - - - - - - - - bridge ontology module - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - bridge ontology module - - - - - - - - - - import ontology module - A subset ontology module that is intended to be imported from another ontology. - TODO: add axioms that indicate this is the output of a module extraction process. - import file - import ontology module - - - - - - - - - - subset ontology module - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - subset ontology module - - - - - - - - - - - curation subset ontology module - A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. - curation subset ontology module - - - - - - - - - analysis ontology module - An ontology module that is intended for usage in analysis or discovery applications. - analysis subset ontology module - - - - - - - - - single layer ontology module - A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. - ribbon subset - single layer subset ontology module - - - - - - - - - exclusion subset ontology module - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - exclusion subset ontology module - - - - - - - - - external import ontology module - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - external import ontology module - - - - - - - - - species subset ontology module - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - species subset ontology module - - - - - - - - - - reasoned ontology module - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - reasoned ontology module - - - - - - - - - - generated ontology module - An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. - TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process - generated ontology module - - - - - - - - - template generated ontology module - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - template generated ontology module - - - - - - - - - - - - taxonomic bridge ontology module - taxonomic bridge ontology module - - - - - - - - - ontology module subsetted by expressivity - ontology module subsetted by expressivity - - - - - - - - - obo basic subset ontology module - A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. - -Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). - -An ontology is OBO Basic if and only if it has the following characteristics: -DAG -Unidirectional -No Dangling Clauses -Fully Asserted -Fully Labeled -No equivalence axioms -Singly labeled edges -No qualifier lists -No disjointness axioms -No owl-axioms header -No imports - obo basic subset ontology module - - - - - - - - - - ontology module subsetted by OWL profile - ontology module subsetted by OWL profile - - - - - - - - - EL++ ontology module - EL++ ontology module - - - - - - - - - planned process - A process that realizes a plan which is the concretization of a plan specification. - - planned process - - - - - - - - - investigation - a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). - - investigation - - - - - - - - - study design execution - a planned process that carries out a study design - - study design execution - - - - - - - - - data transformation - A planned process that produces output data from input data. - - data transformation - - - - - - - - - study design - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - - study design - - - - - - - - - morphology - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - - morphology - - - - - - - - - length - A 1-D extent quality which is equal to the distance between two points. - - length - - - - - - - - - mass - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - - mass - - - - - - - - - physical quality - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - physical object quality - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - length unit - - length unit - - - - - - - - - mass unit - - mass unit - - - - - - - - - time unit - - time unit - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - - failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - - obsolete_core - true - - - - - - - - - - placeholder removed - placeholder removed - - - - - - - - - terms merged - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. - We expect to be able to mine these new reasons and add instances as required. - obsolete_other - true - - - - - - - - - universal - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - defined class - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - named class expression - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 - out of scope - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/tmp/ido-download.owl b/src/ontology/tmp/ido-download.owl deleted file mode 100644 index b9ba582..0000000 --- a/src/ontology/tmp/ido-download.owl +++ /dev/null @@ -1,12111 +0,0 @@ - - - - - Alexander Diehl - - Jie Zheng - Albert Goldfain - Alan Ruttenberg - Bjoern Peters - The core Infectious Disease Ontology is an ontology of entities generally relevant to both the biomedical and clinical aspects of infectious diseases, including terms such as 'pathogen', 'host', 'vector', and 'vaccine'. The structure of IDO adheres to the Basic Formal Ontology. Terms in IDO that are within the scope of other OBO Foundry ontologies, such as the Gene Ontology, are derived from those ontologies. Other terms are defined as cross-products of terms from Foundry ontologies to the extent possible. For more information, see http://www.infectiousdiseaseontology.org/Home.html. - 2017-11-03 - http://www.infectiousdiseaseontology.org - en - Lindsay Cowell - Barry Smith - 2017-11-03T15:13:52 - - - - - - - - - - - - - - - - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - editor preferred term - - - - - - - - example - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - OBI_0000281 - has curation status - - - - - - - - definition - - The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - definition - definition - textual definition - textual definition - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obfoundry.org/obo/obi> - - editor note - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - - - - - - - - alternative term - - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - alternative term - - - - - - - - definition source - - formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition source - - - - - - - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - - - - - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - - curator note - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - - - - - - is denotator type - relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - - - - - - - - imported from - - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - imported from - - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - antisymmetric property - part_of antisymmetric property xsd:true - use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - - - - - - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - - - - - - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - - - - - - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - - - - - - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - - elucidation - - - - - - - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - - has associated axiom(nl) - - - - - - - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - - has associated axiom(fol) - - - - - - - - is allocated id range - Add as annotation triples in the granting ontology - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - is allocated id range - - - - - - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - - has axiom label - - - - - - - - term replaced by - - Add as annotation triples in the granting ontology - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - term replaced by - - - - - - - - temporal interpretation - https://github.com/oborel/obo-relations/wiki/ROAndTime - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - shorthand - - - - - - - - - - - - - - - - - - - - label - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - - - - preceded by - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - preceded by - - - - - - - - - - - precedes - precedes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - results_in - - - - - - - - - has_material_basis_in - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - bearer of - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - disposition of - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - location_of - - location of - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - located in - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - - - - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit - Chris Mungall - David Hill - Tanya Berardini - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - regulates - - - - - - - - - - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y - Chris Mungall - - negatively regulates (process to process) - negatively regulates - - - - - - - - - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y - Chris Mungall - - positively regulates (process to process) - positively regulates - - - - - - - - - - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' - - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) - capable of - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. - Chris Mungall - produces - has output - - - - - - - - - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_formation_of - results in formation of - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - - - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. - obsolete dependent continuant - true - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - - - - - - - - - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - site - - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - - - - - - - - - - - - - - - A part of a multicellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a multicellular organism with granularity above the level of a protein complex. - - anatomical entity - - - - - - - - - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - - molecular entity - - - - - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - - cell - cell - - - - - - - - - An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. - - leukocyte - - - - - - - - - The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. - - reproduction - - - - - - - - - An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). - - adaptive immune response - - - - - - - - - Any process involved in the carrying out of an immune response by a leukocyte. - - leukocyte mediated immunity - - - - - - - - - Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. - - immune response - - - - - - - - - An immune response mediated through a body fluid. - - humoral immune response - - - - - - - - - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - - biological_process - - - - - - - - - A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - - immunoglobulin complex - - - - - - - - - An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. - - B cell receptor complex - - - - - - - - - A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - - developmental process - - - - - - - - - A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - - macromolecular complex - - - - - - - - - The increase in size or mass of an entire organism, a part of an organism or a cell. - - growth - - - - - - - - - A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. - - T cell receptor complex - - - - - - - - - A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells. - - FtsZ-dependent cytokinesis - - - - - - - - - An interaction between two organisms living together in more or less intimate association. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. - - symbiosis, encompassing mutualism through parasitism - - - - - - - - - The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction. - - adhesion of symbiont to host - - - - - - - - - Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. - - entry into host - - - - - - - - - Penetration by an organism into its host organism via active breaching of the physical barriers of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. - - entry into host through host barriers - - - - - - - - - Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. - - innate immune response - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant. - - negative regulation of viral process - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. - - negative regulation of immune response - - - - - - - - - Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). - - negative regulation of developmental process - - - - - - - - - Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. - - Gene Ontology: http://purl.obolibrary.org/obo/go.owl - establishment of localization - establishment of localization - - - - - - - - - A biological process which involves another organism of the same or different species. - - multi-organism process - - - - - - - - - Any process that modulates a measurable attribute of any biological process, quality or function. - - biological regulation - - - - - - - - - An interaction between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other. - - mutualism - - - - - - - - - An interaction between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected. - - commensalism - - - - - - - - - data item - - - - - - - - - information content entity - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - - - - - - - - - - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - _obsolete_process - true - - - - - - - - - _obsolete_role - true - - - - - - - - - _obsolete_quality - true - - - - - - - - - _obsolete_object - true - - - - - - - - - 'the degree of pathogenicitynnpathogenicity and virulence are used in some communities as synonyms.'-ID[O]:0000004: the degree of pathogenicitynnpathogenicity and virulence are used in some communities as synonyms. - id 'virulence'-ID[O]:0000004 from IDO 2007. May have replacement - TBD - _obsolete_virulence - true - - - - - - - - - _obsolete_swollen - true - - - - - - - - - _obsolete_toxicity - true - - - - - - - - - _obsolete_active - true - - - - - - - - - _obsolete_contagious - true - - - - - - - - - 'infection has occurred, but it might not have manifested itselfnquality of being in a non replicative statentime to manifest itself na pathogen when it is in a non replicative state'-ID[O]:0000009: infection has occurred, but it might not have manifested itselfnquality of being in a non replicative statentime to manifest itself na pathogen when it is in a non replicative state - id 'latency'-ID[O]:0000009 from IDO 2007. May have replacement - TBD - _obsolete_latency - true - - - - - - - - - _obsolete_immunosuppressed - true - - - - - - - - - _obsolete_exogenous - true - - - - - - - - - _obsolete_immunity - true - - - - - - - - - _obsolete_protective - true - - - - - - - - - _obsolete_temperature - true - - - - - - - - - _obsolete_inactivated - true - - - - - - - - - _obsolete_mortality - true - - - - - - - - - _obsolete_pandemic - true - - - - - - - - - 'total number of cases of a particular disease at a given time in a particular population divided by the number of individuals in that particular populationnnthe burden of a disease in a population'-ID[O]:0000019: total number of cases of a particular disease at a given time in a particular population divided by the number of individuals in that particular populationnnthe burden of a disease in a population - id 'prevalence'-ID[O]:0000019 from IDO 2007. May have replacement - TBD - _obsolete_prevalence - true - - - - - - - - - _obsolete_epidemic - true - - - - - - - - - _obsolete_infected - true - - - - - - - - - _obsolete_live - true - - - - - - - - - _obsolete_zoonotic - true - - - - - - - - - _obsolete_immunocompromised - true - - - - - - - - - 'the ability of the biotic entity to cause disease in a host of a given typenndo we need to say damage instead of disease?nnpathogenicity and virulence are used as synonyms in some communities'-ID[O]:0000025: the ability of the biotic entity to cause disease in a host of a given typenndo we need to say damage instead of disease?nnpathogenicity and virulence are used as synonyms in some communities - id 'pathogenicity'-ID[O]:0000025 from IDO 2007. May have replacement - TBD - _obsolete_pathogenicity - true - - - - - - - - - _obsolete_tropism - true - - - - - - - - - _obsolete_drug resistance - true - - - - - - - - - _obsolete_antibiotic resistance - true - - - - - - - - - 'number of new cases in a given period of time'-ID[O]:0000029: number of new cases in a given period of time - id 'incidence'-ID[O]:0000029 from IDO 2007. May have replacement - TBD - _obsolete_incidence - true - - - - - - - - - _obsolete_invasive - true - - - - - - - - - _obsolete_endogenous - true - - - - - - - - - _obsolete_attenuated - true - - - - - - - - - _obsolete_morbidity - true - - - - - - - - - _obsolete_endemic - true - - - - - - - - - _obsolete_fusion protein - true - - - - - - - - - _obsolete_colonizer - true - - - - - - - - - _obsolete_commensal - true - - - - - - - - - _obsolete_parasite - true - - - - - - - - - _obsolete_symbiant - true - - - - - - - - - 'role played by a portion of substance to promote virulencennmagnitudendegree of pathogenesis'-ID[O]:0000040: role played by a portion of substance to promote virulencennmagnitudendegree of pathogenesis - id 'virulence factor'-ID[O]:0000040 from IDO 2007. May have replacement - TBD - _obsolete_virulence factor - true - - - - - - - - - _obsolete_route of entry - true - - - - - - - - - _obsolete_invasin - true - - - - - - - - - _obsolete_toxin - true - - - - - - - - - _obsolete_endotoxin - true - - - - - - - - - _obsolete_exotoxin - true - - - - - - - - - _obsolete_sign - true - - - - - - - - - _obsolete_treatment - true - - - - - - - - - 'look at mathias's ontology of cancer to get all the subterms...its under quality there'-ID[O]:0000048: look at mathias's ontology of cancer to get all the subterms...its under quality there - id 'symptom'-ID[O]:0000048 from IDO 2007. May have replacement - TBD - _obsolete_symptom - true - - - - - - - - - _obsolete_antimicrobial - true - - - - - - - - - _obsolete_medicine - true - - - - - - - - - _obsolete_therapeutic - true - - - - - - - - - _obsolete_vaccine - true - - - - - - - - - _obsolete_antibiotic - true - - - - - - - - - 'role played by portion of physical substance which promotes colonization'-ID[O]:0000054: role played by portion of physical substance which promotes colonization - id 'colonization factor'-ID[O]:0000054 from IDO 2007. May have replacement - TBD - _obsolete_colonization factor - true - - - - - - - - - 'role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host'-ID[O]:0000055: role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host - id 'adhesion factor'-ID[O]:0000055 from IDO 2007. May have replacement - TBD - _obsolete_adhesion factor - true - - - - - - - - - _obsolete_host - true - - - - - - - - - _obsolete_carrier - true - - - - - - - - - _obsolete_chronic carrier - true - - - - - - - - - 'holding place for a potential pathogen...animate or inanimate'-ID[O]:0000059: holding place for a potential pathogen...animate or inanimate - id 'reservoir'-ID[O]:0000059 from IDO 2007. May have replacement - TBD - _obsolete_reservoir - true - - - - - - - - - 'inanimate holder, is water a fomite or only a reservoir?'-ID[O]:0000060: inanimate holder, is water a fomite or only a reservoir? - id 'fomite'-ID[O]:0000060 from IDO 2007. May have replacement - TBD - _obsolete_fomite - true - - - - - - - - - _obsolete_mobile genetic element - true - - - - - - - - - _obsolete_pathogenicity island - true - - - - - - - - - 'holder and a carrier (actively transmits) and living: potentially make a cross product. every vector comes into contact with the target. (from one host to another?)'-ID[O]:0000063: holder and a carrier (actively transmits) and living: potentially make a cross product. every vector comes into contact with the target. (from one host to another?) - id 'vector'-ID[O]:0000063 from IDO 2007. May have replacement - TBD - _obsolete_vector - true - - - - - - - - - _obsolete_pathogen - true - - - - - - - - - _obsolete_dependovirus - true - - - - - - - - - _obsolete_infectious agent - true - - - - - - - - - _obsolete_opportunistic pathogen - true - - - - - - - - - _obsolete_emerging pathogen - true - - - - - - - - - _obsolete_primary pathogen - true - - - - - - - - - _obsolete_prion - true - - - - - - - - - _obsolete_initiation of infection - true - - - - - - - - - _obsolete_disruption of body surface - true - - - - - - - - - _obsolete_disruption of normal microbioflora - true - - - - - - - - - 'create cross products for "host" and "pathogen" that will be part of this process.'-ID[O]:0000074: create cross products for "host" and "pathogen" that will be part of this process. - id 'pathogen adherence to host cell'-ID[O]:0000074 from IDO 2007. May have replacement - TBD - _obsolete_pathogen adherence to host cell - true - - - - - - - - - _obsolete_nonspecific adherence - true - - - - - - - - - _obsolete_specific adherence - true - - - - - - - - - _obsolete_afimbrial specific adherence - true - - - - - - - - - _obsolete_fimbrial specific adherence - true - - - - - - - - - _obsolete_penetration of epithelial barrier - true - - - - - - - - - _obsolete_penetration via injury of epithelial barrier - true - - - - - - - - - _obsolete_transcytosis - true - - - - - - - - - _obsolete_utilization of membranous cell gateway - true - - - - - - - - - 'the process by which an infectious agent passes from one organism to another organism'-ID[O]:0000083: the process by which an infectious agent passes from one organism to another organism - id 'transmission'-ID[O]:0000083 from IDO 2007. May have replacement - TBD - _obsolete_transmission - true - - - - - - - - - 'GO:nthe specific processes that generate the ability of an organism to cause disease in anothernnnThis is defined in GO so import.'-ID[O]:0000084: GO:nthe specific processes that generate the ability of an organism to cause disease in anothernnnThis is defined in GO so import. - id 'pathogenesis'-ID[O]:0000084 from IDO 2007. May have replacement - TBD - _obsolete_pathogenesis - true - - - - - - - - - _obsolete_penetration of host cell - true - - - - - - - - - _obsolete_engulfment - true - - - - - - - - - _obsolete_fusion with host cell membrane - true - - - - - - - - - _obsolete_membrane invagination - true - - - - - - - - - _obsolete_passage through cell membrane - true - - - - - - - - - _obsolete_engulfment by nonphagocyte - true - - - - - - - - - _obsolete_engulfment by phagocyte - true - - - - - - - - - _obsolete_damaging host cells and tissues in subepithelial space - true - - - - - - - - - _obsolete_induction of damaging host immune response - true - - - - - - - - - _obsolete_pathogen-induced apoptosis - true - - - - - - - - - _obsolete_pathogen-induced necrosis - true - - - - - - - - - _obsolete_virus-induced cytopathogenesis - true - - - - - - - - - _obsolete_pathogen spread through host - true - - - - - - - - - 'comment about the instances:nncollections of etiologically connected cases of infectious disease in a given population'-ID[O]:0000098: comment about the instances:nncollections of etiologically connected cases of infectious disease in a given population - id 'infectious disease'-ID[O]:0000098 from IDO 2007. May have replacement - TBD - _obsolete_infectious disease - true - - - - - - - - - _obsolete_pathogen evasion of host immune response - true - - - - - - - - - 'the process by which an infectious disease establishes itself in a new population (or at a sufficiently higher rate? higher prevalence and/or higher incidence)'-ID[O]:0000101: the process by which an infectious disease establishes itself in a new population (or at a sufficiently higher rate? higher prevalence and/or higher incidence) - id 'emergence'-ID[O]:0000101 from IDO 2007. May have replacement - TBD - _obsolete_emergence - true - - - - - - - - - _obsolete_epidemiological spread of disease - true - - - - - - - - - _obsolete_outbreak - true - - - - - - - - - _obsolete_infection - true - - - - - - - - - _obsolete_infection treatment process - true - - - - - - - - - _obsolete_immunization - true - - - - - - - - - _obsolete_prevention of infection - true - - - - - - - - - _obsolete_transport by blood - true - - - - - - - - - _obsolete_transport by lymph - true - - - - - - - - - _obsolete_modulation of inflammatory response - true - - - - - - - - - _obsolete_antigenic variation - true - - - - - - - - - _obsolete_resist phagocytosis in subepithelial space - true - - - - - - - - - _obsolete_serum resistance - true - - - - - - - - - _obsolete_phase variation - true - - - - - - - - - _obsolete_genetic diversification - true - - - - - - - - - _obsolete_complement resistance - true - - - - - - - - - _obsolete_epidemic spread of disease - true - - - - - - - - - _obsolete_pandemic spread of disease - true - - - - - - - - - _obsolete_vaccination - true - - - - - - - - - _obsolete_mode of transmission - true - - - - - - - - - _obsolete_end reservoir - true - - - - - - - - - 'Role played by portion of physical substance in a biological process'-ID[O]:0000204: Role played by portion of physical substance in a biological process - id 'factor'-ID[O]:0000204 from IDO 2007. May have replacement - TBD - _obsolete_factor - true - - - - - - - - - 'the process by which a biotic entity establishes multiple copies of itself in a new environment (including an organismal environment).nnfix idn"native" environment term'-ID[O]:0000205: the process by which a biotic entity establishes multiple copies of itself in a new environment (including an organismal environment).nnfix idn"native" environment term - id 'colonization'-ID[O]:0000205 from IDO 2007. May have replacement - TBD - _obsolete_colonization - true - - - - - - - - - _obsolete_biotic - true - - - - - - - - - _obsolete_adhesin - true - - - - - - - - - 'prevalence as measured by antibody'-ID[O]:0000208: prevalence as measured by antibody - id 'seroprevalence'-ID[O]:0000208 from IDO 2007. May have replacement - TBD - _obsolete_seroprevalence - true - - - - - - - - - 'quality [state] of an organism that during its life cycle in which its growth. development, metabolism, etc is temporarily suspended nnnsuspended state, non-replicative state, resting state'-ID[O]:0000209: quality [state] of an organism that during its life cycle in which its growth. development, metabolism, etc is temporarily suspended nnnsuspended state, non-replicative state, resting state - id 'dormancy'-ID[O]:0000209 from IDO 2007. May have replacement - TBD - _obsolete_dormancy - true - - - - - - - - - _obsolete_quality of host - true - - - - - - - - - _obsolete_quality of pathogen - true - - - - - - - - - 'can change depending on environmentnnwhere should susceptibility factors go?'-ID[O]:0000212: can change depending on environmentnnwhere should susceptibility factors go? - id 'susceptibility'-ID[O]:0000212 from IDO 2007. May have replacement - TBD - _obsolete_susceptibility - true - - - - - - - - - _obsolete_resistance - true - - - - - - - - - _obsolete_refractoriness - true - - - - - - - - - _obsolete_quality of host population - true - - - - - - - - - _obsolete_herd immunity - true - - - - - - - - - _obsolete_quality of infectious disease - true - - - - - - - - - _obsolete_case of infectious disease - true - - - - - - - - - 'agent is incubated?ndisease is incubated?'-ID[O]:0000219: agent is incubated?ndisease is incubated? - id 'incubation period'-ID[O]:0000219 from IDO 2007. May have replacement - TBD - _obsolete_incubation period - true - - - - - - - - - _obsolete_infectivity period - true - - - - - - - - - 'the unfolding or course of infectious diseasennwhat do we say about infectious disease that always remain latent nwhat about when a pathogen continues its progression nnwe need to think about whether we need a term called stagenlife cycle?nprogression?ndevelopment?'-ID[O]:0000221: the unfolding or course of infectious diseasennwhat do we say about infectious disease that always remain latent nwhat about when a pathogen continues its progression nnwe need to think about whether we need a term called stagenlife cycle?nprogression?ndevelopment? - id 'infectious disease progression'-ID[O]:0000221 from IDO 2007. May have replacement - TBD - _obsolete_infectious disease progression - true - - - - - - - - - _obsolete_infectious disease course - true - - - - - - - - - _obsolete_host recovery period - true - - - - - - - - - _obsolete_intrinsic incubation period - true - - - - - - - - - _obsolete_extrinsic incubation period - true - - - - - - - - - 'is this just the part of the life cycle of the biotic entity that has role pathogen for the period of time while it has role pathogen?nncan include phases in the existence of the entity before it becomes a pathogen'-ID[O]:0000226: is this just the part of the life cycle of the biotic entity that has role pathogen for the period of time while it has role pathogen?nncan include phases in the existence of the entity before it becomes a pathogen - id 'pathogen life cycle'-ID[O]:0000226 from IDO 2007. May have replacement - TBD - _obsolete_pathogen life cycle - true - - - - - - - - - 'is a period a process?'-ID[O]:0000227: is a period a process? - id 'dormancy period'-ID[O]:0000227 from IDO 2007. May have replacement - TBD - _obsolete_dormancy period - true - - - - - - - - - _obsolete_pathogen outbreak - true - - - - - - - - - _obsolete_oral-fecal transmission - true - - - - - - - - - _obsolete_vertical transmission - true - - - - - - - - - _obsolete_horizontal transmission - true - - - - - - - - - _obsolete_pathogen life cycle stage - true - - - - - - - - - _obsolete_infectious disease progression stage - true - - - - - - - - - _obsolete_progression rate - true - - - - - - - - - _obsolete_rapid progression - true - - - - - - - - - _obsolete_long-term non-progression - true - - - - - - - - - _obsolete_highly exposed persistently seronegative - true - - - - - - - - - _obsolete_co-infected - true - - - - - - - - - 'is a quality relating to both bacteria and host'-ID[O]:0000306: is a quality relating to both bacteria and host - id 'fitness'-ID[O]:0000306 from IDO 2007. May have replacement - TBD - _obsolete_fitness - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an organism in symbiosis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in symbiosis. - symbiont role - - - - - - - - - - - - - - - - - - - - - - - - - A symbiont role borne by an organism in virtue of the fact that both symbionts derive a growth, survival, or fitness advantage from symbiosis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in processes that result in the growth, survival, or fitness advantage of either organism. - mutualist role - - - - - - - - - - - - - - - - - - - - - - - - - A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis, but the other symbiont is neither advantaged nor disadvantaged. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in processes that result in the commensal's growth, survival, or fitness advantage. - commensal role - - - - - - - - - A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen. - The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the other organism's growth, survival, or fitness reduction. - parasite role - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent role - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles. - pathogen role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disposition to become part of a disorder only in organisms whose defenses are compromised. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - opportunitistic pathogenic disposition - The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host. - This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin). - opportunistic infectious disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disposition to become part of a disorder in organisms that have intact defenses. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. - A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease." - primary infectious disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A host role borne by an organism in virtue of the fact that its extended organism contains a second organism and provides an environment supportive for the survival, growth, maturation, or reproduction of that organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The relevant environmental resources may include nutrient resources, warmth, or moisture. - The role is realized in processes in which the host makes the relevant environmental resources available to its partner in symbiosis. A bearer of a symbiont host role is bearer also of a symbiont role. - symbiont host role - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis reaches developmental maturity or reproduces sexually in the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - primary host role - The role is realized in developmental and reproduction processes of the host's partner in symbiosis. - definitive host role - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - secondary host role - The role is realized in developmental processes of the host's partner in symbiosis. - intermediate host role - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, but the host is not required for continuation of the partner's life cycle. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in developmental processes of the host's partner in symbiosis. - paratenic host role - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis has the infectious disposition but cannot be transmitted from the host to the partner's definitive host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - incidental host role - dead-end host role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis derives from the host a growth, survival, or fitness advantage while the host's growth, survival, or fitness is reduced. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The partner in symbiosis bears the parasite role. - The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the host's growth, survival, or fitness reduction. - parasite host role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role. - infectious agent host role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role. - pathogen host role - - - - - - - - - An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent carrier role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that an infectious agent is located in or on the entity and the entity has the capability to transfer (either actively or passively) the infectious agent from one location to another. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process that transfers an infectious organism from one location to another. - infectious agent transporter role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious agent transporter role that is borne by an organism active in the transfer of an infectious agent to an organism of another Species and in which the agent is infectious. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role. - infectious agent vector role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent does not multiply in or on the vector. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - mechanical vector of infectious agent role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in the vector. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - biological vector of infectious agent role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious agent transporter role borne by an entity in virtue of the fact that the entity is not a complete organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles. - infectious agent vehicle role - - - - - - - - - An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is living or contains living cells other than those that have the infectious disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Examples include blood, serum, tissue, or fresh produce. - biological vehicle of infectious agent role - - - - - - - - - An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - fomite role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that it is a habitat in which infectious agents can persist and multiply and from which they can be transmitted in virtue of prevailing practices of potential hosts. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - If the material entity bearing the reservoir role is an organism, then this organism also bears the host role. The organism may also bear the vector role. - The role is realized in a process that has as part life and multiplication processes of an infectious agent and a transmission process. - reservoir of infectious agent role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The virulence factor disposition is typically realized in processes that improve survival of the pathogen in a host, increase the likelihood of transmission to a host, or cause pathological processes in a host. - virulence factor disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - toxin disposition - - - - - - - - - A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in a direct enzymatic process that damages host cells or extracellular matrix. - exotoxin disposition - - - - - - - - - - An exotoxin disposition to damage cells of the host intestinal mucosa. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_enterotoxin disposition - enterotoxin disposition - true - - - - - - - - - - A toxin disposition that inheres in a protein or protein complex that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. - A toxin disposition that inheres in a protein or protein complex that is released from a pathogen only upon cytolysis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_endotoxin disposition - endotoxin disposition - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent enters a host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process by which an infectious agent enters a host. - infectious agent portal of entry role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent exits a host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process by which an infectious agent exists a host. - infectious agent portal of exit role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to a non-living entity. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in the killing and/or growth inhibition of microorganisms on the non-living entity. - disinfectant role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to an anatomical entity of a living organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in the killing and/or growth inhibition of microorganisms on the anatomical entity. - antiseptic role - - - - - - - - - - - - - - - - - - A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had no infectious disorder, and (3) the infectious disorder increases the host's susceptibility to infectious disorders. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process by which the infectious disorder is established in the host. - primary infection role - - - - - - - - - - - - - - - - - A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had a primary infectious disorder, and (3) establishment of the infectious disorder occurs because of increased susceptibility to infectious disorders conferred by the primary infectious disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process by which the infectious disorder is established in the host. - secondary infection role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disease whose physical basis is an infectious disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - tranmissible disease - The disposition is realized in an infectious disease course. - infectious disease - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition borne by a biological macromolecule that is the disposition to participate in adherence to a host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in an adherence to host process. - adhesion disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition borne by a biological macromolecule that is the disposition to facilitate breach of host epithelial barriers or entry into and survival in host cells. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A molecule with the invasion disposition is referred to as an invasion factor or invasin. - invasion disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the development or reproduction of microorganisms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Some instances might be functions, depending on whether the bearer is something that exists and is used for the purpose (alcohol) or something that was designed for the purpose (pine sol). Entities that kill microorganisms are referred to as microbicidal; entities that inhibit the growth of microorganisms are referred to as microbistatic. - The disposition is realized in the killing or inhibition of microorganisms. - antimicrobial disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the lifecycle of viruses. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antiviral disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the development or reproduction of fungal organisms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antifungal disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the reproduction of bacteria. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antibiotic disposition - antibacterial disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the development or reproduction of eukaryotic parasites. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - In the term name, we are using parasite in the medical sense of eukaryotic organisms that are parasitic in humans. - antiparasitic disposition - - - - - - - - - - - - - - - - - - - - - - - - A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Examples include the following: CCR5 mutations protect T cells from HIV invasion. A tumor cell's resistance to chemotherapy protects the cell from damage by the drug (although this harms the patient). An insect's resistance to insecticide protects it from the insecticide. - The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant. - protective resistance - - - - - - - - - - A protective resistance that mitigates the damaging effects of a drug. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - drug resistance - resistance to drug - - - - - - - - - - - - - - - A protective resistance that inheres in an organism and mitigates the damaging effects on that organism of an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - resistance to infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A collective resistance disposition that inheres in an organism population in virtue of the fact that the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from hosts in the population to susceptible individuals in the population and thereby mitigating the damaging effects of the infectious agent on the population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - herd immunity to infectious organism - - - - - - - - - A resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - protective immunity to infectious agent - We don't specify that immunity results from prior exposure, because we want to include innate immunity. In addition, for adaptive immunity, there could be some low level immunity even in a primary immune response. - immunity to infectious agent - - - - - - - - - An immunity to infectious agent that results in elimination of the infectious agent from the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Sterilizing immunity is typically conferred by neutralizing antibodies. - sterilizing immunity to infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to initiate processes that result in a disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pathogenicity - A pathogenic disposition is realized in processes that create a disorder. - The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition. - pathogenic disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - invasive disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder. - infectious disposition - - - - - - - - - An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis. - zoonotic disposition - - - - - - - - - An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. - reverse zoonotic disposition - - - - - - - - - - - - - - - - - - - - - A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - "... in virtue of the individual dispositions of the contstituents" is intended to capture the fact that the collective disposition results from the combination of the individual dispositions. It is not necessary that every constituent of the aggregate have a relevant individual disposition. - The disposition is realized in a process that has as part realizations of some of the individual dispositions. - collective disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism that is experiencing pregnancy-induced or pathologic immunosuppression. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunosuppressed organism - - - - - - - - - - - - - - - - - - - - - An organism that has immunocompetence. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunocompetent organism - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition that inheres in a host of infectious agent and is a disposition to transmit infectious agents to organisms of the same Species through casual contact with a high likelihood of realization. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Highly contagious infections, those with a relatively high likelihood of spread, are referred to as contagious and are those for which spread is likely as a result of day-to-day activities of the host. - The disposition is realized in a horizontal transmission process. - contagiousness - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism that contains a colony in or on its extended organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colonized host - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism that has an infection in or on its extended organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infected organism - - - - - - - - - An organism that has two infections with distinct Species of infectious agents. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - co-infected organism - - - - - - - - - A host exhibiting disease symptoms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_symptomatic host - true - - - - - - - - - - - - - - - A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. - infectious agent transmissibility - - - - - - - - - - - - - - - A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - This quality is measured by the proportion of exposed who become infected. - infectivity - - - - - - - - - - - - - - - A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - This quality is measured by the proportion of clinically apparent cases that are severe or fatal. - virulence - - - - - - - - - - - - - - - A quality that inheres in an entity and is the degree to which it can be harmed by another entity. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. - susceptibility - - - - - - - - - - - - - - - - A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - susceptibility to infectious agent - - - - - - - - - A susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - drug susceptibility - - - - - - - - - - - - - - - A drug susceptibility that inheres in an infectious agent and is the degree to which the infectious agent can be harmed or inhibited from surviving by a drug. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - drug susceptibility of infectious agent - - - - - - - - - An infection comprised of infectious organisms from different Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - mixed infection - polymicrobial infection - complex infection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infection for which the infectious agents that are part of the infection persist in the extracellular space of the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - extracellular infection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infection for which the infectious agents that are part of the infection persist inside host cells. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - intracellular infection - - - - - - - - - - An infection for which the infectious agents that are part of the infection are distributed throughout the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - systemic infection - - - - - - - - - - An infection for which the infectious agents that are part of the infection are limited to a relatively small area of the host's body. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - local infection - - - - - - - - - A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - focal infection - - - - - - - - - An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - acute infectious disease course - - - - - - - - - A quality that inheres in an infection in virtue of the fact that the infection persists for an extended period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - persistent infection - _obsolete_chronic quality of infection - true - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. - infectious disease incidence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. - infection incidence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - cumulative incidence of infectious disease - An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured. - infectious disease incidence proportion - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - cumulative incidence of infection - An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured. - infection incidence proportion - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured. - infectious disease incidence rate - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the infection incidence proportion per unit time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured. - infection incidence rate - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. - infectious disease prevalence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. - infection prevalence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. - infectious disease lifetime prevalence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics. - infectious agent seroprevalence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year. - infectious disease mortality rate - - - - - - - - - - - - - - - A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic. - infectious disease endemicity - - - - - - - - - An infectious disease prevalence that is typical for an infectious disease in an organism population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Infectious disease endemic level is relational to previous prevalences of the disease. - infectious disease endemic level - - - - - - - - - An infectious disease incidence rate that is typical for an infectious disease in an organism population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Infectious disease endemic rate is relational to previous infectious disease incidence rates of the disease. - infectious disease endemic rate - - - - - - - - - An infectious disease endemicity that inheres in an organism population in virtue of the fact that the infectious disease endemic level for an infectious disease is persistently high in the population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Hyper-endemic infectious diseases may have high endemic levels only in certain seasons. A hyper-endemic disease affects all age groups equally. - infectious disease hyper-endemicity - - - - - - - - - - - - - - - A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Sporadic quality of infectious disease is relational to previous prevalence of the disease. - infectious disease sporadicity - - - - - - - - - - - - - - - - - - - - A disease course that is the realization of an infectious disease. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious disease course - - - - - - - - - A chronic infectious disease course that does not progress to severe stages for a long period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - long-term non-progressing infectious disease course - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process by which an organism acquires immunity to an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunization against infectious agent - - - - - - - - - An immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - inoculation - active immunization against infectious agent - - - - - - - - - An active immunization that begins with exposure of an organism to a vaccine. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - vaccination against infectious agent - - - - - - - - - An active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - variolation - - - - - - - - - An immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent. - Examples include the injection of antibodies and the transfer of maternal antibodies to the fetus. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - passive immunization against infectious agent - - - - - - - - - A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. - For a particular instance of infectious disease epidemic, signficance is determined based on the infectious disease incidence that is typical for an infectious disease for the particular population and time period. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious disease outbreak - infectious disease epidemic - - - - - - - - - A process in which multiple infectious disease epidemics of the same type of infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious disease pandemic - - - - - - - - - - - - - - - - - - - An infection that is clinically abnormal. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious disorder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infection that has as part virus particles located in the blood. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - viremia - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infection that has as part bacteria located in the blood. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - bacteremia - - - - - - - - - A bacteremia in which the baceteria are replicating. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_septicemia - true - - - - - - - - - A virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - virion - - - - - - - - - An aggregate of organisms of the same Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. - organism population - - - - - - - - - - - - - - - - - - - - - - - An organism population whose members have an infection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infected population - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism population in whose members an infectious disease is being realized. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - diseased population - - - - - - - - - - - - - - - - - - - - - - - An organism population whose members each have an infectious disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent population - - - - - - - - - An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - at-risk population - susceptible population - - - - - - - - - An organism population whose members are participating in non-parasitic symbiosis with a particular host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - normal resident microflora population - normal resident microbiota population - - - - - - - - - An infectious organism population with a certain configuration quality (OGMS:0000039) (distributed across a spatial region (e.g., anatomical location in a host) in a particular way). Put e.g. In comments - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_configured infectious organism population - true - - - - - - - - - A continuous temporal interval beginning with the extablishment of an infectious agent colony and ending with the onset of symptoms (or infectious disease course?). - Albert Goldfain - Alexander Diehl - Lindsay Cowell - incubation period - - - - - - - - - A continuous temporal interval during which an infectious agent host bears a contagiousness disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - communicability period - - - - - - - - - - - - - - - - - - - - An organism bearing a symbiont role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - symbiont - - - - - - - - - - - - - - - An organism that can only reach developmental maturity, replicate, or persist in symbiosis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - obligatory symbiont - - - - - - - - - - - - - - - - - - - - An organism bearing a mutualist role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - mutualist - - - - - - - - - - - - - - - - - - - - An organism bearing a commensal role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - commensal - - - - - - - - - - - - - - - - - - - - A organism bearing a parasite role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - parasite - - - - - - - - - An infectious agent that is an organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_infectious organism - true - - - - - - - - - - - - - - - - - - - - - - - - A material entity with a pathogenic disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pathogen - - - - - - - - - - - - - - - - - - - - An infectious agent with a primary infectious disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - principal pathogen - primary pathogen - - - - - - - - - - - - - - - - - - - - An organism bearing a host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - host - - - - - - - - - - - - - - - - - - - - An organism bearing a definitive host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - primary host - definitive host - - - - - - - - - - - - - - - - - - - - A organism bearing an intermediate host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - secondary host - intermediate host - - - - - - - - - - - - - - - - - - - - An organism bearing a paratenic host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - paratenic host - - - - - - - - - - - - - - - - - - - - An organism bearing a dead-end host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - incidental host - dead-end host - - - - - - - - - - - - - - - - - - - - An organism bearing a parasite host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - parasite host - - - - - - - - - - - - - - - - - - - - An organism bearing an infectious agent host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent host - - - - - - - - - - - - - - - - - - - - An organism bearing a pathogen host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pathogen host - - - - - - - - - - - - - - - - - - - - An organism bearing the infectious agent carrier role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent carrier - - - - - - - - - - - - - - - - - - - - An organism bearing an infectious agent vector role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent vector - - - - - - - - - - - - - - - - - - - - An infectious agent vector bearing a mechanical vector of infectious agent role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - mechanical vector of infectious agent - - - - - - - - - - - - - - - - - - - - An infectious agent vector bearing a biological vector of infectious agent role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - biological vector of infectious agent - - - - - - - - - - - - - - - - - - - - - A material entity bearing an infectious agent vehicle role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - vehicle of infectious agent - - - - - - - - - - - - - - - - - - - - - - A material entity bearing a fomite role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - fomite - - - - - - - - - - - - - - - - - - - - - A material entity bearing an infectious agent reservoir role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent reservoir - - - - - - - - - A material entity bearing an end reservoir of infectious agent role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - dead-end reservoir of infectious agent - _obsolete_end reservoir of infectious agent - true - - - - - - - - - - - - - - - - - - - - A biological macromolecule produced by a pathogen and that has a virulence factor disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - virulence factor - - - - - - - - - - - - - - - - - - - - A biological macromolecule that has an invasion disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - invasin - invasion factor - - - - - - - - - - - - - - - - - - - - A molecular entity that has a toxin disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - toxin - - - - - - - - - - - - - - - - - - - - A molecular entity bearing an exotoxin disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - exotoxin - - - - - - - - - - - - - - - A molecular entity with an exotoxin disposition, the realization of which damages cells of the host intestinal mucosa. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - enterotoxin - - - - - - - - - - - - - - - A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - endotoxin - - - - - - - - - - - - - - - - - - - - An anatomical entity bearing an infectious agent portal of entry role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent portal of entry - - - - - - - - - - - - - - - - - - - - An anatomical entity bearing an infectious agent portal of exit role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent portal of exit - - - - - - - - - - - - - - - - - - - - - - - A material entity bearing a disinfectant role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - disinfectant - - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antiseptic role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antiseptic - - - - - - - - - - - - - - - - - - - - A biological macromolecule that has an adhesion disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - adhesin - adhesion molecule - adhesion factor - - - - - - - - - - - - - - - - - - - - - - A material entity with an antimicrobial disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antimicrobial - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antiviral disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antiviral - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antifungal disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antifungal - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antiparasitic disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antiparasitic - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antibacterial disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antibiotic - antibacterial - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity with an antimicrobial disposition that is realized in a process of killing microorganisms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - microbicidal [entity] - microbicide - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity with an antiviral disposition that is realized in a process of killing viruses. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - viricide - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity with an antimicrobial disposition that is realized in a process of inhibiting the growth of microorganisms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - microbistatic - - - - - - - - - - - - - - - - - - - - - An infection bearing the primary infection role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - primary infection - - - - - - - - - - - - - - - - - - - - An infection bearing the secondary infection role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - secondary infection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a zoonotic disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - zoonosis - - - - - - - - - - - - - - - An organism that is host to an infectious agent and has no symptoms of the infectious disease associated with the infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - asymptomatic host of infectious agent - - - - - - - - - An infection that is part of an asymptomatic host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - subclinical infection - - - - - - - - - - - - - - - - - - - - - A material entity that has a resistance disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - resistant entity - - - - - - - - - - - - - - - - - - - - An organism who has been bearer of the infectious agent carrier role for an extended period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - chronic carrier of infectious agent - - - - - - - - - - - - - - - An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent - Albert Goldfain - Alexander Diehl - Lindsay Cowell - symptomatic host of infectious agent - - - - - - - - - synonym of invasion factor - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_invasin - true - - - - - - - - - - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_viral latency - true - - - - - - - - - - - - - - - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in an innate immune response. - innate immunity to infectious agent - - - - - - - - - An immunity to infectious agent realized in an adaptive immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_adaptive immunity to infectious agent - true - - - - - - - - - - - - - - - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of components of its circulating body fluid. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - "Circulating body fluid" refers to blood, lymph, and hemolymph. - The disposition is realized in a humoral immune response. - humoral immunity to infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of its leukocytes. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - cell-mediated immunity to infectious agent - The disposition is realized in a leukocyte-mediated immune response. - leukocyte-mediated immunity to infectious agent - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of antibodies not produced by that organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Passive immunity results from a passive immunization. - The disposition is realized in a neutralizing process carried out by the antibodies. - The protective antibodies are typically introduced by injection, breast feeding, or by passing from the placenta to the fetus. - passive immunity to infectious agent - - - - - - - - - A resistance to drug that mitigates the damaging effects of an antibiotic. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antibiotic resistance - - - - - - - - - - - - - - - - - - - - - - - - An organism experiencing a long-term non-progressing infectious disease course. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - long-term non-progressor - - - - - - - - - An infectious agent whose infection incidence is increasing following its first introduction into a new host Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - emerging pathogen - - - - - - - - - - - - - - - A molecular entity with a toxin disposition, the realization of which damages host cells. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - cytotoxin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A collective disposition to initiate processes that result in a disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in processes that create a disorder. - collective pathogenic disposition - - - - - - - - - - - - - - - - - - - - - - - - A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection. - infection - - - - - - - - - A resistance to infectious agent that inheres in an organism in virtue of a specific allele or combination of alleles in its genome. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The resistance of individuals to HIV invasion oonferred by particular CCR5 alleles is an example. Resistance against malaria conferred by the sickle cell gene is another. - genetic resistance to infectious agent - - - - - - - - - A collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - collective resistance disposition - - - - - - - - - - - - - - - - - - - - An organism that has an immunodeficiency. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunocompromised organism - immunodeficient organism - - - - - - - - - An infectious disease course that unfolds over a long period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - persistent infectious disease course - chronic infectious disease course - - - - - - - - - An infectious disposition to be transmitted directly from one human host to another. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_communicable disposition - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism population whose members have acquired immunity to an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immune population - - - - - - - - - A continuous temporal interval during which a transmission process occurs. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - transmission period - - - - - - - - - A process in which a potential host of an infectious agent comes into direct physical contact with the infectious agent. - Bjoern Peters - direct host exposure to infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism that has the capability to bear a host of infectious agent role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - potential host of infectious agent - - - - - - - - - - - - - - - - - - - - - An organism that has an infectious disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent - - - - - - - - - A process in which a potential host of an infectious agent is exposed to an environment in which the infectious agent is present and physical contact between the two can occur, but such contact is not planned. - Bjoern Peters - host exposure to environment containing infectious agent - - - - - - - - - A host exposure to environment with infectious agent where the environment is a household that also has an infected host - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - host living with infected household contact - - - - - - - - - A host exposure to environment with infectious agent where the environment is an area in which an infectious agent is endemic - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - host living in endemic area - - - - - - - - - A host exposure to environment with infectious agent where the exposure is accidental; the environment is a laboratory, and the infectious agent is infectious in humans. - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - release of infectious human pathogen in laboratory - - - - - - - - - A host exposure to environment with infectious agent where the environment contains an infectious agent vector. - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - host coming into contact with vector of infectious agent - - - - - - - - - A host exposure to environment with infectious agent where the environment contains a material entity that has been assessed to confer a risk of infection. - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - host exposure to substance that might have infectious agent - - - - - - - - - A process by which an infectious agent, established in a host, becomes part of an infection in the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - process of establishing an infection - - - - - - - - - - - - - - - - - - - - An establishment of localization in host process in which an organism establishes itself in a host. - Establishment of one organism in the extended organism of another (the host) involves at least one of (1) movement of the organism to a location within the host in which the organism can persist, or (2) adherence or attachment of the organism to part of the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colonization of host - - - - - - - - - A biological object or group of biological objects in close spatial proximity. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_biological object colony - true - - - - - - - - - A colonization of host process that results in a clinically abnormal colony. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - establishment of a clinically abnormal colony - - - - - - - - - A process in which an entity comes into being as a result of the process. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - production - - - - - - - - - A production process in which a participant creates a copy of itself. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - replication - - - - - - - - - A colonization of human process in which the colonized site is the anterior nares. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colonization of human anterior nares - - - - - - - - - - - - - - - - - - - - A process that attenuates an immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunosuppression - - - - - - - - - An immunosuppression which unfolds as part of the natural self-regulation of an immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - physiologic immunosuppression - - - - - - - - - An immunosuppression process which arises as the result of a disorder. - Disorders that result in immunosuppression include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pathologic immunosuppression - - - - - - - - - primitive - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_biological object - true - - - - - - - - - A biological material entity that is capable of replication. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_replicating biological material entity - true - - - - - - - - - An organism population persisting in a site it has colonized. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colony - - - - - - - - - - - - - - - - - - - - - - - - A colony whose members are infectious agents. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent colony - - - - - - - - - - A disorder of an immune system component that results in defective functioning of the immune system. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunodeficiency - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition that is the ability to mount a normal immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response. - immunocompetence - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition whose realization negatively regulates an immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunosuppressive disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of antigen receptors encoded by somatically diversified genes in the organism's genome and expressed by cells that have undergone selection during a primary immune response in that organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - adaptive immunity to infectious agent - immune memory - The disposition is realized in an immune response in which such antigen receptors participate. - acquired immunity to infectious agent - - - - - - - - - - - A disposition to colonize an organism and participate in mutualism or commensalism with that organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - disposition to form a non-parasitic colony - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in a direct, horizontal transmission process between members of the same Species. - communicability - - - - - - - - - A generically dependent continuant that is the set of organism types whose instances have as one of their canonical dispositions, the disposition to bear the host role for a colony of a certain type. - A quality that inheres in an infection and is the likelihood that infectious agents part of the infection will spread to other hosts. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_contagiousness quality - _obsolete_host range - true - - - - - - - - - - - - - - - An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature. - Requested addition of this term to the GO. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA. - establishment of localization in host - - - - - - - - - - - - - - - A process by which a disorder comes into existence. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - appearance of disorder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disorder that is the physical basis for an unfolding acute infectious disease course. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - acute infection - - - - - - - - - An infection that persists for an extended period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - persistent infection - chronic infection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - host role - - - - - - - - - - An infection resulting from a transmission process that unfolds in a hospital. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - nosocomial infection - hospital-acquired infection - - - - - - - - - - An infection resulting from a transmission process that did not unfold in a health care facility. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - community-acquired infection - - - - - - - - - - - - - - - A molecular entity with a toxin disposition, the realization of which damages or interferes with the function of nerve tissue. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - neurotoxin - - - - - - - - - An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - metatstatic infection - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process that has as part a transmission process and a process by which the infectious agent or one of its offspring becomes part of a disorder in the host. - source of infection role - - - - - - - - - A process that is a systemic inflammatory response to infection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - sepsis - - - - - - - - - A sepsis that results in organ dysfunction, hypotension, or hypofusion of at least one organ. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - severe sepsis - - - - - - - - - An infection resulting from a transmission process that unfolds in a nursing home. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - nursing-home acquired infection - - - - - - - - - An infectious agent with a capability to infect human hosts. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious human pathogen - - - - - - - - - - An immunodeficiency that is not caused by a genetic predisposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy). - acquired immunodeficiency - - - - - - - - - An infection comprised of infectious organisms all of the same Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - simple infection - - - - - - - - - An infectious agent whose infection incidence is increasing in a host population as a result of changes in the biology of the host or pathogen, or changes in their interactions. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - re-emerging pathogen - - - - - - - - - An immunosuppression induced by progesterone and other factors upregulated in pregnant women. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pregnancy-induced immunosuppression - - - - - - - - - An infection that has as part organisms of the Genus Candida. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - candidiasis - - - - - - - - - An infection that has as part organisms of the Species Trichomonas vaginalis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - trichomoniasis - - - - - - - - - An infection that has as part organisms of the Genus Leptospira. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - leptospirosis - - - - - - - - - An infection located in the bowel and that has as part organisms of the Genus Shigella. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Shigellosis - - - - - - - - - An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica - Albert Goldfain - Alexander Diehl - Lindsay Cowell - amebiasis - - - - - - - - - A colonization of host process in which the host is of Species Homo sapiens. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colonization of human - - - - - - - - - An immunodeficiency that exists in an organism because of a genetic predisposition. - Albert Goldfain - Alex Diehl - Lindsay Cowell - congenital immunodeficiency - primary immunodeficiency - - - - - - - - - A colonization of human process in which the colonized site is a perineum. - Albert Goldfain - Alex Diehl - Lindsay Cowell - colonization of human perineum - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a reverse zoonotic disposition. - Albert Goldfain - Alex Diehl - Lindsay Cowell - reverse zoonosis - - - - - - - - - - - - - - - - - - - - An infectious agent with an opportunistic infectious disposition. - Albert Goldfain - Alex Diehl - Lindsay Cowell - opportunist - opportunistic pathogen - - - - - - - - - - - - - - - - - - - - - - - - A disposition to undergo a transmission process. - Albert Goldfain - Alex Diehl - Lindsay Cowell - The disposition is realized in a transmission process. - transmissibility disposition - - - - - - - - - A pathogen transmission process in which a pathogen is transmitted from one host to another of the same Species, and the two hosts are not in a parent-child relationship. - Lindsay Cowell - horizontal pathogen transmission process - - - - - - - - - A process that results in death. - Alex Diehl - Lindsay Cowell - process that results in death - - - - - - - - - A process in which a potential host of an infectious agent is exposed to an infectious agent. - Bjoern Peters - host exposure to infectious agent - - - - - - - - - An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent. - Alex Diehl - Lindsay Cowell - susceptible organism - - - - - - - - - A process which is necessary for the survival of an organism. - Alex Diehl - Lindsay Cowell - life-sustaining process - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process. - Alex Diehl - Lindsay Cowell - negative regulation of life-sustaining process - - - - - - - - - - - - - - - - - - - - A material entity bearing a source of infection role. - Albert Goldfain - Alex Diehl - Lindsay Cowell - source of infection - - - - - - - - - A disposition to initiate processes that result in a disorder in a human organism. - human pathogenicity disposition - - - - - - - - - A disposition to participate in a process of symbiosis in which the bearer derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. - parasitic disposition - - - - - - - - - A process by which a part of an organism or something contained in an organism becomes clinically abnormal. - transition to clinical abnormality - - - - - - - - - A pathologic immunosuppression process which arises as the result of an infection and is initiated or dysregulated by the infectious agent population. - The definition should perhaps read "as the result of an infectious disorder". - Alex Diehl - Lindsay Cowell - infection-based immunosuppression - - - - - - - - - An infection-based immunosuppression process which arises as the result of an HIV infection. - Alex Diehl - Lindsay Cowell - HIV-based immunosuppression - - - - - - - - - - - - - - - - - - - - An immunosuppressed organism that is experiencing pathologic immunosuppression. - Alex Diehl - Lindsay Cowell - pathologically immunosuppressed organism - - - - - - - - - - - - - - - - - - - - A pathologically immunosuppressed organism that is experiencing infection-based immunosuppression. - Alex Diehl - Lindsay Cowell - immunosuppressed organism experiencing infection-based immunosuppression - - - - - - - - - A pathologically immunosuppressed organism that is experiencing HIV-based immunosuppression. - These individuals may also be immunodeficient due to depletion of CD4+ T cells and other effects of HIV. - Alex Diehl - Lindsay Cowell - immunosuppressed organism experiencing HIV-based immunosuppression - - - - - - - - - An immunosuppressed organism that is a human experiencing HIV-based immunosuppression. - Alex Diehl - Lindsay Cowell - NCI BBRB - immunosuppressed human experiencing HIV-based immunosuppression - - - - - - - - - A pathologic immunosuppression process which arises as the result of treatment with a drug that attenuates immune responses. - Alex Diehl - Lindsay Cowell - drug-based immunosuppression - - - - - - - - - A drug-based immunosuppression process that results from chronic systemic steroid use. - Alex Diehl - Lindsay Cowell - chronic systemic steroid use-based immunosuppression - - - - - - - - - - - - - - - - - - - - A pathologically immunosuppressed organism that is experiencing drug-based immunosuppression. - Alex Diehl - Lindsay Cowell - immunosuppressed organism experiencing drug-based immunosuppression - - - - - - - - - a pathologically immunosuppressed organism that is experiencing chronic systemic steroid use-based immunosuppression. - Alex Diehl - Lindsay Cowell - immunosuppressed organism experiencing chronic systemic steroid use-based immunosuppression - - - - - - - - - An immunosuppressed organism that is a human experiencing chronic systemic steroid use-based immunosuppression. - Alex Diehl - Lindsay Cowell - NCI BBRB - immunosuppressed human experiencing chronic systemic steroid use-based immunosuppression - - - - - - - - - A pathologically immunosuppressed organism that is a human experiencing drug-based immunosuppression. - Alex Diehl - Lindsay Cowell - NCI BBRB - immunosuppressed human experiencing drug-based immunosuppression due to organ transplant - - - - - - - - - - Viruses - Viruses - - - - - - - - - - Bacteria - - - - - - - - - - Archaea - - - - - - - - - - Eukaryota - - - - - - - - - - Homo sapiens - - - - - - - - - - - - - - - - - - - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - - organism - - - - - - - - - A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease. - - symptom - - - - - - - - - A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. - - disease - - - - - - - - - A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. - - disorder - - - - - - - - - The totality of all processes through which a given disease instance is realized. - - disease course - - - - - - - - - An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. - - extended organism - - - - - - - - - A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. - Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species. - Suggested label: pathogen transmission process - - Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl - transmission process - transmission process - - - - - - - - - Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles. - Suggested label: indirect pathogen transmission process - - indirect - - - - - - - - - A fluid that is composed of blood plasma and erythrocytes. - - blood - - - - - - - - - A life cycle temporal boundary that marks the end of the life cycle of the organism. - - life-death temporal boundary - - - - - - - - - - - - - - - - - - - - - - - - - Obsolete Class - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - example to be eventually removed - - - - - - - - - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - core - - - - - - - - - placeholder removed - - - - - - - - - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - -## Elucidation - -This is used when the statement/axiom is assumed to hold true 'eternally' - -## How to interpret (informal) - -First the "atemporal" FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. - -## Example - - Class: nucleus - SubClassOf: part_of some cell - - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) - -## Notes - -This interpretation is *not* the same as an at-all-times relation - - - axiom holds for all times - - - - - - - - - -## Elucidation - -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. - -## Example: - - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm - - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - - - - relation has no temporal argument - - - - - - - - Person:Alan Ruttenberg - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - - - - - - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/tmp/merged-ogms-edit.ofn b/src/ontology/tmp/merged-ogms-edit.ofn index 77c2479..eeb2b62 100644 --- a/src/ontology/tmp/merged-ogms-edit.ofn +++ b/src/ontology/tmp/merged-ogms-edit.ofn @@ -1,47 +1,1173 @@ Prefix(:=) -Prefix(dce:=) +Prefix(dc:=) +Prefix(obo:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) +Prefix(foaf:=) +Prefix(rdf1:=) Prefix(rdfs:=) -Prefix(dcterms:=) +Prefix(terms:=) +Prefix(protege:=) +Prefix(oboInOwl:=) Ontology( -Annotation(dcterms:description "None") -Annotation(dcterms:license ) -Annotation(dcterms:title "The Ontology for General Medical Science") - -Declaration(Class()) -Declaration(AnnotationProperty(dcterms:description)) -Declaration(AnnotationProperty(dcterms:license)) -Declaration(AnnotationProperty(dcterms:title)) +Annotation(dc:contributor "Matthew Diller"@en) +Annotation(dc:creator "Alan Ruttenberg") +Annotation(dc:creator "Albert Goldfain") +Annotation(dc:creator "Anand Kumar") +Annotation(dc:creator "Barry Smith") +Annotation(dc:creator "Bill Hogan") +Annotation(dc:creator "Brian Aevermann") +Annotation(dc:creator "Cornelius Rosse") +Annotation(dc:creator "Daniel Merico") +Annotation(dc:creator "Jie Zheng") +Annotation(dc:creator "Lindsay Cowell") +Annotation(dc:creator "Richard Scheuermann") +Annotation(dc:creator "Sivaram Arabandi") +Annotation(dc:creator "Werner Ceusters") +Annotation(dc:date "2009-08-07") +Annotation(dc:description "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. + +OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."@en) +Annotation(dc:title "Ontology for General Medical Science") +Annotation(terms:license "http://creativecommons.org/licenses/by/4.0/") +Annotation(rdfs:comment "The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. + +The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl + +The OGMS developer site is https://github.com/OGMS/ogms + +If you are interested in participating in the development of OGMS, please send email to matthew.diller@nih.gov"@en) + +Declaration(Class(obo:BFO_0000001)) +Declaration(Class(obo:BFO_0000015)) +Declaration(Class(obo:BFO_0000016)) +Declaration(Class(obo:BFO_0000019)) +Declaration(Class(obo:BFO_0000023)) +Declaration(Class(obo:BFO_0000031)) +Declaration(Class(obo:BFO_0000040)) +Declaration(Class(obo:COB_0000035)) +Declaration(Class(obo:IAO_0000027)) +Declaration(Class(obo:IAO_0000030)) +Declaration(Class(obo:OBI_0000278)) +Declaration(Class(obo:OGMS_0000014)) +Declaration(Class(obo:OGMS_0000015)) +Declaration(Class(obo:OGMS_0000016)) +Declaration(Class(obo:OGMS_0000017)) +Declaration(Class(obo:OGMS_0000018)) +Declaration(Class(obo:OGMS_0000019)) +Declaration(Class(obo:OGMS_0000020)) +Declaration(Class(obo:OGMS_0000022)) +Declaration(Class(obo:OGMS_0000023)) +Declaration(Class(obo:OGMS_0000024)) +Declaration(Class(obo:OGMS_0000025)) +Declaration(Class(obo:OGMS_0000026)) +Declaration(Class(obo:OGMS_0000027)) +Declaration(Class(obo:OGMS_0000028)) +Declaration(Class(obo:OGMS_0000029)) +Declaration(Class(obo:OGMS_0000030)) +Declaration(Class(obo:OGMS_0000031)) +Declaration(Class(obo:OGMS_0000032)) +Declaration(Class(obo:OGMS_0000033)) +Declaration(Class(obo:OGMS_0000034)) +Declaration(Class(obo:OGMS_0000035)) +Declaration(Class(obo:OGMS_0000037)) +Declaration(Class(obo:OGMS_0000038)) +Declaration(Class(obo:OGMS_0000039)) +Declaration(Class(obo:OGMS_0000040)) +Declaration(Class(obo:OGMS_0000045)) +Declaration(Class(obo:OGMS_0000046)) +Declaration(Class(obo:OGMS_0000047)) +Declaration(Class(obo:OGMS_0000050)) +Declaration(Class(obo:OGMS_0000051)) +Declaration(Class(obo:OGMS_0000055)) +Declaration(Class(obo:OGMS_0000056)) +Declaration(Class(obo:OGMS_0000057)) +Declaration(Class(obo:OGMS_0000059)) +Declaration(Class(obo:OGMS_0000060)) +Declaration(Class(obo:OGMS_0000061)) +Declaration(Class(obo:OGMS_0000063)) +Declaration(Class(obo:OGMS_0000064)) +Declaration(Class(obo:OGMS_0000065)) +Declaration(Class(obo:OGMS_0000066)) +Declaration(Class(obo:OGMS_0000067)) +Declaration(Class(obo:OGMS_0000069)) +Declaration(Class(obo:OGMS_0000070)) +Declaration(Class(obo:OGMS_0000071)) +Declaration(Class(obo:OGMS_0000073)) +Declaration(Class(obo:OGMS_0000074)) +Declaration(Class(obo:OGMS_0000077)) +Declaration(Class(obo:OGMS_0000078)) +Declaration(Class(obo:OGMS_0000079)) +Declaration(Class(obo:OGMS_0000080)) +Declaration(Class(obo:OGMS_0000081)) +Declaration(Class(obo:OGMS_0000082)) +Declaration(Class(obo:OGMS_0000083)) +Declaration(Class(obo:OGMS_0000084)) +Declaration(Class(obo:OGMS_0000085)) +Declaration(Class(obo:OGMS_0000086)) +Declaration(Class(obo:OGMS_0000087)) +Declaration(Class(obo:OGMS_0000088)) +Declaration(Class(obo:OGMS_0000089)) +Declaration(Class(obo:OGMS_0000090)) +Declaration(Class(obo:OGMS_0000091)) +Declaration(Class(obo:OGMS_0000092)) +Declaration(Class(obo:OGMS_0000093)) +Declaration(Class(obo:OGMS_0000094)) +Declaration(Class(obo:OGMS_0000095)) +Declaration(Class(obo:OGMS_0000096)) +Declaration(Class(obo:OGMS_0000097)) +Declaration(Class(obo:OGMS_0000098)) +Declaration(Class(obo:OGMS_0000099)) +Declaration(Class(obo:OGMS_0000100)) +Declaration(Class(obo:OGMS_0000101)) +Declaration(Class(obo:OGMS_0000102)) +Declaration(Class(obo:OGMS_0000103)) +Declaration(Class(obo:OGMS_0000104)) +Declaration(Class(obo:OGMS_0000105)) +Declaration(Class(obo:OGMS_0000106)) +Declaration(Class(obo:OGMS_0000107)) +Declaration(Class(obo:OGMS_0000108)) +Declaration(Class(obo:OGMS_0000109)) +Declaration(Class(obo:OGMS_0000110)) +Declaration(Class(obo:OGMS_0000111)) +Declaration(Class(obo:OGMS_0000112)) +Declaration(Class(obo:OGMS_0000113)) +Declaration(Class(obo:OGMS_0000114)) +Declaration(Class(obo:OGMS_0000115)) +Declaration(Class(obo:OGMS_0000116)) +Declaration(Class(obo:OGMS_0000117)) +Declaration(Class(obo:OGMS_0000118)) +Declaration(Class(obo:OGMS_0000119)) +Declaration(Class(obo:OGMS_0000120)) +Declaration(Class(obo:OGMS_0000121)) +Declaration(Class(obo:OGMS_0000122)) +Declaration(Class(obo:OGMS_0000123)) +Declaration(Class(obo:OGMS_0000124)) +Declaration(Class(obo:OGMS_0000125)) +Declaration(Class(obo:OGMS_0000126)) +Declaration(Class(obo:OGMS_0000127)) +Declaration(Class(obo:OGMS_0000128)) +Declaration(Class(obo:OGMS_0000129)) +Declaration(Class(obo:OGMS_0000130)) +Declaration(Class(obo:OGMS_0000131)) +Declaration(Class(obo:OGMS_0000132)) +Declaration(Class(obo:OGMS_0000133)) +Declaration(Class(obo:OGMS_0000134)) +Declaration(Class(obo:OGMS_0000135)) +Declaration(Class(obo:OGMS_0000136)) +Declaration(Class(obo:OGMS_0000137)) +Declaration(Class(obo:OGMS_0000138)) +Declaration(Class(obo:OGMS_0000139)) +Declaration(Class(obo:OGMS_0000140)) +Declaration(Class(obo:OGMS_0000141)) +Declaration(Class(obo:OGMS_0000142)) +Declaration(Class(obo:OGMS_0000143)) +Declaration(Class(obo:OGMS_0000144)) +Declaration(Class(obo:OGMS_0000145)) +Declaration(Class(obo:OGMS_0000146)) +Declaration(Class(obo:OGMS_0000147)) +Declaration(Class(obo:OGMS_0000148)) +Declaration(Class(obo:OGMS_0000149)) +Declaration(Class(obo:OGMS_0000150)) +Declaration(AnnotationProperty(obo:IAO_0000115)) +Declaration(AnnotationProperty(obo:IAO_0000116)) +Declaration(AnnotationProperty(obo:IAO_0000117)) +Declaration(AnnotationProperty(obo:IAO_0000118)) +Declaration(AnnotationProperty(obo:IAO_0000119)) +Declaration(AnnotationProperty(obo:IAO_0000232)) +Declaration(AnnotationProperty(dc:contributor)) +Declaration(AnnotationProperty(dc:creator)) +Declaration(AnnotationProperty(dc:date)) +Declaration(AnnotationProperty(dc:description)) +Declaration(AnnotationProperty(dc:publisher)) +Declaration(AnnotationProperty(dc:title)) +Declaration(AnnotationProperty(terms:license)) +Declaration(AnnotationProperty(oboInOwl:hasBroadSynonym)) +Declaration(AnnotationProperty(oboInOwl:hasExactSynonym)) + + ############################ -# Annotation Properties +# Classes ############################ -# Annotation Property: dcterms:description (description) +# Class: obo:OGMS_0000014 (clinical finding) -AnnotationAssertion(rdfs:label dcterms:description "description") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000014 "A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000014 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000014 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000014 "creation date: 2010-07-19T10:18:02Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000014 "clinical finding") +SubClassOf(obo:OGMS_0000014 obo:OGMS_0000123) -# Annotation Property: dcterms:license (license) +# Class: obo:OGMS_0000015 (clinical history) -AnnotationAssertion(rdfs:label dcterms:license "license") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000015 "A series of statements representing health-relevant qualities of a patient and of a patient's family."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000015 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000015 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000015 "creation date: 2010-07-19T10:18:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000015 "clinical history") +SubClassOf(obo:OGMS_0000015 obo:OGMS_0000123) -# Annotation Property: dcterms:title (title) +# Class: obo:OGMS_0000016 (clinical picture) -AnnotationAssertion(rdfs:label dcterms:title "title") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000016 "A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000016 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000016 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000016 "creation date: 2010-07-19T10:20:20Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000016 "clinical picture") +SubClassOf(obo:OGMS_0000016 obo:OGMS_0000123) +# Class: obo:OGMS_0000017 (clinical finding from image) +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000017 "An interpretation of an image that is the output of a clinical evaluation and supports an inference to an assertion about some quality of a patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000017 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000017 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000017 "creation date: 2009-06-23T10:21:10Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000017 "clinical finding from image"@en) +SubClassOf(obo:OGMS_0000017 obo:OGMS_0000014) -############################ -# Classes -############################ +# Class: obo:OGMS_0000018 (laboratory finding) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000018 "A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000018 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000018 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000018 "creation date: 2009-06-23T10:21:58Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000018 "laboratory finding") +SubClassOf(obo:OGMS_0000018 obo:OGMS_0000014) + +# Class: obo:OGMS_0000019 (preclinical finding) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000019 "A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000019 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000019 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000019 "creation date: 2009-06-23T10:22:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000019 "preclinical finding") +SubClassOf(obo:OGMS_0000019 obo:IAO_0000027) + +# Class: obo:OGMS_0000020 (symptom) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000020 "A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000020 "note: defined class") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000020 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000020 "creation date: 2010-11-18T11:02:10Z +Updated: 2020-07-06") +AnnotationAssertion(rdfs:label obo:OGMS_0000020 "symptom") +SubClassOf(obo:OGMS_0000020 obo:BFO_0000015) + +# Class: obo:OGMS_0000022 (manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000022 "A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000022 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000022 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000022 "creation date: 2009-06-23T11:12:33Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000022 "manifestation of a disease") +SubClassOf(obo:OGMS_0000022 obo:BFO_0000019) + +# Class: obo:OGMS_0000023 (phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000023 "A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000023 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000023 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000023 "creation date: 2010-07-19T11:13:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000023 "phenotype") +SubClassOf(obo:OGMS_0000023 obo:BFO_0000019) + +# Class: obo:OGMS_0000024 (obsolete_sign) + +AnnotationAssertion(rdfs:comment obo:OGMS_0000024 "The class sign has been replaced by three seperate classes which reflect the different types of signs possible.") +AnnotationAssertion(rdfs:label obo:OGMS_0000024 "obsolete_sign") +AnnotationAssertion(owl:deprecated obo:OGMS_0000024 "true"^^xsd:boolean) + +# Class: obo:OGMS_0000025 (clinical manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000025 "A manifestation of a disease that is detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000025 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000025 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000025 "creation date: 2009-06-23T11:15:43Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000025 "clinical manifestation of a disease") +SubClassOf(obo:OGMS_0000025 obo:OGMS_0000022) + +# Class: obo:OGMS_0000026 (preclinical manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000026 "A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000026 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000026 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000026 "creation date: 2009-06-23T11:16:50Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000026 "preclinical manifestation of a disease") +SubClassOf(obo:OGMS_0000026 obo:OGMS_0000022) + +# Class: obo:OGMS_0000027 (clinical phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000027 "A clinically abnormal phenotype."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000027 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000027 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000027 "creation date: 2009-06-23T11:18:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000027 "clinical phenotype") +SubClassOf(obo:OGMS_0000027 obo:OGMS_0000023) + +# Class: obo:OGMS_0000028 (disease phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000028 "A clinically abnormal phenotype that is characteristic of a single disease."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000028 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000028 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000028 "creation date: 2009-06-23T11:18:39Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000028 "disease phenotype") +SubClassOf(obo:OGMS_0000028 obo:OGMS_0000023) + +# Class: obo:OGMS_0000029 (vital sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000029 "A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000029 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000029 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000029 "creation date: 2009-06-23T11:19:17Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000029 "vital sign") +SubClassOf(obo:OGMS_0000029 obo:OGMS_0000129) + +# Class: obo:OGMS_0000030 (predisposition to disease of type X) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000030 "A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000030 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000030 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000030 "creation date: 2009-06-23T11:20:25Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000030 "predisposition to disease of type X") +SubClassOf(obo:OGMS_0000030 obo:BFO_0000016) + +# Class: obo:OGMS_0000031 (disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000031 "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000031 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000031 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000031 "creation date: 2009-06-23T11:21:20Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000031 "disease") +SubClassOf(obo:OGMS_0000031 obo:BFO_0000016) + +# Class: obo:OGMS_0000032 (homeostasis) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000032 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000032 "creation date: 2009-06-23T11:22:01Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000032 "homeostasis") +SubClassOf(obo:OGMS_0000032 obo:BFO_0000016) + +# Class: obo:OGMS_0000033 (genetic predisposition to disease of type X) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000033 "A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000033 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000033 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000033 "creation date: 2009-06-23T11:23:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000033 "genetic predisposition to disease of type X") +SubClassOf(obo:OGMS_0000033 obo:OGMS_0000030) + +# Class: obo:OGMS_0000034 (acquired genetic disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000034 "A disease whose physical basis is an acquired genetic disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000034 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000034 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000034 "creation date: 2009-06-23T11:24:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000034 "acquired genetic disease") +SubClassOf(obo:OGMS_0000034 obo:OGMS_0000031) + +# Class: obo:OGMS_0000035 (constitutional genetic disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000035 "A disease whose physical basis is a constitutional genetic disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000035 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000035 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000035 "creation date: 2009-06-23T11:24:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000035 "constitutional genetic disease") +SubClassOf(obo:OGMS_0000035 obo:OGMS_0000031) + +# Class: obo:OGMS_0000037 (altered homeostasis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000037 "Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000037 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000037 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000037 "creation date: 2009-06-23T11:26:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000037 "altered homeostasis") +SubClassOf(obo:OGMS_0000037 obo:OGMS_0000032) + +# Class: obo:OGMS_0000038 (normal homeostasis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000038 "Homeostasis of a type that is not clinically abnormal."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000038 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000038 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000038 "creation date: 2009-06-23T11:27:28Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000038 "normal homeostasis") +SubClassOf(obo:OGMS_0000038 obo:OGMS_0000032) + +# Class: obo:OGMS_0000039 (configuration) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000039 "A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000039 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000039 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000039 "creation date: 2009-06-23T11:36:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000039 "configuration") +SubClassOf(obo:OGMS_0000039 obo:BFO_0000019) + +# Class: obo:OGMS_0000040 (pathological physical configuration) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000040 "A configuration which deviates in some way from a canonical configuration for a particular organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000040 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000040 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000040 "creation date: 2009-06-23T11:36:58Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000040 "pathological physical configuration") +SubClassOf(obo:OGMS_0000040 obo:OGMS_0000039) + +# Class: obo:OGMS_0000045 (disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000045 "A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000045 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000045 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000045 "creation date: 2009-06-23T11:39:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000045 "disorder") +SubClassOf(obo:OGMS_0000045 obo:BFO_0000040) + +# Class: obo:OGMS_0000046 (epigenetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000046 "A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000046 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000046 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000046 "creation date: 2009-06-23T11:40:27Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000046 "epigenetic disorder") +SubClassOf(obo:OGMS_0000046 obo:OGMS_0000045) + +# Class: obo:OGMS_0000047 (genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000047 "A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000047 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000047 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000047 "creation date: 2009-06-23T11:41:14Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000047 "genetic disorder") +SubClassOf(obo:OGMS_0000047 obo:OGMS_0000045) + +# Class: obo:OGMS_0000050 (acquired genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000050 "A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000050 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000050 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000050 "creation date: 2009-06-23T11:43:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000050 "acquired genetic disorder") +SubClassOf(obo:OGMS_0000050 obo:OGMS_0000047) + +# Class: obo:OGMS_0000051 (constitutional genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000051 "A genetic disorder inherited during conception that is part of all cells in the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000051 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000051 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000051 "creation date: 2009-06-23T11:43:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000051 "constitutional genetic disorder") +SubClassOf(obo:OGMS_0000051 obo:OGMS_0000047) + +# Class: obo:OGMS_0000055 (clinical history taking) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000055 "A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000055 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000055 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000055 "creation date: 2009-06-23T11:49:16Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000055 "clinical history taking") +SubClassOf(obo:OGMS_0000055 obo:OGMS_0000108) + +# Class: obo:OGMS_0000056 (clinical laboratory test) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000056 "A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000056 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000056 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000056 "creation date: 2009-06-23T11:49:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000056 "clinical laboratory test") +SubClassOf(obo:OGMS_0000056 obo:OGMS_0000108) + +# Class: obo:OGMS_0000057 (physical examination) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000057 "A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000057 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000057 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000057 "creation date: 2010-07-19T11:50:18Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000057 "physical examination") +SubClassOf(obo:OGMS_0000057 obo:OGMS_0000108) + +# Class: obo:OGMS_0000059 (etiological process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000059 "A process in an organism that leads to a subsequent disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000059 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000059 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000059 "creation date: 2009-06-23T11:53:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000059 "etiological process") +SubClassOf(obo:OGMS_0000059 obo:BFO_0000015) + +# Class: obo:OGMS_0000060 (bodily process) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000060 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000060 "creation date: 2009-06-23T11:53:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000060 "bodily process") +SubClassOf(obo:OGMS_0000060 obo:BFO_0000015) + +# Class: obo:OGMS_0000061 (pathological bodily process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000061 "A bodily process that is clinically abnormal."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000061 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000061 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000061 "creation date: 2009-06-23T11:54:29Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000061 "pathological bodily process") +SubClassOf(obo:OGMS_0000061 obo:OGMS_0000060) + +# Class: obo:OGMS_0000063 (disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000063 "The totality of all processes through which a given disease instance is realized."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000063 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000063 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000063 "creation date: 2009-06-23T11:55:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000063 "disease course") +SubClassOf(obo:OGMS_0000063 obo:BFO_0000015) + +# Class: obo:OGMS_0000064 (chronic disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000064 "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000064 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000064 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000064 "creation date: 2009-06-23T11:56:26Z + +10212020 + +for definition use: +http://purl.obolibrary.org/obo/PATO_0001863") +AnnotationAssertion(rdfs:label obo:OGMS_0000064 "chronic disease course") +SubClassOf(obo:OGMS_0000064 obo:OGMS_0000063) + +# Class: obo:OGMS_0000065 (progressive disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000065 "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000065 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000065 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000065 "creation date: 2009-06-23T11:57:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000065 "progressive disease course") +SubClassOf(obo:OGMS_0000065 obo:OGMS_0000063) + +# Class: obo:OGMS_0000066 (transient disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000066 "A disease course that terminates in a return to normal homeostasis."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000066 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000066 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000066 "creation date: 2009-06-23T11:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000066 "transient disease course") +SubClassOf(obo:OGMS_0000066 obo:OGMS_0000063) + +# Class: obo:OGMS_0000067 (_undefined primitive term) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000067 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000067 "creation date: 2009-06-23T11:58:22Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000067 "_undefined primitive term") +SubClassOf(obo:OGMS_0000067 obo:BFO_0000001) + +# Class: obo:OGMS_0000069 (clinically abnormal) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000069 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000069 "creation date: 2009-06-23T11:59:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000069 "clinically abnormal") +SubClassOf(obo:OGMS_0000069 obo:OGMS_0000067) + +# Class: obo:OGMS_0000070 (physical basis) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000070 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000070 "creation date: 2009-06-23T12:00:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000070 "physical basis") +SubClassOf(obo:OGMS_0000070 obo:OGMS_0000067) + +# Class: obo:OGMS_0000071 (realization) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000071 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000071 "creation date: 2009-06-23T12:00:39Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000071 "realization") +SubClassOf(obo:OGMS_0000071 obo:OGMS_0000067) + +# Class: obo:OGMS_0000073 (diagnosis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000073 "The representation of a conclusion of a diagnostic process."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000073 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000073 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000073 "creation date: 2009-06-23T12:42:23Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000073 "diagnosis") +SubClassOf(obo:OGMS_0000073 obo:OGMS_0000123) + +# Class: obo:OGMS_0000074 (normal value) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000074 "A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000074 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000074 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000074 "creation date: 2009-06-26T10:31:34Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000074 "normal value") +SubClassOf(obo:OGMS_0000074 obo:BFO_0000031) + +# Class: obo:OGMS_0000077 (pathological formation) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000077 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000077 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000077 "creation date: 2009-07-13T02:14:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000077 "pathological formation") +SubClassOf(obo:OGMS_0000077 obo:BFO_0000040) + +# Class: obo:OGMS_0000078 (pathological anatomical structure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000078 "An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000078 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000078 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000078 "creation date: 2009-07-13T02:14:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000078 "pathological anatomical structure") +SubClassOf(obo:OGMS_0000078 obo:BFO_0000040) + +# Class: obo:OGMS_0000079 (portion of pathological body substance) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000079 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000079 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000079 "creation date: 2009-07-13T02:15:17Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000079 "portion of pathological body substance") +SubClassOf(obo:OGMS_0000079 obo:BFO_0000040) + +# Class: obo:OGMS_0000080 (pathological transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000080 "A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000080 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000080 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000080 "creation date: 2009-07-13T02:17:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000080 "pathological transformation") +SubClassOf(obo:OGMS_0000080 obo:OGMS_0000061) + +# Class: obo:OGMS_0000081 (pathological derivation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000081 "A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000081 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000081 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000081 "creation date: 2009-07-13T02:17:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000081 "pathological derivation") +SubClassOf(obo:OGMS_0000081 obo:OGMS_0000061) + +# Class: obo:OGMS_0000082 (pathological invasion) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000082 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000082 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000082 "creation date: 2009-07-13T02:17:47Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000082 "pathological invasion") +SubClassOf(obo:OGMS_0000082 obo:OGMS_0000061) + +# Class: obo:OGMS_0000083 (physical examination finding) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000083 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000083 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000083 "physical examination finding") +SubClassOf(obo:OGMS_0000083 obo:OGMS_0000014) + +# Class: obo:OGMS_0000084 (organism population) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000084 "An aggregate of organisms of the same type."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000084 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000084 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000084 "organism population") +SubClassOf(obo:OGMS_0000084 obo:BFO_0000040) + +# Class: obo:OGMS_0000085 (pain) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000085 "A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000085 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000085 "https://philarchive.org/rec/SMITAO-12") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000085 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000085 "pain") +SubClassOf(obo:OGMS_0000085 obo:OGMS_0000020) + +# Class: obo:OGMS_0000086 (syndrome) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000086 "A pattern of signs and symptoms that typically co-occur."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000086 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000086 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000086 "syndrome") +SubClassOf(obo:OGMS_0000086 obo:BFO_0000019) + +# Class: obo:OGMS_0000087 (extended organism) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000087 "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000087 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000087 "creation date: 2010-01-25T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000087 "extended organism") +SubClassOf(obo:OGMS_0000087 obo:BFO_0000040) + +# Class: obo:OGMS_0000088 (patient symptom report) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000088 "A communication from a patient about something they perceive as being abnormal about their body or life."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000088 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000088 "creation date: 2010-01-25T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000088 "patient symptom report") +SubClassOf(obo:OGMS_0000088 obo:IAO_0000030) + +# Class: obo:OGMS_0000089 (congenital disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000089 "A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000089 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000089 "congenital malformation") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000089 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000089 "congenital disorder") +SubClassOf(obo:OGMS_0000089 obo:BFO_0000040) + +# Class: obo:OGMS_0000090 (treatment) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000090 "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000090 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000090 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:OGMS_0000090 "medical intervention"@en) +AnnotationAssertion(rdfs:label obo:OGMS_0000090 "treatment") +SubClassOf(obo:OGMS_0000090 obo:OGMS_0000096) + +# Class: obo:OGMS_0000091 (convalescence) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000091 "A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000091 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000091 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000091 "convalescence") +SubClassOf(obo:OGMS_0000091 obo:BFO_0000015) + +# Class: obo:OGMS_0000092 (life course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000092 "A process which has as parts all the processes in which a given organism is participant."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000092 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000092 "creation date: 2010-03-31T04:51:11Z + +EDIT: 10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000092 "life course") +SubClassOf(obo:OGMS_0000092 obo:BFO_0000015) + +# Class: obo:OGMS_0000093 (prognosis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000093 "A hypothesis about some future part of a disease course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000093 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000093 "creation date: 2010-03-31T12:42:23Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000093 "prognosis") +SubClassOf(obo:OGMS_0000093 obo:IAO_0000027) + +# Class: obo:OGMS_0000094 (acute disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000094 "A disease course with an acute onset"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000094 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000094 "creation date: 2010-07-19T11:57:44Z + +10212020 + +for definition use + +http://purl.obolibrary.org/obo/PATO_0000389") +AnnotationAssertion(rdfs:label obo:OGMS_0000094 "acute disease course") +SubClassOf(obo:OGMS_0000094 obo:OGMS_0000063) + +# Class: obo:OGMS_0000095 (inflammatory process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000095 "A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000095 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000095 "creation date: 2010-07-19T11:57:44Z + +Updated: 10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000095 "inflammatory process") +SubClassOf(obo:OGMS_0000095 obo:OGMS_0000060) + +# Class: obo:OGMS_0000096 (health care process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000096 "A planned process with the objective to improve or maintain the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000096 "Albert Goldfain +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000096 "creation date: 2011-02-21T09:57:44Z +editor date: 2017-04-18") +AnnotationAssertion(rdfs:label obo:OGMS_0000096 "health care process") +SubClassOf(obo:OGMS_0000096 obo:COB_0000035) + +# Class: obo:OGMS_0000097 (health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000097 "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000097 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000097 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000097 "health care encounter") +SubClassOf(obo:OGMS_0000097 obo:OGMS_0000096) + +# Class: obo:OGMS_0000098 (hospitalization) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000098 "A health care process in which a person is admitted to a hospital for treatment, diagnosis, or monitoring."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000098 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000098 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000098 "hospitalization") +SubClassOf(obo:OGMS_0000098 obo:OGMS_0000096) + +# Class: obo:OGMS_0000099 (outpatient encounter) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000099 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000099 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000099 "outpatient encounter") +SubClassOf(obo:OGMS_0000099 obo:OGMS_0000097) + +# Class: obo:OGMS_0000100 (inpatient encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000100 "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000100 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000100 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000100 "inpatient encounter") +SubClassOf(obo:OGMS_0000100 obo:OGMS_0000097) + +# Class: obo:OGMS_0000101 (emergency department encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000101 "A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000101 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000101 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000101 "emergency department encounter") +SubClassOf(obo:OGMS_0000101 obo:OGMS_0000097) + +# Class: obo:OGMS_0000102 (injury) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000102 "A disorder that involves some structural damage that is immediately caused by a catastrophic external force."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000102 "At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. + +Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.") +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000102 "Albert Goldfain +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000102 "creation date: 2011-09-20T09:57:44Z +edited date: 30 SEPT 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000102 "injury") +SubClassOf(obo:OGMS_0000102 obo:OGMS_0000045) + +# Class: obo:OGMS_0000103 (disease prophylaxis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000103 "A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000103 "Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question.") +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000103 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000103 "creation date: 2011-09-20T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000103 "disease prophylaxis") +SubClassOf(obo:OGMS_0000103 obo:COB_0000035) + +# Class: obo:OGMS_0000104 (diagnostic process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000104 "A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000104 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000104 "creation date: 2011-09-20T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000104 "diagnostic process") +SubClassOf(obo:OGMS_0000104 obo:OGMS_0000096) + +# Class: obo:OGMS_0000105 (relapse) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000105 "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease.") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000105 "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000105 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000105 "recurrent") +AnnotationAssertion(dc:date obo:OGMS_0000105 "10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000105 "relapse"@en) +SubClassOf(obo:OGMS_0000105 obo:OBI_0000278) + +# Class: obo:OGMS_0000106 (remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000106 "A disease stage which is characterized by the lack of a manifestation of a disease") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000106 "A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000106 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(dc:date obo:OGMS_0000106 "10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000106 "remission"@en) +SubClassOf(obo:OGMS_0000106 obo:OBI_0000278) + +# Class: obo:OGMS_0000107 (ancillary health care process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000107 "A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient.") +AnnotationAssertion(dc:date obo:OGMS_0000107 "2017-04-18") +AnnotationAssertion(dc:publisher obo:OGMS_0000107 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000107 "ancillary health care process") +SubClassOf(obo:OGMS_0000107 obo:COB_0000035) + +# Class: obo:OGMS_0000108 (health care process assay) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000108 "A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.") +AnnotationAssertion(dc:date obo:OGMS_0000108 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000108 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000108 "health care process assay") +SubClassOf(obo:OGMS_0000108 obo:OGMS_0000096) + +# Class: obo:OGMS_0000109 (health care process biomaterial transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000109 "A health care process which results in physical changes in a specified input material") +AnnotationAssertion(dc:date obo:OGMS_0000109 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000109 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000109 "health care process biomaterial transformation") +SubClassOf(obo:OGMS_0000109 obo:OGMS_0000096) + +# Class: obo:OGMS_0000110 (health care process data transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000110 "A health care process that produces output from input data") +AnnotationAssertion(dc:date obo:OGMS_0000110 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000110 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000110 "health care process data transformation") +SubClassOf(obo:OGMS_0000110 obo:OGMS_0000096) + +# Class: obo:OGMS_0000111 (prophylactic treatment) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000111 "A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000111 "Creation date: 2018-11-27") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:OGMS_0000111 "preventive intervention"@en) +AnnotationAssertion(rdfs:label obo:OGMS_0000111 "prophylactic treatment"@en) +SubClassOf(obo:OGMS_0000111 obo:OGMS_0000090) + +# Class: obo:OGMS_0000112 (therapeutic procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000112 "A treatment whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder or pathological process.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000112 "Creation data: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000112 "therapeutic procedure"@en) +SubClassOf(obo:OGMS_0000112 obo:OGMS_0000090) + +# Class: obo:OGMS_0000113 (chemotherapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000113 "A therapeutic procedure that uses synthetic or naturally-occurring chemicals") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000113 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000113 "chemotherapy procedure"@en) +SubClassOf(obo:OGMS_0000113 obo:OGMS_0000112) + +# Class: obo:OGMS_0000114 (immunotherapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000114 "A therapeutic procedure that uses immune system derived entities.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000114 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000114 "immunotherapy procedure"@en) +SubClassOf(obo:OGMS_0000114 obo:OGMS_0000112) + +# Class: obo:OGMS_0000115 (physical therapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000115 "A therapeutic procedure that uses physical conditioning") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000115 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000115 "physical therapy procedure"@en) +SubClassOf(obo:OGMS_0000115 obo:OGMS_0000112) + +# Class: obo:OGMS_0000116 (radiation therapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000116 "A therapeutic procedure that uses radiation.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000116 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000116 "radiation therapy procedure"@en) +SubClassOf(obo:OGMS_0000116 obo:OGMS_0000112) + +# Class: obo:OGMS_0000117 (asymptomatic) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000117 "A disease stage characterized by the lack of symptoms associated with a given disease") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000117 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000117 "asymptomatic"@en) +SubClassOf(obo:OGMS_0000117 obo:OBI_0000278) + +# Class: obo:OGMS_0000118 (onset) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000118 "A disease stage that marks the beginning of a disease") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000118 "creation date 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000118 "onset"@en) +SubClassOf(obo:OGMS_0000118 obo:OBI_0000278) + +# Class: obo:OGMS_0000119 (acute onset) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000119 "A disease stage with a rapid unfolding of signs and symptoms") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000119 "creation date 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000119 "acute onset"@en) +SubClassOf(obo:OGMS_0000119 obo:OGMS_0000118) + +# Class: obo:OGMS_0000120 (complete remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000120 "A remission which is characterized by a prolonged lack of all manifestations of a disease") +AnnotationAssertion(rdfs:label obo:OGMS_0000120 "complete remission"@en) +SubClassOf(obo:OGMS_0000120 obo:OGMS_0000106) + +# Class: obo:OGMS_0000121 (partial remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000121 "A remission which is characterized by a prolonged lack of some manifestations of a disease") +AnnotationAssertion(rdfs:label obo:OGMS_0000121 "partial remission"@en) +SubClassOf(obo:OGMS_0000121 obo:OGMS_0000106) + +# Class: obo:OGMS_0000122 (recovered from disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000122 "A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000122 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000122 "recovered from disease"@en) +SubClassOf(obo:OGMS_0000122 obo:BFO_0000019) + +# Class: obo:OGMS_0000123 (clinical data item) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000123 "A data item that is about a patient and is the specified output of a health care process assay or diagnostic process") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000123 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000123 "clinical data item"@en) +SubClassOf(obo:OGMS_0000123 obo:IAO_0000027) + +# Class: obo:OGMS_0000124 (routine health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000124 "A health care encounter that is regularly scheduled for the purpose of health monitoring.") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000124 "routine clinical visit") +AnnotationAssertion(rdfs:label obo:OGMS_0000124 "routine health care encounter") +SubClassOf(obo:OGMS_0000124 obo:OGMS_0000099) + +# Class: obo:OGMS_0000125 (follow-up health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000125 "A health care encounter that is scheduled for the purpose of assessing a known set of specific issues") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000125 "follow-up clinical visit") +AnnotationAssertion(rdfs:label obo:OGMS_0000125 "follow-up health care encounter") +SubClassOf(obo:OGMS_0000125 obo:OGMS_0000099) + +# Class: obo:OGMS_0000126 (congenital infection) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000126 "A congenital disorder arising as a result of an infectious process") +AnnotationAssertion(rdfs:label obo:OGMS_0000126 "congenital infection") +SubClassOf(obo:OGMS_0000126 obo:OGMS_0000089) + +# Class: obo:OGMS_0000127 (drug induced congenital malformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000127 "A congenital disorder arising as a result of a drug exposure causing an anatomical abnormality") +AnnotationAssertion(rdfs:label obo:OGMS_0000127 "drug induced congenital malformation") +SubClassOf(obo:OGMS_0000127 obo:OGMS_0000089) + +# Class: obo:OGMS_0000128 (congenital process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000128 "A pathological bodily process that occurs in the fetus during fetal development") +AnnotationAssertion(rdfs:label obo:OGMS_0000128 "congenital process") +SubClassOf(obo:OGMS_0000128 obo:OGMS_0000061) + +# Class: obo:OGMS_0000129 (physical sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000129 "An abnormal material entity that is part of a patient and hypothesized to be clinically relevant.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000129 "Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension") +AnnotationAssertion(rdfs:label obo:OGMS_0000129 "physical sign") +SubClassOf(obo:OGMS_0000129 obo:BFO_0000040) + +# Class: obo:OGMS_0000130 (allergic disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000130 "The process in which an allergic disease unfolds.") +AnnotationAssertion(rdfs:label obo:OGMS_0000130 "allergic disease process") +SubClassOf(obo:OGMS_0000130 obo:OGMS_0000061) + +# Class: obo:OGMS_0000131 (cancer process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000131 "The process in which cancer unfolds") +AnnotationAssertion(rdfs:label obo:OGMS_0000131 "cancer process") +SubClassOf(obo:OGMS_0000131 obo:OGMS_0000061) + +# Class: obo:OGMS_0000132 (autoimmune disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000132 "The process in which an autoimmune disease unfolds.") +AnnotationAssertion(rdfs:label obo:OGMS_0000132 "autoimmune disease process") +SubClassOf(obo:OGMS_0000132 obo:OGMS_0000061) + +# Class: obo:OGMS_0000133 (progression stage) + +AnnotationAssertion(rdfs:label obo:OGMS_0000133 "progression stage") +SubClassOf(obo:OGMS_0000133 obo:OBI_0000278) + +# Class: obo:OGMS_0000134 (cancer progression stage) + +AnnotationAssertion(rdfs:label obo:OGMS_0000134 "cancer progression stage") +SubClassOf(obo:OGMS_0000134 obo:OGMS_0000133) + +# Class: obo:OGMS_0000135 (cancer progression stage 0) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000135 "A cancer progression stage characterized by abnormal cellular growth contained within normal tissue boundaries (e.g. carcinoma in situ).") +AnnotationAssertion(rdfs:label obo:OGMS_0000135 "cancer progression stage 0") +SubClassOf(obo:OGMS_0000135 obo:OGMS_0000134) + +# Class: obo:OGMS_0000136 (cancer progression stage I) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000136 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass.") +AnnotationAssertion(rdfs:label obo:OGMS_0000136 "cancer progression stage I") +SubClassOf(obo:OGMS_0000136 obo:OGMS_0000134) + +# Class: obo:OGMS_0000137 (cancer progression stage II) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000137 "A cancer progression stage characterized by abnormal cellular growth that extends well beyond normal local tissue boundaries as a contiguous mass.") +AnnotationAssertion(rdfs:label obo:OGMS_0000137 "cancer progression stage II") +SubClassOf(obo:OGMS_0000137 obo:OGMS_0000134) + +# Class: obo:OGMS_0000138 (cancer progression stage III) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000138 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to one or more regional draining lymph nodes.") +AnnotationAssertion(rdfs:label obo:OGMS_0000138 "cancer progression stage III") +SubClassOf(obo:OGMS_0000138 obo:OGMS_0000134) + +# Class: obo:OGMS_0000139 (cancer progression stage IV) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000139 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to other distant tissues besides lymph nodes.") +AnnotationAssertion(rdfs:label obo:OGMS_0000139 "cancer progression stage IV") +SubClassOf(obo:OGMS_0000139 obo:OGMS_0000134) + +# Class: obo:OGMS_0000140 (infectious disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000140 "The process in which an infectious disease unfolds") +AnnotationAssertion(rdfs:label obo:OGMS_0000140 "infectious disease process") +SubClassOf(obo:OGMS_0000140 obo:OGMS_0000061) + +# Class: obo:OGMS_0000141 (processual sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000141 "An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant.") +AnnotationAssertion(rdfs:label obo:OGMS_0000141 "processual sign") +SubClassOf(obo:OGMS_0000141 obo:BFO_0000015) + +# Class: obo:OGMS_0000142 (qualitative sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000142 "An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000142 "Example: the color of a rash; the shape of a melanoma") +AnnotationAssertion(rdfs:label obo:OGMS_0000142 "qualitative sign") +SubClassOf(obo:OGMS_0000142 obo:BFO_0000019) + +# Class: obo:OGMS_0000143 (transplantation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000143 "A therapeutic procedure in which a body part is transferred into a organism") +AnnotationAssertion(rdfs:label obo:OGMS_0000143 "transplantation") +SubClassOf(obo:OGMS_0000143 obo:OGMS_0000112) + +# Class: obo:OGMS_0000144 (solid organ transplant) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000144 "A transplantation in which the body part is a non-fluid tissue") +AnnotationAssertion(rdfs:label obo:OGMS_0000144 "solid organ transplant") +SubClassOf(obo:OGMS_0000144 obo:OGMS_0000143) + +# Class: obo:OGMS_0000145 (transfusion) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000145 "A transplantation in which the body part is a bodily fluid") +AnnotationAssertion(rdfs:label obo:OGMS_0000145 "transfusion") +SubClassOf(obo:OGMS_0000145 obo:OGMS_0000143) + +# Class: obo:OGMS_0000146 (tissue disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000146 "A disorder of some macroscopic part of a tissue") +AnnotationAssertion(rdfs:label obo:OGMS_0000146 "tissue disorder") +SubClassOf(obo:OGMS_0000146 obo:OGMS_0000045) + +# Class: obo:OGMS_0000147 (neoplasm) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000147 "A tissue disorder that has resulted from a dysregulation of cell proliferation leading to a net increase in mass") +AnnotationAssertion(rdfs:label obo:OGMS_0000147 "neoplasm") +SubClassOf(obo:OGMS_0000147 obo:OGMS_0000146) + +# Class: obo:OGMS_0000148 (medication role) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000148 "A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000148 "Originally OBIB_0000026") +AnnotationAssertion(rdfs:label obo:OGMS_0000148 "medication role") +SubClassOf(obo:OGMS_0000148 obo:BFO_0000023) + +# Class: obo:OGMS_0000149 (patient-reported outcome) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000149 "A data item that is about a patient’s health that comes directly from the patient. A patient reported outcome can include subjective feelings regarding symptoms, functions in daily life, physical, mental, emotional, spiritual, and social well-being, and satisfaction with healthcare that has been received."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000149 "https://orcid.org/0000-0001-6378-1703") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000149 "https://www.cancer.gov/publications/dictionaries/cancer-terms/def/patient-reported-outcome") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0000-0001-9625-1899") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0000-0001-9990-8331") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0009-0003-7246-1252") +AnnotationAssertion(oboInOwl:hasBroadSynonym obo:OGMS_0000149 "PRO"@en) +AnnotationAssertion(rdfs:comment obo:OGMS_0000149 "The outcome does not necessarily need to be related to a healthcare intervention. For example, it can be about a patient's overall quality of life related to a disease."@en) +AnnotationAssertion(rdfs:label obo:OGMS_0000149 "patient-reported outcome"@en) +SubClassOf(obo:OGMS_0000149 obo:IAO_0000027) -# Class: (root node) +# Class: obo:OGMS_0000150 (healthcare outcome report) -AnnotationAssertion(rdfs:label "root node"@en) +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000150 "A data item about a persont's health status or condition resulting from healthcare interventions, treatments, or services."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000150 "https://orcid.org/0000-0001-6378-1703") +AnnotationAssertion(dc:contributor obo:OGMS_0000150 "https://orcid.org/0000-0001-9990-8331") +AnnotationAssertion(dc:contributor obo:OGMS_0000150 "https://orcid.org/0009-0003-7246-1252") +AnnotationAssertion(rdfs:label obo:OGMS_0000150 "healthcare outcome report"@en) +SubClassOf(obo:OGMS_0000150 obo:IAO_0000027) ) \ No newline at end of file diff --git a/src/ontology/tmp/mirror-bfo.owl b/src/ontology/tmp/mirror-bfo.owl deleted file mode 100644 index 405f02f..0000000 --- a/src/ontology/tmp/mirror-bfo.owl +++ /dev/null @@ -1,1715 +0,0 @@ - - - - - BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation. - BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science. - BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms. - Alan Ruttenberg - Albert Goldfain - Barry Smith - Bill Duncan - Bjoern Peters - Chris Mungall - David Osumi-Sutherland - Fabian Neuhaus - Holger Stenzhorn - James A. Overton - Janna Hastings - Jie Zheng - Jonathan Bona - Larry Hunter - Leonard Jacuzzo - Ludger Jansen - Mark Ressler - Mathias Brochhausen - Mauricio Almeida - Melanie Courtot - Pierre Grenon - Randall Dipert - Ron Rudnicki - Selja Seppälä - Stefan Schulz - Thomas Bittner - Werner Ceusters - Yongqun "Oliver" He - - Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. - The BSD license on the BFO project site refers to code used to build BFO. - This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version. - - - - - - - - - - - - - - - - - - - - - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - - - - - - editor preferred term - - - - - - - - - example of usage - - - - - - - - - definition - - - - - - - - - editor note - - - - - - - - - term editor - - - - - - - - - alternative term - - - - - - - - - definition source - - - - - - - - - curator note - - - - - - - - - imported from - - - - - - - - - elucidation - - - - - - - - - has associated axiom(nl) - - - - - - - - - has associated axiom(fol) - - - - - - - - - has axiom label - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - continuant - Continuant - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - - - - - occurrent - Occurrent - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - - - - - - - - - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - site - - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of requited love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - diff --git a/src/ontology/tmp/mirror-iao.owl b/src/ontology/tmp/mirror-iao.owl deleted file mode 100644 index 2e2f9b4..0000000 --- a/src/ontology/tmp/mirror-iao.owl +++ /dev/null @@ -1,8152 +0,0 @@ - - - - - en - Adam Goldstein - Alan Ruttenberg - Albert Goldfain - Barry Smith - Bjoern Peters - Carlo Torniai - Chris Mungall - Chris Stoeckert - Christian A. Boelling - Clint Dowland - Darren Natale - David Osumi-Sutherland - Gwen Frishkoff - Holger Stenzhorn - James A. Overton - James Malone - Jennifer Fostel - Jie Zheng - Jonathan Rees - Larisa Soldatova - Lawrence Hunter - Mathias Brochhausen - Matt Brush - Melanie Courtot - Michel Dumontier - Paolo Ciccarese - Pat Hayes - Philippe Rocca-Serra - Randy Dipert - Ron Rudnicki - Satya Sahoo - Sivaram Arabandi - Werner Ceusters - William Duncan - William Hogan - Yongqun (Oliver) He - The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. - Information Artifact Ontology (IAO) - - An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO - IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 - IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 - - 2022-11-07 - - - - - - - - - - - - - - - - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - editor preferred term - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - has curation status - - - - - - - - definition - - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - - editor note - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - - - - - - - - alternative label - - A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. - OBO Operations committee - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - - - - - - - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition source - - - - - - - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - - - - - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - - curator note - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - ontology term requester - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - - - - - - is denotator type - Relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - - - - - - - - imported from - - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - imported from - - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - antisymmetric property - part_of antisymmetric property xsd:true - Use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - has ID digit count - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - - - - - - has ID range allocated - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - - - - - - has ID policy for - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - - - - - - has ID prefix - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - - - - - - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - - elucidation - - - - - - - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - - has associated axiom(nl) - - - - - - - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - - has associated axiom(fol) - - - - - - - - is allocated id range - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - Add as annotation triples in the granting ontology - is allocated id range - - - - - - - - retired from use as of - relates a class of CRID to the date after which further instances should not be made, according to the central authority - In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp - Alan Ruttenberg - retired from use as of - - - - - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - - - - - may be identical to - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - #40 - VFB - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - may be identical to - - - - - - - - scheduled for obsoletion on or after - Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. - Chris Mungall, Jie Zheng - https://github.com/geneontology/go-ontology/issues/15532 - https://github.com/information-artifact-ontology/ontology-metadata/issues/32 - GO ontology - scheduled for obsoletion on or after - - - - - - - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - - has axiom label - - - - - - - - term replaced by - - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - Add as annotation triples in the granting ontology - term replaced by - - - - - - - - This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. - OBO Operations call - - logical characteristic of object property - - - - - - - - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } - Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. - - - - defined by construct - - - - - - - - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - has broad synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - - - - - - - - - An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - has exact synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - - - - - - - - - An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 - has narrow synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 - - - - - - - - - An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 - has related synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - - - - has measurement unit label - - - - - - - - - The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. - -Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. - -c = pattern in the ink -b = paper + ink -r = friend - - c specifically denotes r =def -r is a portion of reality -& c is a particular quality -& c depends specifically on some independent continuant b -& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. - -Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. - -Case 1 -Memory trace as mark created when reading some description of some friend. The trace can denote. - -Case 2 -Pattern of ink arrayed on paper as mark when writing down a friend's name - -Case 3 -Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. - 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_specifically denotes - true - - - - - - - - - This document is about information artifacts and their representations - - A (currently) primitive relation that relates an information artifact to an entity. - 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. - -We will try to build it back up by elaborating the various subproperties that are more precisely defined. - -Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. - person:Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - is about - - - - - - - - - - - An information artifact IA mentions an entity E exactly when it has a component/part that denotes E - 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) - 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition - PERSON: Jonathan Rees - Person: Alan Ruttenberg - mentions - - - - - - - - Inverse of the relation 'mentions' - - - 2022-01-28T07:20:08Z - mentioned by - - - - - - - - - - - - A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. - A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. -g denotes r =def -r is a portion of reality -there is some c that is a concretization of g -every c that is a concretization of g specifically denotes r - person:Alan Ruttenberg - Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan - - denotes - - - - - - - - - see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote - - obsolete_materially denotes - true - - - - - - - - - - - - m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later - From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] - -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] - -unit of measure is a quality, e.g. the length of a ruler. - -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] - -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] - -a represents b means either a denotes b or a describes - -describe: -a describes b means a is about b and a allows an inference of at least one quality of b - -We have had a long discussion about denotes versus describes. - From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. - -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. - From the second meeting on IAO: - -An attempt at defining assay using Barry's "reliability" wording - -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input. - This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. - -Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. - Alan Ruttenberg - is quality measurement of - - - - - - - - - - obsolete_describes - true - - - - - - - - - - obsolete_represents - true - - - - - - - - - - inverse of the relation 'denotes' - Person: Jie Zheng, Chris Stoeckert, Mike Conlon - - denoted by - - - - - - - - - - - - relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point - has coordinate unit label - - - - - - - - - - - - relates a process to a time-measurement-datum that represents the duration of the process - Person:Alan Ruttenberg - is duration of - - - - - - - - - inverse of the relation of is quality measurement of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - is quality measured as - - - - - - - - - - - A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. - Person:Alan Ruttenberg - Person:Bjoern Peters - is quality specification of - - - - - - - - - inverse of the relation of is quality specification of - 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship - Person:Alan Ruttenberg - Person:Bjoern Peters - quality is specified as - - - - - - - - - - - - - relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken - Alan Ruttenberg - has time stamp - - - - - - - - - - - - - - - - - - - - - relates a time stamped measurement datum to the measurement datum that was measured - Alan Ruttenberg - has measurement datum - - - - - - - - - - - - - - - has_specified_input - has_specified_input - see is_input_of example_of_usage - - The inverse property of is_specified_input_of - 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Coutot - - has_specified_input - - - - - - - - is_specified_input_of - - - - - - - - - - - - - - - has_specified_output - has_specified_output - - The inverse property of is_specified_output_of - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Larry Hunter - PERSON: Melanie Courtot - - has_specified_output - - - - - - - - - - is_specified_output_of - is_specified_output_of - - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. - Alan Ruttenberg - PERSON:Bjoern Peters - - is_specified_output_of - - - - - - - - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple - a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. - characteristic of - - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - has characteristic - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - disposition of - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - location of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - located in - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true - - - - - - - - DEPRECATED bearer of - true - - - - - - - - - - - - - - - - - - - - - - has measurement value - - - - - - - - - - - has x coordinate value - - - - - - - - - - - has z coordinate value - - - - - - - - - - - has y coordinate value - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A planned process that has specified output a software product and that involves the creation of source code. - Mathias Brochhausen - William R. Hogan - http://en.wikipedia.org/wiki/Software_development - A planned process resulting in a software product involving the creation of source code. - software development - - - - - - - - - - - - - - - - - - - - A measurement datum that is the output of counting. - Mathias Brochhausen - A measurement datum that is the output of counting. - count - - - - - - - - - - - - - - - - - - - - The planned process of finding the number of elements in a finite set of objects. - Mathias Brochhausen - http://en.wikipedia.org/wiki/Counting - The planned process of finding the number of elements in a finite set of objects. - counting - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - software source code version control repository - A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. - William R. Hogan - Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based - source code repository - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - process of compiling software - A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. - William R. Hogan - It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). - Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. - compiling software - - - - - - - - - - - - - - - - - - - - creating a data set - A planned process that has a data set as its specified output. - William R. Hogan - data set creation - dataset creation - dataset creating - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object-part - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object part - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - - - - - - - - - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - site - - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of requited love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - - - conditional specification - - A directive information entity that specifies what should happen if the trigger condition is fulfilled. - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000349 - conditional specification - - - - - - - - - measurement unit label - Examples of measurement unit labels are liters, inches, weight per volume. - - A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - 2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term. - 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - measurement unit label - - - - - - - - - objective specification - In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. - - A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." - 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. - Answers the question, why did you do this experiment? - PERSON: Alan Ruttenberg - PERSON: Barry Smith - PERSON: Bjoern Peters - PERSON: Jennifer Fostel - goal specification - OBI Plan and Planned Process/Roles Branch - OBI_0000217 - objective specification - - - - - - - - - narrative object - Examples of narrative objects are reports, journal articles, and patents submission. - - A narrative object is an information content entity that is a set of propositions. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions - person:Chris Stoeckert - OBI_0000013 - group:OBI - narrative object - - - - - - - - - Pour the contents of flask 1 into flask 2 - - A directive information entity that describes an action the bearer will take. - Alan Ruttenberg - OBI Plan and Planned Process branch - action specification - - - - - - - - - - obsolete_artifact - true - - - - - - - - - datum label - - A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n - GROUP: IAO - 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. - - datum label - - - - - - - - - software - - Software is a plan specification composed of a series of instructions that can be -interpreted by or directly executed by a processing unit. - see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI - software - - - - - - - - - obsolete_digital entity - A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - -Superclass was 'digitial quality' - person:Chris Stoeckert - group:OBI - OBI_0000261 - - obsolete2_digital entity - true - - - - - - - - - - - - - - - - - - - - - - journal article - Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. - - A report that is published in a journal. - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - OBI_0000159 - group:OBI - journal article - - - - - - - - - - - - - - - - - - - - information carrier - In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. - - A quality of an information bearer that imparts the information content - 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. - 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. - PERSON: Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - information carrier - - - - - - - - - model number - - A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers - Person: Alan Ruttenberg - model number - - - - - - - - - - obsolete_material_entity - true - - - - - - - - - binary digital entity - MS Word document, ZIP file, DICOM file, JPEG file - A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -Superclass was 'digital entity' - digital_entity - person:Chris Stoeckert - group:OBI - OBI_0000244 - - obsolete2_binary digital entity - true - - - - - - - - - The length of a ruler. - a unit of measure is the quality of some material entity compared to which another quality is some multiple of. - Alan Ruttenberg - Smith, Ceusters, Ruttenberg, 2000 years of philosophy - - obsolete_unit of measure - true - - - - - - - - - programming language - R, Perl, Java - - A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000058 - group:OBI - programming language - - - - - - - - - data item - Data items include counts of things, analyte concentrations, and statistical summaries. - - An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. - 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. - 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. - 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ - JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Jonathan Rees - data - data item - - - - - - - - - symbol - a serial number such as "12324X" - a stop sign - a written proper name such as "OBI" - - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - 20091104, MC: this needs work and will most probably change - 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). - PERSON: James A. Overton - PERSON: Jonathan Rees - based on Oxford English Dictionary - symbol - - - - - - - - - numeral - - A symbol that denotes a number. - PERSON: Jonathan Rees - numeral - - - - - - - - - - - - - - - information content entity - Examples of information content entites include journal articles, data, graphical layouts, and graphs. - - A generically dependent continuant that is about some thing. - 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). - information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. - PERSON: Chris Stoeckert - OBI_0000142 - information content entity - - - - - - - - - integer numeral - - A numeral that denotes an integer - PERSON: Jonathan Rees - integer numeral - - - - - - - - - - - - 1 - - - - - - 1 - - - 10 feet. 3 ml. - - A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form - Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - scalar measurement datum - - - - - - - - - - - - - - - - An information content entity whose concretizations indicate to their bearer how to realize them in a process. - 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. - 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO - Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan - PERSON: Alan Ruttenberg - PERSON: Bjoern Peters - directive information entity - - - - - - - - - time trigger - - PlanAndPlannedProcess Branch - time trigger - - - - - - - - - obsolete_study interpretation - - A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses - The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. - 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - Lawrence Hunter - PERSON: Jennifer Fostel - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - conclusion - OBI_0000005 - - obsolete_study interpretation - true - - - - - - - - - dot plot - Dot plot of SSC-H and FSC-H. - - A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000123 - group:OBI - dot plot - - - - - - - - - graph - - A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - PERSON: Lawrence Hunter - person:Alan Ruttenberg - person:Allyson Lister - OBI_0000240 - group:OBI - graph - - - - - - - - - text based digital entity - XML file, C++ source code file - A text based digital entity is a digital entity that is encoded so that it only contains text characters. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital document' - digital_entity - person:Chris Stoeckert - OBI_0000132 - group:OBI - - obsolete2_text based digital entity - true - - - - - - - - - rule - example to be added - - A rule is an executable which guides, defines, restricts actions. - MSI - PRS - OBI_0500021 - PRS - rule - - - - - - - - - contour plot - Contour plot of SSC-H, FSC-H, and FL1-H. - - generically_dependent_continuants - person:Allyson Lister - person:Chris Stoeckert - OBI_0000246 - group:Flow Cytometry community - contour plot - - - - - - - - - report figure - - A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements - I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report - Replaced by defined version of figure - person:Alan Ruttenberg - person:Allyson Lister - group:OBI - OBI_0000027 - - obsolete2_report figure - true - - - - - - - - - algorithm - PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. - - A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - Philippe Rocca-Serra - PlanAndPlannedProcess Branch - OBI_0000270 - adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) - algorithm - - - - - - - - - software interpreter - R program, Perl interpreter, Java virtual machine - - A software interpreter is a software application that executes some specified input software. - Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000199 - group:OBI - software interpreter - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - density plot - Density plot of SSC-H and FSC-H. - - A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000179 - group:Flow Cytometry community - density plot - - - - - - - - - report - Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. - - A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on -something that has completed." Should it be restricted to those things -that are completed? For example, a progress report is (usually) about -something that definitely has *not* been completed, or may include -(only) projections. I think the definition would not suffer if the -whole sentence is deleted. - 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion - disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification - PERSON: Alan Ruttenberg - PERSON: Chris Stoeckert - PERSON: Melanie Courtot - GROUP: OBI - OBI_0000099 - report - - - - - - - - - report element - - A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). - There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text - 2009-03-16: needs some more work (clarify relations). - 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. - 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion - Replaced by textual entity and figure - PERSON: Alan Ruttenberg - PERSON: Allyson Lister - PERSON: Melanie Courtot - GROUP:OBI - OBI_0000001 - - obsolete_report element - true - - - - - - - - - binary executable - Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital entity' - person:Jennifer Fostel - group:OBI - OBI_0000222 - - obsolete2_binary executable - true - - - - - - - - - source code module - The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. - - A source code module is a directive information entity that specifies, using a programming language, some algorithm. - person:Alan Ruttenberg - person:Chris Stoeckert - OBI_0000039 - group:OBI - source code module - - - - - - - - - report table - - A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content - 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion - person:Alan Ruttenberg - person:Allyson Lister - group:OBI - OBI_0000265 - - obsolete_report table - true - - - - - - - - - data format specification - - A data format specification is the information content borne by the document published defining the specification. -Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file" - PERSON: Alan Ruttenberg - PlanAndPlannedProcess Branch - OBI branch derived - OBI_0000187 - data format specification - - - - - - - - - data set - Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). - - A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type - 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. - person:Allyson Lister - person:Chris Stoeckert - OBI_0000042 - group:OBI - data set - - - - - - - - - image - - An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - person:Alan Ruttenberg - person:Allyson - person:Chris Stoeckert - OBI_0000030 - group:OBI - image - - - - - - - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - - plan specification - PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. - - A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. - 2014-03-31: A plan specification can have other parts, such as conditional specifications. - 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. - Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved - Alan Ruttenberg - Clint Dowland - OBI Plan and Planned Process branch - OBI_0000344 - 2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them - plan specification - https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 - - - - - - - - - digital document - A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digial entity' - person:Jennifer Fostel - group:OBI - OBI_0000195 - - obsolete2_digital document - true - - - - - - - - - measurement datum - Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. - - A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - 2/2/2009 is_specified_output of some assay? - person:Chris Stoeckert - OBI_0000305 - group:OBI - measurement datum - - - - - - - - - - _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - -Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. - - obsolete_identifier - true - - - - - - - - - version number - - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. - Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version - GROUP: IAO - version number - - - - - - - - - serial number - - A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) - GROUP: IAO - serial number - - - - - - - - - lot number - - A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. - GROUP: IAO - batch number - lot number - - - - - - - - - - A settings datum is a datum that denotes some configuration of an instrument. - 2/3/2009 Feedback from OBI - -This should be a "setting specification". There is a question of whether it is information about a realizable or not. - -Pro other specification are about realizables. -Cons sometimes specifies a quality which is not a realizable. - Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. - setting datum - - - - - - - - - 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - Need to rework digital entity. Digital quality was suggested by Barry. - - obsolete_digital quality - true - - - - - - - - - conclusion textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - 2009/10/23 Alan Ruttenberg: We need to work on the definition still - Person:Alan Ruttenberg - conclusion textual entity - - - - - - - - - - - - - - - - - - - - - - - - - material information bearer - A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. - a brain - a hard drive - - A material entity in which a concretization of an information content entity inheres. - GROUP: IAO - material information bearer - - - - - - - - - histogram - - A histogram is a report graph which is a statistical description of a -distribution in terms of occurrence frequencies of different event classes. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - histogram - - - - - - - - - heatmap - - A heatmap is a report graph which is a graphical representation of data -where the values taken by a variable(s) are shown as colors in a -two-dimensional map. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - GROUP:OBI - heatmap - - - - - - - - - Venn diagram - - A Venn diagram is a report graph showing all hypothetically possible -logical relations between a finite collection of sets. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Venn_diagram - Venn diagram - - - - - - - - - obsolete_survival curve - - A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://www.graphpad.com/www/book/survive.htm - - obsolete_survival curve - true - - - - - - - - - dendrogram - Dendrograms are often used in computational biology to -illustrate the clustering of genes. - - A dendrogram is a report graph which is a tree diagram -frequently used to illustrate the arrangement of the clusters produced by a -clustering algorithm. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - WEB: http://en.wikipedia.org/wiki/Dendrogram - dendrogram - - - - - - - - - scatter plot - Comparison of gene expression values in two samples can be displayed in a scatter plot - - A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - PERSON:Chris Stoeckert - PERSON:James Malone - PERSON:Melanie Courtot - scattergraph - WEB: http://en.wikipedia.org/wiki/Scatterplot - scatter plot - - - - - - - - - - A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. - PERSON:Alan Ruttenberg - PERSON:Joanne Luciano - PERSON:Melanie Courtot - WEB: http://en.wiktionary.org/wiki/photograph - photograph - - - - - - - - - - - - - - - - - - - - - - - - - photographic print - - A photographic print is a material entity upon which a photograph generically depends. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - photographic print - - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - textual entity - Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities - - A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. - MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. - PERSON: Lawrence Hunter - text - textual entity - - - - - - - - - - - - - - - citation - Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. - - A textual entity intended to identify a particular publication. - PERSON: Lawrence Hunter - citation - - - - - - - - - author identification - L. Hunter - - A textual entity intended to identify a particular author - PERSON: Lawrence Hunter - author identification - - - - - - - - - institutional identification - University of Colorado Denver School of Medicine - - A textual entity intended to identify a particular institution - PERSON: Lawrence Hunter - institutional identification - - - - - - - - - - - - - - - caption - Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. - - A textual entity that describes a figure - PERSON: Lawrence Hunter - caption - - - - - - - - - document title - Textual characteristics of traditional and Open Access scientific journals are similar - - A textual entity that names a document - PERSON: Lawrence Hunter - document title - - - - - - - - - table - | T F ---+----- -T | T F -F | F F - - A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions - PERSON: Lawrence Hunter - table - - - - - - - - - table of abbreviations - IAO information artifact ontology -OBI ontology of biomedical investiations -GO gene ontology - - A table where the constituent texts are abbreviations and their expansions - PERSON: Lawrence Hunter - table of abbreviations - - - - - - - - - figure - Any picture, diagram or table - - An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - PERSON: Lawrence Hunter - figure - - - - - - - - - diagram - A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. - - A figure that expresses one or more propositions - PERSON: Lawrence Hunter - diagram - - - - - - - - - document - A journal article, patent application, laboratory notebook, or a book - - A collection of information content entities intended to be understood together as a whole - PERSON: Lawrence Hunter - document - - - - - - - - - - - - - - - - - - - - publication - journal article, newspaper story, book, etc. - - A document that is the output of a publishing process. - PERSON: Chris Stoeckert - PERSON: Jie Zheng - PERSON: Lawrence Hunter - published document - - Revisit the term in Octorber 2020. Improve the defintion. - publication - - - - - - - - - - - - - - - publication about an investigation - Most scientific journal articles - - A publication that is about an investigation - PERSON: Lawrence Hunter - scientific publication - publication about an investigation - - - - - - - - - patent - US Patent 6,449,603 - - A document that has been accepted by a patent authority - PERSON: Lawrence Hunter - patent - - - - - - - - - - - - - - - document part - An abstract, introduction, method or results section. - - An information content entity that is part of a document. - PERSON: Lawrence Hunter - document part - - - - - - - - - - - - - - - abstract - The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. - - A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. - PERSON: Lawrence Hunter - precis - - abstract - - - - - - - - - - - - - - - introduction to a publication about an investigation - Section labelled 'introduction' of a typical scientific journal article - - A part of a publication about an investigation that is about the objective specification (why the investigation is being done) - PERSON: Lawrence Hunter - background - introduction - overview - - introduction to a publication about an investigation - - - - - - - - - - - - - - - methods section - The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. - - A part of a publication about an investigation that is about the study design of the investigation - PERSON: Lawrence Hunter - experimental - experimental methods - experimental procedures - experimental section - method - methodology - methods - - methods section - - - - - - - - - - - - - - - results section - The section labelled 'results' in a typical scientific journal article - - A part of a publication about an investigation that is about a study design execution - PERSON: Lawrence Hunter - results - results section - - - - - - - - - discussion section of a publication about an investigation - - A part of a publication about an investigation that is about the study interpretation of the investigation - PERSON: Lawrence Hunter - discussion - discussion section - discussions - - discussion section of a publication about an investigation - - - - - - - - - - - - - - - references section - The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" - - A part of a document that has citations as parts - PERSON: Lawrence Hunter - literature cited - reference - reference list - references - - references section - - - - - - - - - - - - - - - author list - Lawrence Hunter and Kevin Brettonel Cohen - - A part of a document that enumerates the authors of the document - PERSON: Lawrence Hunter - author list - - - - - - - - - - - - - - - institution list - The University of Colorado Denver School of Medicine and the University of Colorado Boulder. - - A part of a document that has parts that are institution identifications associated with the authors of the document - PERSON: Lawrence Hunter - institution list - - - - - - - - - author contributions section - LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. - - A part of a publication that is about the specific contributions of each author - PERSON: Lawrence Hunter - author contributions - authors' contribution - authors' contributions - authors' roles - contributions by the authors - contributorship - - author contributions section - - - - - - - - - acknowledgements section - The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript - - Part of a publication that is about the contributions of people or institutions other than the authors. - PERSON: Lawrence Hunter - acknowledgement - acknowledgements - acknowledgment - acknowledgments - - acknowledgements section - - - - - - - - - - - - - - - footnote - The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. - - A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. - PERSON: Lawrence Hunter - endnote - footnotes - - footnote - - - - - - - - - supplementary material to a document - - A part of a document that is segregated from the rest of the document due to its size - PERSON: Lawrence Hunter - additional file - additional files - additional information - appendix - electronic supplementary material - electronic supplementary materials - supplemental data - supplemental information - supplemental material - supplementary data - supplementary files - supplementary information - supplementary material - supplementary materials - supporting information - - supplementary material to a document - - - - - - - - - table of contents - - A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of contents - - - - - - - - - table of figures - - A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). - PERSON: Lawrence Hunter - table of figures - - - - - - - - - running title - - A shorter version of a document title - PERSON: Lawrence Hunter - running title - - - - - - - - - copyright section - This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. - - A document part that describes legal restrictions on making or distributing copies of the document - PERSON: Lawrence Hunter - copyright section - - - - - - - - - - - - - - - - - - 1 - - - - A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude - 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - Alan Ruttenberg - AR notes: We need to discuss whether it should include site. - cartesian spatial coordinate datum - http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region - Alan Ruttenberg - one dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region - Alan Ruttenberg - two dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - 1 - - - - - - 1 - - - - A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region - Alan Ruttenberg - three dimensional cartesian spatial coordinate datum - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of length quality - Alan Ruttenberg - length measurement datum - - - - - - - - - - - - - - - - - - denotator type - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measurement of mass quality - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - mass measurement datum - - - - - - - - - hypothesis textual entity - that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 - - A textual entity that expresses an assertion that is intended to be tested. - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - hypothesis textual entity - - - - - - - - - - - - - - - - - - - - - - - - A scalar measurement datum that is the result of measuring a temporal interval - 2009/09/28 Alan Ruttenberg. Fucoidan-use-case - Person:Alan Ruttenberg - time measurement datum - - - - - - - - - - A textual entity that is used as directive to deliver something to a person, or organization - 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 - postal address - - - - - - - - - email address - - Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 - Person:Alan Ruttenberg - Person:Chris Stoeckart - email address - - - - - - - - - author role - - A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - author role - - - - - - - - - - - - - - - - - - - - - - A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing - Person:Alan Ruttenberg - data item extraction from journal article - - - - - - - - - - A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. - Person: Jie Zheng - https://en.wikipedia.org/wiki/Publishing - - VEuPathDB - publishing process - - - - - - - - - - A document that is in preparation for submission to be published. - PERSON: Jie Zheng - EFO_0001795 in preparation - - VEuPathDB - document in preparation for publication - - - - - - - - - - - - - - - - - - - - - Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. - - A planned process in which a document is created or added to by including the specified input in it. - 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape - Bjoern Peters - wikipedia http://en.wikipedia.org/wiki/Documenting - documenting - - - - - - - - - line graph - - A line graph is a type of graph created by connecting a series of data -points together with a line. - PERSON:Chris Stoeckert - PERSON:Melanie Courtot - line chart - GROUP:OBI - WEB: http://en.wikipedia.org/wiki/Line_chart - line graph - - - - - - - - - - - - - - - - - - - - - A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. - - A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. - Person:Alan Ruttenberg - Person:Bjoern Peters - Person:Melanie Courtot - assigning a CRID - assigning a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - - - - Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. - - A planned process in which a CRID registry associates an information content entity with a CRID symbol - PERSON:Alan Ruttenberg - associating information with a CRID in the CRID registry - associating information with a centrally registered identifier in its registry - - - - - - - - - a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. - MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. - - obsolete_establishing a CRID registry - true - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID symbol - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier symbol - - - - - - - - - - - - - - - - - - - - - - - - - - The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed. - - An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. - 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records'). - Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation. - Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered. - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID - Original proposal from Bjoern, discussions at IAO calls - centrally registered identifier - - - - - - - - - PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. - - A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. - Justin Whorton - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - CRID registry - Original proposal from Bjoern, discussions at IAO calls - https://github.com/information-artifact-ontology/IAO/issues/237 - centrally registered identifier registry - - - - - - - - - - - - - - - - - - - - - - - - - - - Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. - - A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol - PERSON: Alan Ruttenberg - PERSON: Bill Hogan - PERSON: Bjoern Peters - PERSON: Melanie Courtot - looking up a CRID - looking up a centrally registered identifier - - - - - - - - - - - - - - - - - - - - - - - - time stamped measurement datum - - - - - - - - - - - - - - - pmid:20604925 - time-lapse live cell microscopy - - A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. - Alan Ruttenberg - experimental time series - time sampled measurement data set - - - - - - - - - written name - "Bill Clinton" - "The Eiffel Tower" - "United States of America" - - A textual entity that denotes a particular in reality. - PERSON: Bill Hogan - https://github.com/information-artifact-ontology/IAO/issues/114 - The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. - written name - - - - - - - - - - A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software method - - - - - - - - - - A software module is software composed of a collection of software methods. - PERSON: Melanei Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software module - - - - - - - - - - A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software library - - - - - - - - - - A software application is software that can be directly executed by some processing unit. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software application - - - - - - - - - - A software script is software whose instructions can be executed using a software interpreter. - PERSON: Melanie Courtot - PERSON: Michel Dumontier - https://github.com/information-artifact-ontology/IAO/issues/80 - software script - - - - - - - - - abbreviation textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. - A textual entity listing abbreviations and their expansions that are used in a document. - PERSON: Bill Baumgartner - - abbreviation textual entity - - - - - - - - - - - - - - - abbreviations section - The section labelled 'abbreviations' in a typical scientific journal article. - A part of a document where abbreviations and their long-forms used within the document are listed. - PERSON: Bill Baumgartner - abbreviation and acronyms - abbreviation list - abbreviations - abbreviations and acronyms - abbreviations list - abbreviations used - definitions for abbreviations - list of abbreviations - list of abbreviations used - non-standard abbreviations - nonstandard abbreviations - nonstandard abbreviations and acronyms - - - abbreviations section - - - - - - - - - - - - - - - author information section - The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) - A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - author information - authors’ information - biographies - contributor information - - - author information section - - - - - - - - - author information textual entity - From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): - -IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. - A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. - PERSON: Bill Baumgartner - - author information textual entity - - - - - - - - - - - - - - - author summary section - The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) - A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. - PERSON: Bill Baumgartner - author summary - summary - synopsis - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) - - author summary section - - - - - - - - - author summary textual entity - From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): - - -The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. - A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - PERSON: Bill Baumgartner - Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). - - author summary textual entity - - - - - - - - - - - - - - - availability section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. - PERSON: Bill Baumgartner - availability - availability of data - data archiving - data availability - data availability statement - data sharing statement - - - availability section - - - - - - - - - availability textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -Project home page:http://krux.googlecode.com - A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. - PERSON: Bill Baumgartner - - availability textual entity - - - - - - - - - - - - - - - case report section - The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) - A part of a document about the medical history of a specific patient as it relates to the topic of the document. - PERSON: Bill Baumgartner - case presentation - case report - - case report section - - - - - - - - - case report textual entity - Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): - -The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. - A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. - PERSON: Bill Baumgartner - - case report textual entity - - - - - - - - - - - - - - - conclusion section - The section labelled 'conclusion' in a typical scientific journal article. - A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. - PERSON: Bill Baumgartner - concluding remarks - conclusion - conclusions - findings - summary - - conclusion section - - - - - - - - - - - - - - - conflict of interest section - The section labelled 'conflict of interest statement' in a typical scientific journal article. - A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. - PERSON: Bill Baumgartner - authors' disclosures of potential conflicts of interest - competing financial interests - competing interests - conflict of interest - conflict of interest statement - conflict of interests - conflicts of interest - declaration of competing interest - declaration of competing interests - declaration of interest - declaration of interests - disclosure of conflict of interest - disclosure of potential conflicts of interest - duality of interest - statement of interest - - - conflict of interest section - - - - - - - - - conflict of interest statement - SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] - A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. - PERSON: Bill Baumgartner - - conflict of interest textual entity - - - - - - - - - - - - - - - consent section - The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) - A part of a document about the consent process that was used to enroll patients in a study. - PERSON: Bill Baumgartner - consent - - consent section - - - - - - - - - consent textual entity - From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. - A textual entity that documents the consenting process used to enroll patients in a study. - PERSON: Bill Baumgartner - - consent textual entity - - - - - - - - - - - - - - - ethical approval section - The section labelled 'ethical approval' in a typical scientific journal article. - A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. - PERSON: Bill Baumgartner - ethical approval - ethical requirements - ethics - ethics statement - - - ethical approval section - - - - - - - - - - - - - - - ethical approval textual entity - From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - -The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. - A textual entity that documents the ethical approval of some study design. - PERSON: Bill Baumgartner - - ethical approval textual entity - - - - - - - - - - - - - - - figures section - The section labelled 'figures' in a typical scientific journal article. - A part of a document that contains one or more figures. - PERSON: Bill Baumgartner - figures - - figures section - - - - - - - - - - - - - - - funding source declaration section - The section labelled 'funding' in a typical scientific journal article. - A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. - PERSON: Bill Baumgartner - financial support - funding - funding information - funding sources - funding statement - funding/support - grants - role of the funding source - source of funding - sources of funding - study funding - - - funding source declaration section - - - - - - - - - funding souce declaration textual entity - From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): - -This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. - A textual entity documenting the source of funding that supported some study. - PERSON: Bill Baumgartner - - funding source declaration textual entity - - - - - - - - - - - - - - - future directions section - The section labelled 'future directions' in a typical scientific journal article. - A part of a document detailing extensions of the described work that may be implemented at some future point in time. - PERSON: Bill Baumgartner - future challenges - future considerations - future developments - future directions - future outlook - future perspectives - future plans - future prospects - future research - future research directions - future studies - future work - outlook - - - future directions section - - - - - - - - - future directions textual entity - Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): - -In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. - A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. - PERSON: Bill Baumgartner - - future directions textual entity - - - - - - - - - - - - - - - genome announcement section - The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) - A document part announcing the publication of a novel draft genome sequence. - PERSON: Bill Baumgartner - genome announcement - - genome announcement section - - - - - - - - - genome announcement textual entity - Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): - -Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). - A textual entity that describes the generation and public release of a novel, draft genome sequence. - PERSON: Bill Baumgartner - - genome announcement textual entity - - - - - - - - - keyword textual entity - From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): - -Exon orthology; alternative splicing; exon duplication; intron-exon structure. - A textual entity listing keywords indicating the major theme(s) of a document. - PERSON: Bill Baumgartner - - keyword textual entity - - - - - - - - - - - - - - - keywords section - The section labelled 'keywords' in a typical scientific journal article. - A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. - PERSON: Bill Baumgartner - keywords - - keywords section - - - - - - - - - - - - - - - - - - - - - study limitations section - The section labelled 'limitations' in a typical scientific journal article. - A part of a document about biases or short comings related to the study design and execution. - PERSON: Bill Baumgartner - limitations - study limitations - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations section - - - - - - - - - study limitations textual entity - Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). - -Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. - A textual entity addressing a shortcoming or bias of a study design or execution. - PERSON: Bill Baumgartner - Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) - - study limitations textual entity - - - - - - - - - materials section - The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) - A part of a document about the materials required to reproduce the content of the document. - PERSON: Bill Baumgartner - materials - - materials section - - - - - - - - - notes section - The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. - PERSON: Bill Baumgartner - notes - - notes section - - - - - - - - - - - - - - - patients section - The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) - A part of a document about the patients that participated in a study. - PERSON: Bill Baumgartner - - patients section - - - - - - - - - patients textual entity - Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): - -Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. - A textual entity expressing information regarding the patients used in a study. - PERSON: Bill Baumgartner - - patients textual entity - - - - - - - - - - - - - - - pre-publication history section - The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) - A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. - PERSON: Bill Baumgartner - notice of republication - pre-publication history - - pre-publication history section - - - - - - - - - pre-publication history textual entity - From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): - -The pre-publication history for this paper can be accessed here: -http://www.biomedcentral.com/1471-2253/13/33/prepub - A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. - PERSON: Bill Baumgartner - - pre-publication history textual entity - - - - - - - - - - - - - - - related work section - The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) - A part of a document about work in other publications that is relevant to the content of the document. - PERSON: Bill Baumgartner - related literature - related work - - related work section - - - - - - - - - related work textual entity - Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): - -Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). - - - A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. - PERSON: Bill Baumgartner - - related work textual entity - - - - - - - - - - - - - - - requirements section - The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). - A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. - PERSON: Bill Baumgartner - requirements - - requirements section - - - - - - - - - requirements textual entity - From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -• Operating systems: Platform independent - -• Programming language: Matlab, R, Python - -• Other requirements: None - -• License: GNU GPL v3 - -• Any restrictions to use by non-academics: None - A textual entity that expresses the requirements necessary to use a resource, e.g. software. - PERSON: Bill Baumgartner - - requirements textual entity - - - - - - - - - statistical analysis textual entity - From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): - -Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. - A textual entity documenting statistical analysis tools and techniques employed. - PERSON: Bill Baumgartner - - statistical analysis textual entity - - - - - - - - - - - - - - - statistical analysis section - The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) - A part of the document used to describe the statistical methodologies employed in the work presented in the document. - PERSON: Bill Baumgartner - statistical analysis - - statistical analysis section - - - - - - - - - - - - - - - tables section - The section labelled 'tables' in a typical scientific journal article. - A part of a document that contains one or more tables. - PERSON: Bill Baumgartner - tables - - tables section - - - - - - - - - An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. - Mathias Brochhausen - postal code - - - - - - - - - A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. - Mathias Brochhausen - Postal delivery route - - - - - - - - - A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. - Mathias Brochhausen - ZIP code - zone improvement plan code - - - - - - - - - - - - - - - - - - - - - database extract, transform, and load process - A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. - Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second - Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. - PERSON:Alan Ruttenberg - ETL - WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load - - - database extract, transform, and load process - - - - - - - - - - descriptive data section - - A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made. - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.equator-network.org/reporting-guidelines/prisma/ - - ONE ontology - descriptive data section - - - - - - - - - additional results section - - A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.) - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.equator-network.org/reporting-guidelines/consort/ - https://www.equator-network.org/reporting-guidelines/prisma/ - https://www.equator-network.org/reporting-guidelines/strobe/ - - ONE ontology - additional results section - - - - - - - - - research participants section - - A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.). - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.equator-network.org/reporting-guidelines/consort/ - https://www.equator-network.org/reporting-guidelines/prisma/ - https://www.equator-network.org/reporting-guidelines/strobe-nut/ - - ONE ontology - research participants section - - - - - - - - - measurement methods section - - A methods section that describes details of data assessment methods (data measurement). - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.equator-network.org/reporting-guidelines/strobe/ - - ONE ontology - measurement methods section - - - - - - - - - research settings section - - A document part that describes the physical/social/cultural conditions around a research trial. - PERSON: Chen Yang - PERSON: Jie Zheng - https://www.ncbi.nlm.nih.gov/books/NBK262175/ - - ONE ontology - research settings section - - - - - - - - - study bias section - - A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others. - PERSON: Chen Yang - PERSON: Jie Zheng - DOI: 10.1097/PRS.0b013e3181de24bc - - ONE ontology - study bias section - - - - - - - - - graphical abstract - - An abstract that is pictorial summary of the main findings described in the document. - PERSON: Jie Zheng - PERSON: Tim Beck - visual abstract - https://www.elsevier.com/authors/journal-authors/graphical-abstract - - Biomedical literature NLP project - graphical abstract - - - - - - - - - - A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor. - "You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/] - This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25) - http://orcid.org/0000-0002-1595-3213 - ORCID ID - ORCiD - Open Researcher and Contributor ID - Open Researcher and Contributor Identifier - https://orcid.org/ - https://github.com/information-artifact-ontology/IAO/issues/259 - ORCID identifier - - - - - - - - - - - - - - - - - - - - - - - - identifier - An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. - Justin Whorton - Mathias Brochhausen - proper name - https://github.com/information-artifact-ontology/IAO/issues/237 - Mathias Brochhausen - Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) - identifier - - - - - - - - - alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems - An information content entity that is a fundamental unit in a written language. - Justin Whorton - http://en.wikipedia.org/wiki/Grapheme - https://github.com/information-artifact-ontology/IAO/issues/237 - Mathias Brochhausen - Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there. - grapheme - - - - - - - - - - - - - - - - - - - - A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. - Justin Whorton - Mathias Brochhausen - dubbing process - naming - https://github.com/information-artifact-ontology/IAO/issues/237 - Mathias Brochhausen - identifier creating process - - - - - - - - - An identifier referring to an individual entity that is ascribed personhood by the user of the identifier. - Justin Whorton - Mathias Brochhausen - http://en.wikipedia.org/wiki/Personal_name - https://github.com/information-artifact-ontology/IAO/issues/237 - Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name) - Personal names to not include names of fictional characters, e.g. Sherlock Holmes. - Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB) - personal name - - - - - - - - - A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name - Justin Whorton - Mathias Brochhausen - first name - http://en.wikipedia.org/wiki/Given_name - https://github.com/information-artifact-ontology/IAO/issues/237 - given name - - - - - - - - - An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. - Justin Whorton - Mathias Brochhausen - last name - surname - http://en.wikipedia.org/wiki/Family_name - https://github.com/information-artifact-ontology/IAO/issues/237 - family name - - - - - - - - - - - - - - - An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. - Alan Ruttenberg - Justin Whorton - Mathias Brochhausen - code map - code system - codeset - coding system - controlled vocabulary - https://github.com/information-artifact-ontology/IAO/issues/237 - Alan Ruttenberg - Clint Dowland - Matt Diller - Sarah Bost - William R. Hogan - Code sets might include non-entities/things (e.g. missing thumbs). - Does not imply absence vs. presence of any taxonomy. - Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. - Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. - -When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). - For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). - For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. - Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. - The information content entities do not denote each other. - code set - - - - - - - - - ontology module - I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. - ontology file - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - ontology module - - - - - - - - - base ontology module - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - base ontology module - - - - - - - - - - editors ontology module - An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. - source ontology module - editors ontology module - - - - - - - - - main release ontology module - An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. - TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module - main release ontology module - - - - - - - - - bridge ontology module - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - bridge ontology module - - - - - - - - - - import ontology module - A subset ontology module that is intended to be imported from another ontology. - TODO: add axioms that indicate this is the output of a module extraction process. - import file - import ontology module - - - - - - - - - - subset ontology module - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - subset ontology module - - - - - - - - - - - curation subset ontology module - A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. - curation subset ontology module - - - - - - - - - analysis ontology module - An ontology module that is intended for usage in analysis or discovery applications. - analysis subset ontology module - - - - - - - - - single layer ontology module - A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. - ribbon subset - single layer subset ontology module - - - - - - - - - exclusion subset ontology module - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - exclusion subset ontology module - - - - - - - - - external import ontology module - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - external import ontology module - - - - - - - - - species subset ontology module - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - species subset ontology module - - - - - - - - - - reasoned ontology module - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - reasoned ontology module - - - - - - - - - - generated ontology module - An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. - TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process - generated ontology module - - - - - - - - - template generated ontology module - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - template generated ontology module - - - - - - - - - - - - taxonomic bridge ontology module - taxonomic bridge ontology module - - - - - - - - - ontology module subsetted by expressivity - ontology module subsetted by expressivity - - - - - - - - - obo basic subset ontology module - A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. - -Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). - -An ontology is OBO Basic if and only if it has the following characteristics: -DAG -Unidirectional -No Dangling Clauses -Fully Asserted -Fully Labeled -No equivalence axioms -Singly labeled edges -No qualifier lists -No disjointness axioms -No owl-axioms header -No imports - obo basic subset ontology module - - - - - - - - - - ontology module subsetted by OWL profile - ontology module subsetted by OWL profile - - - - - - - - - EL++ ontology module - EL++ ontology module - - - - - - - - - planned process - A process that realizes a plan which is the concretization of a plan specification. - - planned process - - - - - - - - - investigation - a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). - - investigation - - - - - - - - - study design execution - a planned process that carries out a study design - - study design execution - - - - - - - - - data transformation - A planned process that produces output data from input data. - - data transformation - - - - - - - - - study design - A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. - - study design - - - - - - - - - morphology - A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. - - morphology - - - - - - - - - length - A 1-D extent quality which is equal to the distance between two points. - - length - - - - - - - - - mass - A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. - - mass - - - - - - - - - physical quality - A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. - - physical quality - - - - - - - - - physical object quality - A quality which inheres in a continuant. - - physical object quality - - - - - - - - - length unit - - length unit - - - - - - - - - mass unit - - mass unit - - - - - - - - - time unit - - time unit - - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - - - failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - ready for release - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - - obsolete_core - true - - - - - - - - - - placeholder removed - placeholder removed - - - - - - - - - terms merged - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. - We expect to be able to mine these new reasons and add instances as required. - obsolete_other - true - - - - - - - - - universal - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - defined class - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - named class expression - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 - out of scope - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/tmp/mirror-ido.owl b/src/ontology/tmp/mirror-ido.owl deleted file mode 100644 index 75d3031..0000000 --- a/src/ontology/tmp/mirror-ido.owl +++ /dev/null @@ -1,12112 +0,0 @@ - - - - - en - Jie Zheng - Alan Ruttenberg - Albert Goldfain - Alexander Diehl - Barry Smith - Bjoern Peters - Lindsay Cowell - 2017-11-03T15:13:52 - - The core Infectious Disease Ontology is an ontology of entities generally relevant to both the biomedical and clinical aspects of infectious diseases, including terms such as 'pathogen', 'host', 'vector', and 'vaccine'. The structure of IDO adheres to the Basic Formal Ontology. Terms in IDO that are within the scope of other OBO Foundry ontologies, such as the Gene Ontology, are derived from those ontologies. Other terms are defined as cross-products of terms from Foundry ontologies to the extent possible. For more information, see http://www.infectiousdiseaseontology.org/Home.html. - http://www.infectiousdiseaseontology.org - 2017-11-03 - - - - - - - - - - - - - - - - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - editor preferred term - - - - - - - - example - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - example of usage - - - - - - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - OBI_0000281 - has curation status - - - - - - - - definition - - The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - definition - definition - textual definition - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obfoundry.org/obo/obi> - - editor note - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - term editor - - - - - - - - alternative term - - An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - alternative term - - - - - - - - definition source - - formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - - definition source - - - - - - - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - - - - - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - - curator note - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - - - - - - is denotator type - relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - - - - - - - - imported from - - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - - imported from - - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - antisymmetric property - part_of antisymmetric property xsd:true - use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - - - - - - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - - - - - - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - - - - - - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - - - - - - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - - elucidation - - - - - - - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - - has associated axiom(nl) - - - - - - - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - - has associated axiom(fol) - - - - - - - - is allocated id range - Add as annotation triples in the granting ontology - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - is allocated id range - - - - - - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - - has axiom label - - - - - - - - term replaced by - - Add as annotation triples in the granting ontology - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - term replaced by - - - - - - - - temporal interpretation - https://github.com/oborel/obo-relations/wiki/ROAndTime - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - shorthand - - - - - - - - - - - - - - - - - - - - label - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - part of - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - - - - preceded by - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - preceded by - - - - - - - - - - - precedes - precedes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - results_in - - - - - - - - - has_material_basis_in - - - - - - - - - inheres in - this fragility inheres in this vase - this red color inheres in this apple - a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence - A dependent inheres in its bearer at all times for which the dependent exists. - inheres_in - - inheres in - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - bearer of - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. - is concretized as - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - disposition of - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - location_of - - location of - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - located in - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - - - - x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y - We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit - Chris Mungall - David Hill - Tanya Berardini - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - regulates - - - - - - - - - - x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y - Chris Mungall - - negatively regulates (process to process) - negatively regulates - - - - - - - - - x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y - Chris Mungall - - positively regulates (process to process) - positively regulates - - - - - - - - - - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' - - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) - capable of - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. - Chris Mungall - produces - has output - - - - - - - - - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - Chris Mungall - GOC:mtg_berkeley_2013 - results_in_formation_of - results in formation of - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - - - - - - - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. - obsolete dependent continuant - true - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - process - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - - - - - - - - - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - disposition - - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - - - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - realizable entity - - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - specifically dependent continuant - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - - - - - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - role - - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - - - - - - - - - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - site - - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - - - - - - - - - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - function - - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - - - - - - - material - MaterialEntity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - material entity - - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - - - - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - - immaterial entity - - - - - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - - - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history - - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - - - - - - - - - - - - - - - - - - - - - A part of a multicellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a multicellular organism with granularity above the level of a protein complex. - - anatomical entity - - - - - - - - - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - - molecular entity - - - - - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - - cell - cell - - - - - - - - - An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. - - leukocyte - - - - - - - - - The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. - - reproduction - - - - - - - - - An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). - - adaptive immune response - - - - - - - - - Any process involved in the carrying out of an immune response by a leukocyte. - - leukocyte mediated immunity - - - - - - - - - Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. - - immune response - - - - - - - - - An immune response mediated through a body fluid. - - humoral immune response - - - - - - - - - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - - biological_process - - - - - - - - - A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. - - immunoglobulin complex - - - - - - - - - An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. - - B cell receptor complex - - - - - - - - - A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition. - - developmental process - - - - - - - - - A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. - - macromolecular complex - - - - - - - - - The increase in size or mass of an entire organism, a part of an organism or a cell. - - growth - - - - - - - - - A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. - - T cell receptor complex - - - - - - - - - A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells. - - FtsZ-dependent cytokinesis - - - - - - - - - An interaction between two organisms living together in more or less intimate association. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. - - symbiosis, encompassing mutualism through parasitism - - - - - - - - - The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction. - - adhesion of symbiont to host - - - - - - - - - Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. - - entry into host - - - - - - - - - Penetration by an organism into its host organism via active breaching of the physical barriers of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. - - entry into host through host barriers - - - - - - - - - Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. - - innate immune response - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant. - - negative regulation of viral process - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. - - negative regulation of immune response - - - - - - - - - Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). - - negative regulation of developmental process - - - - - - - - - Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation. - - Gene Ontology: http://purl.obolibrary.org/obo/go.owl - establishment of localization - - - - - - - - - A biological process which involves another organism of the same or different species. - - multi-organism process - - - - - - - - - Any process that modulates a measurable attribute of any biological process, quality or function. - - biological regulation - - - - - - - - - An interaction between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other. - - mutualism - - - - - - - - - An interaction between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected. - - commensalism - - - - - - - - - data item - - - - - - - - - information content entity - - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - - - - - - - - - - - - - - - - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - - - - - - - - - - - - - - - - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - - - - - - - _obsolete_process - true - - - - - - - - - _obsolete_role - true - - - - - - - - - _obsolete_quality - true - - - - - - - - - _obsolete_object - true - - - - - - - - - 'the degree of pathogenicitynnpathogenicity and virulence are used in some communities as synonyms.'-ID[O]:0000004: the degree of pathogenicitynnpathogenicity and virulence are used in some communities as synonyms. - id 'virulence'-ID[O]:0000004 from IDO 2007. May have replacement - TBD - _obsolete_virulence - true - - - - - - - - - _obsolete_swollen - true - - - - - - - - - _obsolete_toxicity - true - - - - - - - - - _obsolete_active - true - - - - - - - - - _obsolete_contagious - true - - - - - - - - - 'infection has occurred, but it might not have manifested itselfnquality of being in a non replicative statentime to manifest itself na pathogen when it is in a non replicative state'-ID[O]:0000009: infection has occurred, but it might not have manifested itselfnquality of being in a non replicative statentime to manifest itself na pathogen when it is in a non replicative state - id 'latency'-ID[O]:0000009 from IDO 2007. May have replacement - TBD - _obsolete_latency - true - - - - - - - - - _obsolete_immunosuppressed - true - - - - - - - - - _obsolete_exogenous - true - - - - - - - - - _obsolete_immunity - true - - - - - - - - - _obsolete_protective - true - - - - - - - - - _obsolete_temperature - true - - - - - - - - - _obsolete_inactivated - true - - - - - - - - - _obsolete_mortality - true - - - - - - - - - _obsolete_pandemic - true - - - - - - - - - 'total number of cases of a particular disease at a given time in a particular population divided by the number of individuals in that particular populationnnthe burden of a disease in a population'-ID[O]:0000019: total number of cases of a particular disease at a given time in a particular population divided by the number of individuals in that particular populationnnthe burden of a disease in a population - id 'prevalence'-ID[O]:0000019 from IDO 2007. May have replacement - TBD - _obsolete_prevalence - true - - - - - - - - - _obsolete_epidemic - true - - - - - - - - - _obsolete_infected - true - - - - - - - - - _obsolete_live - true - - - - - - - - - _obsolete_zoonotic - true - - - - - - - - - _obsolete_immunocompromised - true - - - - - - - - - 'the ability of the biotic entity to cause disease in a host of a given typenndo we need to say damage instead of disease?nnpathogenicity and virulence are used as synonyms in some communities'-ID[O]:0000025: the ability of the biotic entity to cause disease in a host of a given typenndo we need to say damage instead of disease?nnpathogenicity and virulence are used as synonyms in some communities - id 'pathogenicity'-ID[O]:0000025 from IDO 2007. May have replacement - TBD - _obsolete_pathogenicity - true - - - - - - - - - _obsolete_tropism - true - - - - - - - - - _obsolete_drug resistance - true - - - - - - - - - _obsolete_antibiotic resistance - true - - - - - - - - - 'number of new cases in a given period of time'-ID[O]:0000029: number of new cases in a given period of time - id 'incidence'-ID[O]:0000029 from IDO 2007. May have replacement - TBD - _obsolete_incidence - true - - - - - - - - - _obsolete_invasive - true - - - - - - - - - _obsolete_endogenous - true - - - - - - - - - _obsolete_attenuated - true - - - - - - - - - _obsolete_morbidity - true - - - - - - - - - _obsolete_endemic - true - - - - - - - - - _obsolete_fusion protein - true - - - - - - - - - _obsolete_colonizer - true - - - - - - - - - _obsolete_commensal - true - - - - - - - - - _obsolete_parasite - true - - - - - - - - - _obsolete_symbiant - true - - - - - - - - - 'role played by a portion of substance to promote virulencennmagnitudendegree of pathogenesis'-ID[O]:0000040: role played by a portion of substance to promote virulencennmagnitudendegree of pathogenesis - id 'virulence factor'-ID[O]:0000040 from IDO 2007. May have replacement - TBD - _obsolete_virulence factor - true - - - - - - - - - _obsolete_route of entry - true - - - - - - - - - _obsolete_invasin - true - - - - - - - - - _obsolete_toxin - true - - - - - - - - - _obsolete_endotoxin - true - - - - - - - - - _obsolete_exotoxin - true - - - - - - - - - _obsolete_sign - true - - - - - - - - - _obsolete_treatment - true - - - - - - - - - 'look at mathias's ontology of cancer to get all the subterms...its under quality there'-ID[O]:0000048: look at mathias's ontology of cancer to get all the subterms...its under quality there - id 'symptom'-ID[O]:0000048 from IDO 2007. May have replacement - TBD - _obsolete_symptom - true - - - - - - - - - _obsolete_antimicrobial - true - - - - - - - - - _obsolete_medicine - true - - - - - - - - - _obsolete_therapeutic - true - - - - - - - - - _obsolete_vaccine - true - - - - - - - - - _obsolete_antibiotic - true - - - - - - - - - 'role played by portion of physical substance which promotes colonization'-ID[O]:0000054: role played by portion of physical substance which promotes colonization - id 'colonization factor'-ID[O]:0000054 from IDO 2007. May have replacement - TBD - _obsolete_colonization factor - true - - - - - - - - - 'role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host'-ID[O]:0000055: role played by portion of physical substance utilized by an organism in order to establish adherence to a surface in a host - id 'adhesion factor'-ID[O]:0000055 from IDO 2007. May have replacement - TBD - _obsolete_adhesion factor - true - - - - - - - - - _obsolete_host - true - - - - - - - - - _obsolete_carrier - true - - - - - - - - - _obsolete_chronic carrier - true - - - - - - - - - 'holding place for a potential pathogen...animate or inanimate'-ID[O]:0000059: holding place for a potential pathogen...animate or inanimate - id 'reservoir'-ID[O]:0000059 from IDO 2007. May have replacement - TBD - _obsolete_reservoir - true - - - - - - - - - 'inanimate holder, is water a fomite or only a reservoir?'-ID[O]:0000060: inanimate holder, is water a fomite or only a reservoir? - id 'fomite'-ID[O]:0000060 from IDO 2007. May have replacement - TBD - _obsolete_fomite - true - - - - - - - - - _obsolete_mobile genetic element - true - - - - - - - - - _obsolete_pathogenicity island - true - - - - - - - - - 'holder and a carrier (actively transmits) and living: potentially make a cross product. every vector comes into contact with the target. (from one host to another?)'-ID[O]:0000063: holder and a carrier (actively transmits) and living: potentially make a cross product. every vector comes into contact with the target. (from one host to another?) - id 'vector'-ID[O]:0000063 from IDO 2007. May have replacement - TBD - _obsolete_vector - true - - - - - - - - - _obsolete_pathogen - true - - - - - - - - - _obsolete_dependovirus - true - - - - - - - - - _obsolete_infectious agent - true - - - - - - - - - _obsolete_opportunistic pathogen - true - - - - - - - - - _obsolete_emerging pathogen - true - - - - - - - - - _obsolete_primary pathogen - true - - - - - - - - - _obsolete_prion - true - - - - - - - - - _obsolete_initiation of infection - true - - - - - - - - - _obsolete_disruption of body surface - true - - - - - - - - - _obsolete_disruption of normal microbioflora - true - - - - - - - - - 'create cross products for "host" and "pathogen" that will be part of this process.'-ID[O]:0000074: create cross products for "host" and "pathogen" that will be part of this process. - id 'pathogen adherence to host cell'-ID[O]:0000074 from IDO 2007. May have replacement - TBD - _obsolete_pathogen adherence to host cell - true - - - - - - - - - _obsolete_nonspecific adherence - true - - - - - - - - - _obsolete_specific adherence - true - - - - - - - - - _obsolete_afimbrial specific adherence - true - - - - - - - - - _obsolete_fimbrial specific adherence - true - - - - - - - - - _obsolete_penetration of epithelial barrier - true - - - - - - - - - _obsolete_penetration via injury of epithelial barrier - true - - - - - - - - - _obsolete_transcytosis - true - - - - - - - - - _obsolete_utilization of membranous cell gateway - true - - - - - - - - - 'the process by which an infectious agent passes from one organism to another organism'-ID[O]:0000083: the process by which an infectious agent passes from one organism to another organism - id 'transmission'-ID[O]:0000083 from IDO 2007. May have replacement - TBD - _obsolete_transmission - true - - - - - - - - - 'GO:nthe specific processes that generate the ability of an organism to cause disease in anothernnnThis is defined in GO so import.'-ID[O]:0000084: GO:nthe specific processes that generate the ability of an organism to cause disease in anothernnnThis is defined in GO so import. - id 'pathogenesis'-ID[O]:0000084 from IDO 2007. May have replacement - TBD - _obsolete_pathogenesis - true - - - - - - - - - _obsolete_penetration of host cell - true - - - - - - - - - _obsolete_engulfment - true - - - - - - - - - _obsolete_fusion with host cell membrane - true - - - - - - - - - _obsolete_membrane invagination - true - - - - - - - - - _obsolete_passage through cell membrane - true - - - - - - - - - _obsolete_engulfment by nonphagocyte - true - - - - - - - - - _obsolete_engulfment by phagocyte - true - - - - - - - - - _obsolete_damaging host cells and tissues in subepithelial space - true - - - - - - - - - _obsolete_induction of damaging host immune response - true - - - - - - - - - _obsolete_pathogen-induced apoptosis - true - - - - - - - - - _obsolete_pathogen-induced necrosis - true - - - - - - - - - _obsolete_virus-induced cytopathogenesis - true - - - - - - - - - _obsolete_pathogen spread through host - true - - - - - - - - - 'comment about the instances:nncollections of etiologically connected cases of infectious disease in a given population'-ID[O]:0000098: comment about the instances:nncollections of etiologically connected cases of infectious disease in a given population - id 'infectious disease'-ID[O]:0000098 from IDO 2007. May have replacement - TBD - _obsolete_infectious disease - true - - - - - - - - - _obsolete_pathogen evasion of host immune response - true - - - - - - - - - 'the process by which an infectious disease establishes itself in a new population (or at a sufficiently higher rate? higher prevalence and/or higher incidence)'-ID[O]:0000101: the process by which an infectious disease establishes itself in a new population (or at a sufficiently higher rate? higher prevalence and/or higher incidence) - id 'emergence'-ID[O]:0000101 from IDO 2007. May have replacement - TBD - _obsolete_emergence - true - - - - - - - - - _obsolete_epidemiological spread of disease - true - - - - - - - - - _obsolete_outbreak - true - - - - - - - - - _obsolete_infection - true - - - - - - - - - _obsolete_infection treatment process - true - - - - - - - - - _obsolete_immunization - true - - - - - - - - - _obsolete_prevention of infection - true - - - - - - - - - _obsolete_transport by blood - true - - - - - - - - - _obsolete_transport by lymph - true - - - - - - - - - _obsolete_modulation of inflammatory response - true - - - - - - - - - _obsolete_antigenic variation - true - - - - - - - - - _obsolete_resist phagocytosis in subepithelial space - true - - - - - - - - - _obsolete_serum resistance - true - - - - - - - - - _obsolete_phase variation - true - - - - - - - - - _obsolete_genetic diversification - true - - - - - - - - - _obsolete_complement resistance - true - - - - - - - - - _obsolete_epidemic spread of disease - true - - - - - - - - - _obsolete_pandemic spread of disease - true - - - - - - - - - _obsolete_vaccination - true - - - - - - - - - _obsolete_mode of transmission - true - - - - - - - - - _obsolete_end reservoir - true - - - - - - - - - 'Role played by portion of physical substance in a biological process'-ID[O]:0000204: Role played by portion of physical substance in a biological process - id 'factor'-ID[O]:0000204 from IDO 2007. May have replacement - TBD - _obsolete_factor - true - - - - - - - - - 'the process by which a biotic entity establishes multiple copies of itself in a new environment (including an organismal environment).nnfix idn"native" environment term'-ID[O]:0000205: the process by which a biotic entity establishes multiple copies of itself in a new environment (including an organismal environment).nnfix idn"native" environment term - id 'colonization'-ID[O]:0000205 from IDO 2007. May have replacement - TBD - _obsolete_colonization - true - - - - - - - - - _obsolete_biotic - true - - - - - - - - - _obsolete_adhesin - true - - - - - - - - - 'prevalence as measured by antibody'-ID[O]:0000208: prevalence as measured by antibody - id 'seroprevalence'-ID[O]:0000208 from IDO 2007. May have replacement - TBD - _obsolete_seroprevalence - true - - - - - - - - - 'quality [state] of an organism that during its life cycle in which its growth. development, metabolism, etc is temporarily suspended nnnsuspended state, non-replicative state, resting state'-ID[O]:0000209: quality [state] of an organism that during its life cycle in which its growth. development, metabolism, etc is temporarily suspended nnnsuspended state, non-replicative state, resting state - id 'dormancy'-ID[O]:0000209 from IDO 2007. May have replacement - TBD - _obsolete_dormancy - true - - - - - - - - - _obsolete_quality of host - true - - - - - - - - - _obsolete_quality of pathogen - true - - - - - - - - - 'can change depending on environmentnnwhere should susceptibility factors go?'-ID[O]:0000212: can change depending on environmentnnwhere should susceptibility factors go? - id 'susceptibility'-ID[O]:0000212 from IDO 2007. May have replacement - TBD - _obsolete_susceptibility - true - - - - - - - - - _obsolete_resistance - true - - - - - - - - - _obsolete_refractoriness - true - - - - - - - - - _obsolete_quality of host population - true - - - - - - - - - _obsolete_herd immunity - true - - - - - - - - - _obsolete_quality of infectious disease - true - - - - - - - - - _obsolete_case of infectious disease - true - - - - - - - - - 'agent is incubated?ndisease is incubated?'-ID[O]:0000219: agent is incubated?ndisease is incubated? - id 'incubation period'-ID[O]:0000219 from IDO 2007. May have replacement - TBD - _obsolete_incubation period - true - - - - - - - - - _obsolete_infectivity period - true - - - - - - - - - 'the unfolding or course of infectious diseasennwhat do we say about infectious disease that always remain latent nwhat about when a pathogen continues its progression nnwe need to think about whether we need a term called stagenlife cycle?nprogression?ndevelopment?'-ID[O]:0000221: the unfolding or course of infectious diseasennwhat do we say about infectious disease that always remain latent nwhat about when a pathogen continues its progression nnwe need to think about whether we need a term called stagenlife cycle?nprogression?ndevelopment? - id 'infectious disease progression'-ID[O]:0000221 from IDO 2007. May have replacement - TBD - _obsolete_infectious disease progression - true - - - - - - - - - _obsolete_infectious disease course - true - - - - - - - - - _obsolete_host recovery period - true - - - - - - - - - _obsolete_intrinsic incubation period - true - - - - - - - - - _obsolete_extrinsic incubation period - true - - - - - - - - - 'is this just the part of the life cycle of the biotic entity that has role pathogen for the period of time while it has role pathogen?nncan include phases in the existence of the entity before it becomes a pathogen'-ID[O]:0000226: is this just the part of the life cycle of the biotic entity that has role pathogen for the period of time while it has role pathogen?nncan include phases in the existence of the entity before it becomes a pathogen - id 'pathogen life cycle'-ID[O]:0000226 from IDO 2007. May have replacement - TBD - _obsolete_pathogen life cycle - true - - - - - - - - - 'is a period a process?'-ID[O]:0000227: is a period a process? - id 'dormancy period'-ID[O]:0000227 from IDO 2007. May have replacement - TBD - _obsolete_dormancy period - true - - - - - - - - - _obsolete_pathogen outbreak - true - - - - - - - - - _obsolete_oral-fecal transmission - true - - - - - - - - - _obsolete_vertical transmission - true - - - - - - - - - _obsolete_horizontal transmission - true - - - - - - - - - _obsolete_pathogen life cycle stage - true - - - - - - - - - _obsolete_infectious disease progression stage - true - - - - - - - - - _obsolete_progression rate - true - - - - - - - - - _obsolete_rapid progression - true - - - - - - - - - _obsolete_long-term non-progression - true - - - - - - - - - _obsolete_highly exposed persistently seronegative - true - - - - - - - - - _obsolete_co-infected - true - - - - - - - - - 'is a quality relating to both bacteria and host'-ID[O]:0000306: is a quality relating to both bacteria and host - id 'fitness'-ID[O]:0000306 from IDO 2007. May have replacement - TBD - _obsolete_fitness - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an organism in symbiosis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in symbiosis. - symbiont role - - - - - - - - - - - - - - - - - - - - - - - - - A symbiont role borne by an organism in virtue of the fact that both symbionts derive a growth, survival, or fitness advantage from symbiosis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in processes that result in the growth, survival, or fitness advantage of either organism. - mutualist role - - - - - - - - - - - - - - - - - - - - - - - - - A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis, but the other symbiont is neither advantaged nor disadvantaged. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in processes that result in the commensal's growth, survival, or fitness advantage. - commensal role - - - - - - - - - A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - In the medical community, the term 'parasite' is used with the narrower meaning of eukaryotic pathogen. - The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the other organism's growth, survival, or fitness reduction. - parasite role - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an infectious agent when contained in a host in which its infectious disposition can be realized. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent role - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Clostridium botulinum is an example of an entity with the capability to bear the pathogen role but that does not have the capability to bear the infectious agent role or the parasite role. The influenza viruses are examples of organisms that can bear both the infectious agent and pathogen roles. - pathogen role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disposition to become part of a disorder only in organisms whose defenses are compromised. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - opportunitistic pathogenic disposition - The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host. - This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin). - opportunistic infectious disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disposition to become part of a disorder in organisms that have intact defenses. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A pathogen with a primary infectious disposition can cause disease or death in both immunocompromised and immunocompetent hosts. - A quote from page 3 of Mandell's "Principles and Practice of Infectious Diseases" (Sixth edition): "It is useful to distinguish "principal" pathogens, which regularly cause disease in some proportion of susceptible individuals with apparently intact defense systems, from other potentially pathogenic microorganisms. ... even for most organisms classified as principal pathogens, for example, Staphylococcus aureus and the pneumococcus, some impairment or local breakdown in normal host defense mechanisms must occur for these bacteria to cause disease. ... Thus, it seems clear that the capacity of certain microorganisms to cause disease in seemingly uncompromised human hosts on a regular basis reflects some fundamental difference in their virulence capabilities from those of opportunists and the more numerous commensal species that rarely, if ever, cause disease." - primary infectious disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A host role borne by an organism in virtue of the fact that its extended organism contains a second organism and provides an environment supportive for the survival, growth, maturation, or reproduction of that organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The relevant environmental resources may include nutrient resources, warmth, or moisture. - The role is realized in processes in which the host makes the relevant environmental resources available to its partner in symbiosis. A bearer of a symbiont host role is bearer also of a symbiont role. - symbiont host role - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis reaches developmental maturity or reproduces sexually in the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - primary host role - The role is realized in developmental and reproduction processes of the host's partner in symbiosis. - definitive host role - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - secondary host role - The role is realized in developmental processes of the host's partner in symbiosis. - intermediate host role - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis utilizes the host to undergo a developmental stage transition, but the host is not required for continuation of the partner's life cycle. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in developmental processes of the host's partner in symbiosis. - paratenic host role - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis has the infectious disposition but cannot be transmitted from the host to the partner's definitive host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - incidental host role - dead-end host role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A symbiont host role borne by an organism in virtue of the fact that its partner in symbiosis derives from the host a growth, survival, or fitness advantage while the host's growth, survival, or fitness is reduced. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The partner in symbiosis bears the parasite role. - The role is realized in processes that result in the parasite's growth, survival, or fitness advantage or in the host's growth, survival, or fitness reduction. - parasite host role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role. - infectious agent host role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role. - pathogen host role - - - - - - - - - An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent carrier role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that an infectious agent is located in or on the entity and the entity has the capability to transfer (either actively or passively) the infectious agent from one location to another. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process that transfers an infectious organism from one location to another. - infectious agent transporter role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious agent transporter role that is borne by an organism active in the transfer of an infectious agent to an organism of another Species and in which the agent is infectious. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a transmission process. A bearer of a vector role is also a bearer of a host role. - infectious agent vector role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent does not multiply in or on the vector. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - mechanical vector of infectious agent role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious agent vector role borne by an organism in virtue of the fact that the infectious agent multiplies in the vector. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - biological vector of infectious agent role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious agent transporter role borne by an entity in virtue of the fact that the entity is not a complete organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Drinking water bears the infectious agent vehicle role, but does not bear either of the subtype roles. - infectious agent vehicle role - - - - - - - - - An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is living or contains living cells other than those that have the infectious disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Examples include blood, serum, tissue, or fresh produce. - biological vehicle of infectious agent role - - - - - - - - - An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - fomite role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that it is a habitat in which infectious agents can persist and multiply and from which they can be transmitted in virtue of prevailing practices of potential hosts. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - If the material entity bearing the reservoir role is an organism, then this organism also bears the host role. The organism may also bear the vector role. - The role is realized in a process that has as part life and multiplication processes of an infectious agent and a transmission process. - reservoir of infectious agent role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The virulence factor disposition is typically realized in processes that improve survival of the pathogen in a host, increase the likelihood of transmission to a host, or cause pathological processes in a host. - virulence factor disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - toxin disposition - - - - - - - - - A toxin disposition to damage cells or extracellular matrix by a direct enzymatic process. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in a direct enzymatic process that damages host cells or extracellular matrix. - exotoxin disposition - - - - - - - - - - An exotoxin disposition to damage cells of the host intestinal mucosa. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_enterotoxin disposition - enterotoxin disposition - true - - - - - - - - - - A toxin disposition that inheres in a protein or protein complex that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. - A toxin disposition that inheres in a protein or protein complex that is released from a pathogen only upon cytolysis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_endotoxin disposition - endotoxin disposition - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent enters a host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process by which an infectious agent enters a host. - infectious agent portal of entry role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an anatomical entity in virtue of the fact that it serves as the site through which an infectious agent exits a host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process by which an infectious agent exists a host. - infectious agent portal of exit role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to a non-living entity. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in the killing and/or growth inhibition of microorganisms on the non-living entity. - disinfectant role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that it has an antimicrobial disposition and is applied to an anatomical entity of a living organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in the killing and/or growth inhibition of microorganisms on the anatomical entity. - antiseptic role - - - - - - - - - - - - - - - - - - A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had no infectious disorder, and (3) the infectious disorder increases the host's susceptibility to infectious disorders. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process by which the infectious disorder is established in the host. - primary infection role - - - - - - - - - - - - - - - - - A role borne by an infectious disorder in virtue of the fact that (1) the host has at least two distinct infectious disorders, where neither arose from the other through metastasis, (2) at the time the infectious disorder was established in the host, the host had a primary infectious disorder, and (3) establishment of the infectious disorder occurs because of increased susceptibility to infectious disorders conferred by the primary infectious disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process by which the infectious disorder is established in the host. - secondary infection role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disease whose physical basis is an infectious disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - tranmissible disease - The disposition is realized in an infectious disease course. - infectious disease - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition borne by a biological macromolecule that is the disposition to participate in adherence to a host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in an adherence to host process. - adhesion disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition borne by a biological macromolecule that is the disposition to facilitate breach of host epithelial barriers or entry into and survival in host cells. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A molecule with the invasion disposition is referred to as an invasion factor or invasin. - invasion disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the development or reproduction of microorganisms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Some instances might be functions, depending on whether the bearer is something that exists and is used for the purpose (alcohol) or something that was designed for the purpose (pine sol). Entities that kill microorganisms are referred to as microbicidal; entities that inhibit the growth of microorganisms are referred to as microbistatic. - The disposition is realized in the killing or inhibition of microorganisms. - antimicrobial disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the lifecycle of viruses. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antiviral disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the development or reproduction of fungal organisms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antifungal disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the reproduction of bacteria. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antibiotic disposition - antibacterial disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to kill or inhibit the development or reproduction of eukaryotic parasites. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - In the term name, we are using parasite in the medical sense of eukaryotic organisms that are parasitic in humans. - antiparasitic disposition - - - - - - - - - - - - - - - - - - - - - - - - A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Examples include the following: CCR5 mutations protect T cells from HIV invasion. A tumor cell's resistance to chemotherapy protects the cell from damage by the drug (although this harms the patient). An insect's resistance to insecticide protects it from the insecticide. - The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant. - protective resistance - - - - - - - - - - A protective resistance that mitigates the damaging effects of a drug. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - drug resistance - resistance to drug - - - - - - - - - - - - - - - A protective resistance that inheres in an organism and mitigates the damaging effects on that organism of an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - resistance to infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A collective resistance disposition that inheres in an organism population in virtue of the fact that the proportion of the population with immunity to an infectious agent is high resulting in a low number of transmissions from hosts in the population to susceptible individuals in the population and thereby mitigating the damaging effects of the infectious agent on the population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - herd immunity to infectious organism - - - - - - - - - A resistance to infectious agent that inheres in an organism in virtue of immune system components in the extended organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - protective immunity to infectious agent - We don't specify that immunity results from prior exposure, because we want to include innate immunity. In addition, for adaptive immunity, there could be some low level immunity even in a primary immune response. - immunity to infectious agent - - - - - - - - - An immunity to infectious agent that results in elimination of the infectious agent from the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Sterilizing immunity is typically conferred by neutralizing antibodies. - sterilizing immunity to infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition to initiate processes that result in a disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pathogenicity - A pathogenic disposition is realized in processes that create a disorder. - The use of 'initiates' is intended to convey that a pathogenic disposition is realized when processes resulting in a disorder begin because of some action on the part of the bearer of the disposition. By this interpretation of 'initiates', disorder-causing entities such as glass, UV light, and toxins do not have a pathogenic disposition. - pathogenic disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - invasive disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A pathogenic disposition that inheres in an organism and is a disposition for that organism (1) to be transmitted to a host, (2) to establish itself in the host, (3) to initiate processes that result in a disorder in the host, and (4) to become part of that disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in a process that has as part a transmission process, an establishment in host process, a process that results in a disorder, and a process in which the bearer of the disposition becomes part of that disorder. The infectious disposition has a complementary disposition that inheres in an organism and is the capability to be host to an organism with an infectious disposition and to undergo processes initiated by that infectious organism that result in a disorder. - infectious disposition - - - - - - - - - An infectious disposition that is the disposition to be transmitted from an infected, non-human host to a human host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An infectious disease associated with an infectious agent that bears the zoonotic disposition is referred to as a zoonosis. - zoonotic disposition - - - - - - - - - An infectious disposition that is the disposition to be transmitted from an infected, human host to a non-human host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An infectious disease associated with an infectious agent that bears the reverse zoonotic disposition is referred to as a reverse zoonosis. - reverse zoonotic disposition - - - - - - - - - - - - - - - - - - - - - A disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - "... in virtue of the individual dispositions of the contstituents" is intended to capture the fact that the collective disposition results from the combination of the individual dispositions. It is not necessary that every constituent of the aggregate have a relevant individual disposition. - The disposition is realized in a process that has as part realizations of some of the individual dispositions. - collective disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism that is experiencing pregnancy-induced or pathologic immunosuppression. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunosuppressed organism - - - - - - - - - - - - - - - - - - - - - An organism that has immunocompetence. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunocompetent organism - - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition that inheres in a host of infectious agent and is a disposition to transmit infectious agents to organisms of the same Species through casual contact with a high likelihood of realization. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Highly contagious infections, those with a relatively high likelihood of spread, are referred to as contagious and are those for which spread is likely as a result of day-to-day activities of the host. - The disposition is realized in a horizontal transmission process. - contagiousness - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism that contains a colony in or on its extended organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colonized host - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism that has an infection in or on its extended organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infected organism - - - - - - - - - An organism that has two infections with distinct Species of infectious agents. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - co-infected organism - - - - - - - - - A host exhibiting disease symptoms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_symptomatic host - true - - - - - - - - - - - - - - - A quality that inheres in an infectious agent and is the likelihood that the infectious agent will undergo a horizontal transmission process. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The transmissibility quality varies with both the type of organism being transmitted and the type of organism to which transmission is happening. - infectious agent transmissibility - - - - - - - - - - - - - - - A quality that inheres in an infectious agent and is the liklihood that the infectious disposition will be realized upon exposure of a susceptible organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - This quality is measured by the proportion of exposed who become infected. - infectivity - - - - - - - - - - - - - - - A quality that inheres in an infectious agent and is the degree to which realizations of the infectious disease caused by the infectious agent become severe or fatal. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - This quality is measured by the proportion of clinically apparent cases that are severe or fatal. - virulence - - - - - - - - - - - - - - - A quality that inheres in an entity and is the degree to which it can be harmed by another entity. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Low susceptibility is often referred to as resistance. In this sense, resistance is a quality. - susceptibility - - - - - - - - - - - - - - - - A susceptibility that inheres in an organism and is the degree to which it can be harmed by an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - susceptibility to infectious agent - - - - - - - - - A susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - drug susceptibility - - - - - - - - - - - - - - - A drug susceptibility that inheres in an infectious agent and is the degree to which the infectious agent can be harmed or inhibited from surviving by a drug. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - drug susceptibility of infectious agent - - - - - - - - - An infection comprised of infectious organisms from different Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - mixed infection - polymicrobial infection - complex infection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infection for which the infectious agents that are part of the infection persist in the extracellular space of the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - extracellular infection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infection for which the infectious agents that are part of the infection persist inside host cells. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - intracellular infection - - - - - - - - - - An infection for which the infectious agents that are part of the infection are distributed throughout the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - systemic infection - - - - - - - - - - An infection for which the infectious agents that are part of the infection are limited to a relatively small area of the host's body. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - local infection - - - - - - - - - A local infection for which symptoms are observed in parts of the host's extended organism that are distant from the infection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - focal infection - - - - - - - - - An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - acute infectious disease course - - - - - - - - - A quality that inheres in an infection in virtue of the fact that the infection persists for an extended period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - persistent infection - _obsolete_chronic quality of infection - true - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A particular instance of infectious disease incidence will depend on a type of infectious disease, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. - infectious disease incidence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of organisms in the population that become infected with an infectious agent during a specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A particular instance of infection incidence will depend on a type of infectious agent, a population, and a period of time. Incidence is used as a measure of risk. Actual measures of incidence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. These constraints will vary with the context of the incidence measure. - infection incidence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the proportion of members of the population not experiencing an infectious disease course at the beginning of a specified period of time and in whom the infectious disease begins during the specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - cumulative incidence of infectious disease - An instance of infectious disease incidence proportion is measured by dividing a measure of an instance of infectious disease incidence by the number of members of the population in which the infectious disease course had not begun at the beginning of the specified period of time over which the incidence was measured. - infectious disease incidence proportion - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - cumulative incidence of infection - An instance of infection incidence proportion is measured by dividing a measure of an instance of infection incidence by the number of members of the population not infected at the beginning of the specified period of time over which the incidence was measured. - infection incidence proportion - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the infectious disease incidence proportion per unit time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An instance of infectious disease incidence rate is measured by dividing a measure of an instance of the infectious disease incidence proportion by the length of the period of time over which the incidence was measured. - infectious disease incidence rate - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the infection incidence proportion per unit time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An instance of infection incidence rate is measured by dividing a measure of an instance of infection incidence proportion by the length of the period of time over which the incidence was measured. - infection incidence rate - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease prevalence will depend on a type of infectious disease, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. - infectious disease prevalence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of organisms in the population infected with an infectious agent at a specified time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infection prevalence will depend on a type of infectious agent, a population, and a period of time. Actual measures of prevalence are based only on reported cases and usually specify a time interval and geographic location. Other constraints may include population demographics. - infection prevalence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious disease lifetime prevalence will depend on a type of infectious disease and a population. Actual measures of prevalence are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. - infectious disease lifetime prevalence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for an infectious agent in their serum at a specified time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Prevalence is sometimes defined as a proportion with total population size in the denominator. A particular instance of infectious agent seroprevalence will depend on a type of infectious agent and a population. Actual measures of seroprevalence are based only on tested individuals and usually specify a geographic location. Other constraints may include population demographics. - infectious agent seroprevalence - - - - - - - - - - - - - - - A quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A particular instance of infectious disease mortality rate will depend on a type of infectious disease and a population. Actual measures of mortality rate are based only on reported cases and usually specify a geographic location. Other constraints may include population demographics. Mortality rate is typically expressed in units of deaths per 1000 individuals per year. - infectious disease mortality rate - - - - - - - - - - - - - - - A quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - A particular instance of infectious disease endemicity will depend on a type of infectious agent and a population. The population may be specified by temporal, geographic, or demographic constraints. Infectious diseases that are typical or common to a particular population are referred to as endemic. - infectious disease endemicity - - - - - - - - - An infectious disease prevalence that is typical for an infectious disease in an organism population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Infectious disease endemic level is relational to previous prevalences of the disease. - infectious disease endemic level - - - - - - - - - An infectious disease incidence rate that is typical for an infectious disease in an organism population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Infectious disease endemic rate is relational to previous infectious disease incidence rates of the disease. - infectious disease endemic rate - - - - - - - - - An infectious disease endemicity that inheres in an organism population in virtue of the fact that the infectious disease endemic level for an infectious disease is persistently high in the population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Hyper-endemic infectious diseases may have high endemic levels only in certain seasons. A hyper-endemic disease affects all age groups equally. - infectious disease hyper-endemicity - - - - - - - - - - - - - - - A quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Sporadic quality of infectious disease is relational to previous prevalence of the disease. - infectious disease sporadicity - - - - - - - - - - - - - - - - - - - - A disease course that is the realization of an infectious disease. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious disease course - - - - - - - - - A chronic infectious disease course that does not progress to severe stages for a long period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - long-term non-progressing infectious disease course - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process by which an organism acquires immunity to an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunization against infectious agent - - - - - - - - - An immunization that begins with exposure of an organism to antigen and results in immunity against an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - inoculation - active immunization against infectious agent - - - - - - - - - An active immunization that begins with exposure of an organism to a vaccine. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - vaccination against infectious agent - - - - - - - - - An active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - variolation - - - - - - - - - An immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against an infectious agent. - Examples include the injection of antibodies and the transfer of maternal antibodies to the fetus. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - passive immunization against infectious agent - - - - - - - - - A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. - For a particular instance of infectious disease epidemic, signficance is determined based on the infectious disease incidence that is typical for an infectious disease for the particular population and time period. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious disease outbreak - infectious disease epidemic - - - - - - - - - A process in which multiple infectious disease epidemics of the same type of infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious disease pandemic - - - - - - - - - - - - - - - - - - - An infection that is clinically abnormal. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious disorder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infection that has as part virus particles located in the blood. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - viremia - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infection that has as part bacteria located in the blood. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - bacteremia - - - - - - - - - A bacteremia in which the baceteria are replicating. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_septicemia - true - - - - - - - - - A virus that is in its assembled state consisting of genomic material (DNA or RNA) surrounded by coating molecules. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - virion - - - - - - - - - An aggregate of organisms of the same Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. - organism population - - - - - - - - - - - - - - - - - - - - - - - An organism population whose members have an infection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infected population - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism population in whose members an infectious disease is being realized. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - diseased population - - - - - - - - - - - - - - - - - - - - - - - An organism population whose members each have an infectious disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent population - - - - - - - - - An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - at-risk population - susceptible population - - - - - - - - - An organism population whose members are participating in non-parasitic symbiosis with a particular host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - normal resident microflora population - normal resident microbiota population - - - - - - - - - An infectious organism population with a certain configuration quality (OGMS:0000039) (distributed across a spatial region (e.g., anatomical location in a host) in a particular way). Put e.g. In comments - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_configured infectious organism population - true - - - - - - - - - A continuous temporal interval beginning with the extablishment of an infectious agent colony and ending with the onset of symptoms (or infectious disease course?). - Albert Goldfain - Alexander Diehl - Lindsay Cowell - incubation period - - - - - - - - - A continuous temporal interval during which an infectious agent host bears a contagiousness disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - communicability period - - - - - - - - - - - - - - - - - - - - An organism bearing a symbiont role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - symbiont - - - - - - - - - - - - - - - An organism that can only reach developmental maturity, replicate, or persist in symbiosis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - obligatory symbiont - - - - - - - - - - - - - - - - - - - - An organism bearing a mutualist role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - mutualist - - - - - - - - - - - - - - - - - - - - An organism bearing a commensal role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - commensal - - - - - - - - - - - - - - - - - - - - A organism bearing a parasite role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - parasite - - - - - - - - - An infectious agent that is an organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_infectious organism - true - - - - - - - - - - - - - - - - - - - - - - - - A material entity with a pathogenic disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pathogen - - - - - - - - - - - - - - - - - - - - An infectious agent with a primary infectious disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - principal pathogen - primary pathogen - - - - - - - - - - - - - - - - - - - - An organism bearing a host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - host - - - - - - - - - - - - - - - - - - - - An organism bearing a definitive host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - primary host - definitive host - - - - - - - - - - - - - - - - - - - - A organism bearing an intermediate host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - secondary host - intermediate host - - - - - - - - - - - - - - - - - - - - An organism bearing a paratenic host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - paratenic host - - - - - - - - - - - - - - - - - - - - An organism bearing a dead-end host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - incidental host - dead-end host - - - - - - - - - - - - - - - - - - - - An organism bearing a parasite host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - parasite host - - - - - - - - - - - - - - - - - - - - An organism bearing an infectious agent host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent host - - - - - - - - - - - - - - - - - - - - An organism bearing a pathogen host role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pathogen host - - - - - - - - - - - - - - - - - - - - An organism bearing the infectious agent carrier role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent carrier - - - - - - - - - - - - - - - - - - - - An organism bearing an infectious agent vector role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent vector - - - - - - - - - - - - - - - - - - - - An infectious agent vector bearing a mechanical vector of infectious agent role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - mechanical vector of infectious agent - - - - - - - - - - - - - - - - - - - - An infectious agent vector bearing a biological vector of infectious agent role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - biological vector of infectious agent - - - - - - - - - - - - - - - - - - - - - A material entity bearing an infectious agent vehicle role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - vehicle of infectious agent - - - - - - - - - - - - - - - - - - - - - - A material entity bearing a fomite role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - fomite - - - - - - - - - - - - - - - - - - - - - A material entity bearing an infectious agent reservoir role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent reservoir - - - - - - - - - A material entity bearing an end reservoir of infectious agent role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - dead-end reservoir of infectious agent - _obsolete_end reservoir of infectious agent - true - - - - - - - - - - - - - - - - - - - - A biological macromolecule produced by a pathogen and that has a virulence factor disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - virulence factor - - - - - - - - - - - - - - - - - - - - A biological macromolecule that has an invasion disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - invasin - invasion factor - - - - - - - - - - - - - - - - - - - - A molecular entity that has a toxin disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - toxin - - - - - - - - - - - - - - - - - - - - A molecular entity bearing an exotoxin disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - exotoxin - - - - - - - - - - - - - - - A molecular entity with an exotoxin disposition, the realization of which damages cells of the host intestinal mucosa. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - enterotoxin - - - - - - - - - - - - - - - A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - endotoxin - - - - - - - - - - - - - - - - - - - - An anatomical entity bearing an infectious agent portal of entry role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent portal of entry - - - - - - - - - - - - - - - - - - - - An anatomical entity bearing an infectious agent portal of exit role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent portal of exit - - - - - - - - - - - - - - - - - - - - - - - A material entity bearing a disinfectant role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - disinfectant - - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antiseptic role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antiseptic - - - - - - - - - - - - - - - - - - - - A biological macromolecule that has an adhesion disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - adhesin - adhesion molecule - adhesion factor - - - - - - - - - - - - - - - - - - - - - - A material entity with an antimicrobial disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antimicrobial - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antiviral disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antiviral - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antifungal disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antifungal - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antiparasitic disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antiparasitic - - - - - - - - - - - - - - - - - - - - - - A material entity bearing an antibacterial disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antibiotic - antibacterial - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity with an antimicrobial disposition that is realized in a process of killing microorganisms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - microbicidal [entity] - microbicide - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity with an antiviral disposition that is realized in a process of killing viruses. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - viricide - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A material entity with an antimicrobial disposition that is realized in a process of inhibiting the growth of microorganisms. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - microbistatic - - - - - - - - - - - - - - - - - - - - - An infection bearing the primary infection role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - primary infection - - - - - - - - - - - - - - - - - - - - An infection bearing the secondary infection role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - secondary infection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a zoonotic disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - zoonosis - - - - - - - - - - - - - - - An organism that is host to an infectious agent and has no symptoms of the infectious disease associated with the infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - asymptomatic host of infectious agent - - - - - - - - - An infection that is part of an asymptomatic host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - subclinical infection - - - - - - - - - - - - - - - - - - - - - A material entity that has a resistance disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - resistant entity - - - - - - - - - - - - - - - - - - - - An organism who has been bearer of the infectious agent carrier role for an extended period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - chronic carrier of infectious agent - - - - - - - - - - - - - - - An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent - Albert Goldfain - Alexander Diehl - Lindsay Cowell - symptomatic host of infectious agent - - - - - - - - - synonym of invasion factor - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_invasin - true - - - - - - - - - - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_viral latency - true - - - - - - - - - - - - - - - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in an innate immune response. - innate immunity to infectious agent - - - - - - - - - An immunity to infectious agent realized in an adaptive immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_adaptive immunity to infectious agent - true - - - - - - - - - - - - - - - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of components of its circulating body fluid. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - "Circulating body fluid" refers to blood, lymph, and hemolymph. - The disposition is realized in a humoral immune response. - humoral immunity to infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of its leukocytes. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - cell-mediated immunity to infectious agent - The disposition is realized in a leukocyte-mediated immune response. - leukocyte-mediated immunity to infectious agent - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of antibodies not produced by that organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Passive immunity results from a passive immunization. - The disposition is realized in a neutralizing process carried out by the antibodies. - The protective antibodies are typically introduced by injection, breast feeding, or by passing from the placenta to the fetus. - passive immunity to infectious agent - - - - - - - - - A resistance to drug that mitigates the damaging effects of an antibiotic. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - antibiotic resistance - - - - - - - - - - - - - - - - - - - - - - - - An organism experiencing a long-term non-progressing infectious disease course. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - long-term non-progressor - - - - - - - - - An infectious agent whose infection incidence is increasing following its first introduction into a new host Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - emerging pathogen - - - - - - - - - - - - - - - A molecular entity with a toxin disposition, the realization of which damages host cells. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - cytotoxin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A collective disposition to initiate processes that result in a disorder. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in processes that create a disorder. - collective pathogenic disposition - - - - - - - - - - - - - - - - - - - - - - - - A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The organism corresponding to the extended organism is host to the infectious agents. By this definition, parts of the host can be considered part of the infection. - infection - - - - - - - - - A resistance to infectious agent that inheres in an organism in virtue of a specific allele or combination of alleles in its genome. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The resistance of individuals to HIV invasion oonferred by particular CCR5 alleles is an example. Resistance against malaria conferred by the sickle cell gene is another. - genetic resistance to infectious agent - - - - - - - - - A collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - collective resistance disposition - - - - - - - - - - - - - - - - - - - - An organism that has an immunodeficiency. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunocompromised organism - immunodeficient organism - - - - - - - - - An infectious disease course that unfolds over a long period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - persistent infectious disease course - chronic infectious disease course - - - - - - - - - An infectious disposition to be transmitted directly from one human host to another. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_communicable disposition - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism population whose members have acquired immunity to an infectious agent. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immune population - - - - - - - - - A continuous temporal interval during which a transmission process occurs. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - transmission period - - - - - - - - - A process in which a potential host of an infectious agent comes into direct physical contact with the infectious agent. - Bjoern Peters - direct host exposure to infectious agent - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An organism that has the capability to bear a host of infectious agent role. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - potential host of infectious agent - - - - - - - - - - - - - - - - - - - - - An organism that has an infectious disposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent - - - - - - - - - A process in which a potential host of an infectious agent is exposed to an environment in which the infectious agent is present and physical contact between the two can occur, but such contact is not planned. - Bjoern Peters - host exposure to environment containing infectious agent - - - - - - - - - A host exposure to environment with infectious agent where the environment is a household that also has an infected host - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - host living with infected household contact - - - - - - - - - A host exposure to environment with infectious agent where the environment is an area in which an infectious agent is endemic - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - host living in endemic area - - - - - - - - - A host exposure to environment with infectious agent where the exposure is accidental; the environment is a laboratory, and the infectious agent is infectious in humans. - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - release of infectious human pathogen in laboratory - - - - - - - - - A host exposure to environment with infectious agent where the environment contains an infectious agent vector. - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - host coming into contact with vector of infectious agent - - - - - - - - - A host exposure to environment with infectious agent where the environment contains a material entity that has been assessed to confer a risk of infection. - Alan Ruttenberg 2010/05/20- Tentative definition. Needs review by Bjoern - host exposure to substance that might have infectious agent - - - - - - - - - A process by which an infectious agent, established in a host, becomes part of an infection in the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - process of establishing an infection - - - - - - - - - - - - - - - - - - - - An establishment of localization in host process in which an organism establishes itself in a host. - Establishment of one organism in the extended organism of another (the host) involves at least one of (1) movement of the organism to a location within the host in which the organism can persist, or (2) adherence or attachment of the organism to part of the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colonization of host - - - - - - - - - A biological object or group of biological objects in close spatial proximity. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_biological object colony - true - - - - - - - - - A colonization of host process that results in a clinically abnormal colony. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - establishment of a clinically abnormal colony - - - - - - - - - A process in which an entity comes into being as a result of the process. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - production - - - - - - - - - A production process in which a participant creates a copy of itself. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - replication - - - - - - - - - A colonization of human process in which the colonized site is the anterior nares. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colonization of human anterior nares - - - - - - - - - - - - - - - - - - - - A process that attenuates an immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunosuppression - - - - - - - - - An immunosuppression which unfolds as part of the natural self-regulation of an immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - physiologic immunosuppression - - - - - - - - - An immunosuppression process which arises as the result of a disorder. - Disorders that result in immunosuppression include those that result from infection, stress, malnutrition, and treatments such as chemotherapy or calcineurin inhibition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pathologic immunosuppression - - - - - - - - - primitive - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_biological object - true - - - - - - - - - A biological material entity that is capable of replication. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_replicating biological material entity - true - - - - - - - - - An organism population persisting in a site it has colonized. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colony - - - - - - - - - - - - - - - - - - - - - - - - A colony whose members are infectious agents. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious agent colony - - - - - - - - - - A disorder of an immune system component that results in defective functioning of the immune system. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunodeficiency - - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition that is the ability to mount a normal immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition inheres in a bearer in virtue of the fact that the bearer has all canonical immune system components and none are disordered. The disposition is realized in a successful immune response. - immunocompetence - - - - - - - - - - - - - - - - - - - - - - - - - - A disposition whose realization negatively regulates an immune response. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - immunosuppressive disposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An immunity to infectious agent that inheres in an organism in virtue of antigen receptors encoded by somatically diversified genes in the organism's genome and expressed by cells that have undergone selection during a primary immune response in that organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - adaptive immunity to infectious agent - immune memory - The disposition is realized in an immune response in which such antigen receptors participate. - acquired immunity to infectious agent - - - - - - - - - - - A disposition to colonize an organism and participate in mutualism or commensalism with that organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - disposition to form a non-parasitic colony - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disposition to be transmitted directly from one organism to another of the same Species by horizontal transmission. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The disposition is realized in a direct, horizontal transmission process between members of the same Species. - communicability - - - - - - - - - A generically dependent continuant that is the set of organism types whose instances have as one of their canonical dispositions, the disposition to bear the host role for a colony of a certain type. - A quality that inheres in an infection and is the likelihood that infectious agents part of the infection will spread to other hosts. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - _obsolete_contagiousness quality - _obsolete_host range - true - - - - - - - - - - - - - - - An establishment of localization process in which a material entity reaches a site in an organism in which it can survive, grow, multiply, or mature. - Requested addition of this term to the GO. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA. - establishment of localization in host - - - - - - - - - - - - - - - A process by which a disorder comes into existence. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - appearance of disorder - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disorder that is the physical basis for an unfolding acute infectious disease course. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - acute infection - - - - - - - - - An infection that persists for an extended period of time. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - persistent infection - chronic infection - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - host role - - - - - - - - - - An infection resulting from a transmission process that unfolds in a hospital. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - nosocomial infection - hospital-acquired infection - - - - - - - - - - An infection resulting from a transmission process that did not unfold in a health care facility. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - community-acquired infection - - - - - - - - - - - - - - - A molecular entity with a toxin disposition, the realization of which damages or interferes with the function of nerve tissue. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - neurotoxin - - - - - - - - - An infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - metatstatic infection - - - - - - - - - - - - - - - A role borne by a material entity in virtue of the fact that it contains a site from which an infectious agent is transmitted. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - The role is realized in a process that has as part a transmission process and a process by which the infectious agent or one of its offspring becomes part of a disorder in the host. - source of infection role - - - - - - - - - A process that is a systemic inflammatory response to infection. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - sepsis - - - - - - - - - A sepsis that results in organ dysfunction, hypotension, or hypofusion of at least one organ. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - severe sepsis - - - - - - - - - An infection resulting from a transmission process that unfolds in a nursing home. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - nursing-home acquired infection - - - - - - - - - An infectious agent with a capability to infect human hosts. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - infectious human pathogen - - - - - - - - - - An immunodeficiency that is not caused by a genetic predisposition. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Causes of acquired immunodeficiences include infection and drug treatments (e.g. chemotherapy). - acquired immunodeficiency - - - - - - - - - An infection comprised of infectious organisms all of the same Species. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - simple infection - - - - - - - - - An infectious agent whose infection incidence is increasing in a host population as a result of changes in the biology of the host or pathogen, or changes in their interactions. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - re-emerging pathogen - - - - - - - - - An immunosuppression induced by progesterone and other factors upregulated in pregnant women. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - pregnancy-induced immunosuppression - - - - - - - - - An infection that has as part organisms of the Genus Candida. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - candidiasis - - - - - - - - - An infection that has as part organisms of the Species Trichomonas vaginalis. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - trichomoniasis - - - - - - - - - An infection that has as part organisms of the Genus Leptospira. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - leptospirosis - - - - - - - - - An infection located in the bowel and that has as part organisms of the Genus Shigella. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - Shigellosis - - - - - - - - - An infection located in the colon and that has as part organisms of the Species Entamoeba histolytica - Albert Goldfain - Alexander Diehl - Lindsay Cowell - amebiasis - - - - - - - - - A colonization of host process in which the host is of Species Homo sapiens. - Albert Goldfain - Alexander Diehl - Lindsay Cowell - colonization of human - - - - - - - - - An immunodeficiency that exists in an organism because of a genetic predisposition. - Albert Goldfain - Alex Diehl - Lindsay Cowell - congenital immunodeficiency - primary immunodeficiency - - - - - - - - - A colonization of human process in which the colonized site is a perineum. - Albert Goldfain - Alex Diehl - Lindsay Cowell - colonization of human perineum - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An infectious disease that has as its physical basis an infectious disorder composed of infectious agents that have a reverse zoonotic disposition. - Albert Goldfain - Alex Diehl - Lindsay Cowell - reverse zoonosis - - - - - - - - - - - - - - - - - - - - An infectious agent with an opportunistic infectious disposition. - Albert Goldfain - Alex Diehl - Lindsay Cowell - opportunist - opportunistic pathogen - - - - - - - - - - - - - - - - - - - - - - - - A disposition to undergo a transmission process. - Albert Goldfain - Alex Diehl - Lindsay Cowell - The disposition is realized in a transmission process. - transmissibility disposition - - - - - - - - - A pathogen transmission process in which a pathogen is transmitted from one host to another of the same Species, and the two hosts are not in a parent-child relationship. - Lindsay Cowell - horizontal pathogen transmission process - - - - - - - - - A process that results in death. - Alex Diehl - Lindsay Cowell - process that results in death - - - - - - - - - A process in which a potential host of an infectious agent is exposed to an infectious agent. - Bjoern Peters - host exposure to infectious agent - - - - - - - - - An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent. - Alex Diehl - Lindsay Cowell - susceptible organism - - - - - - - - - A process which is necessary for the survival of an organism. - Alex Diehl - Lindsay Cowell - life-sustaining process - - - - - - - - - - - - - - - Any process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process. - Alex Diehl - Lindsay Cowell - negative regulation of life-sustaining process - - - - - - - - - - - - - - - - - - - - A material entity bearing a source of infection role. - Albert Goldfain - Alex Diehl - Lindsay Cowell - source of infection - - - - - - - - - A disposition to initiate processes that result in a disorder in a human organism. - human pathogenicity disposition - - - - - - - - - A disposition to participate in a process of symbiosis in which the bearer derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. - parasitic disposition - - - - - - - - - A process by which a part of an organism or something contained in an organism becomes clinically abnormal. - transition to clinical abnormality - - - - - - - - - A pathologic immunosuppression process which arises as the result of an infection and is initiated or dysregulated by the infectious agent population. - The definition should perhaps read "as the result of an infectious disorder". - Alex Diehl - Lindsay Cowell - infection-based immunosuppression - - - - - - - - - An infection-based immunosuppression process which arises as the result of an HIV infection. - Alex Diehl - Lindsay Cowell - HIV-based immunosuppression - - - - - - - - - - - - - - - - - - - - An immunosuppressed organism that is experiencing pathologic immunosuppression. - Alex Diehl - Lindsay Cowell - pathologically immunosuppressed organism - - - - - - - - - - - - - - - - - - - - A pathologically immunosuppressed organism that is experiencing infection-based immunosuppression. - Alex Diehl - Lindsay Cowell - immunosuppressed organism experiencing infection-based immunosuppression - - - - - - - - - A pathologically immunosuppressed organism that is experiencing HIV-based immunosuppression. - These individuals may also be immunodeficient due to depletion of CD4+ T cells and other effects of HIV. - Alex Diehl - Lindsay Cowell - immunosuppressed organism experiencing HIV-based immunosuppression - - - - - - - - - An immunosuppressed organism that is a human experiencing HIV-based immunosuppression. - Alex Diehl - Lindsay Cowell - NCI BBRB - immunosuppressed human experiencing HIV-based immunosuppression - - - - - - - - - A pathologic immunosuppression process which arises as the result of treatment with a drug that attenuates immune responses. - Alex Diehl - Lindsay Cowell - drug-based immunosuppression - - - - - - - - - A drug-based immunosuppression process that results from chronic systemic steroid use. - Alex Diehl - Lindsay Cowell - chronic systemic steroid use-based immunosuppression - - - - - - - - - - - - - - - - - - - - A pathologically immunosuppressed organism that is experiencing drug-based immunosuppression. - Alex Diehl - Lindsay Cowell - immunosuppressed organism experiencing drug-based immunosuppression - - - - - - - - - a pathologically immunosuppressed organism that is experiencing chronic systemic steroid use-based immunosuppression. - Alex Diehl - Lindsay Cowell - immunosuppressed organism experiencing chronic systemic steroid use-based immunosuppression - - - - - - - - - An immunosuppressed organism that is a human experiencing chronic systemic steroid use-based immunosuppression. - Alex Diehl - Lindsay Cowell - NCI BBRB - immunosuppressed human experiencing chronic systemic steroid use-based immunosuppression - - - - - - - - - A pathologically immunosuppressed organism that is a human experiencing drug-based immunosuppression. - Alex Diehl - Lindsay Cowell - NCI BBRB - immunosuppressed human experiencing drug-based immunosuppression due to organ transplant - - - - - - - - - - Viruses - - - - - - - - - - Bacteria - - - - - - - - - - Archaea - - - - - - - - - - Eukaryota - - - - - - - - - - Homo sapiens - - - - - - - - - - - - - - - - - - - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - - organism - - - - - - - - - A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease. - - symptom - - - - - - - - - A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. - - disease - - - - - - - - - A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. - - disorder - - - - - - - - - The totality of all processes through which a given disease instance is realized. - - disease course - - - - - - - - - An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. - - extended organism - - - - - - - - - A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host. - Suggested definition: A process by which a pathogen passes from one host organism to a second host organism of the same Species. - Suggested label: pathogen transmission process - - Transmission Ontology: http://purl.obolibrary.org/obo/trans.owl - transmission process - - - - - - - - - Indirect transmission is a transmission process during which the pathogen is indirectly transferred from a reservoir, source or host to another host by intermediary vehicles, vectors or as airborne dust particles. - Suggested label: indirect pathogen transmission process - - indirect - - - - - - - - - A fluid that is composed of blood plasma and erythrocytes. - - blood - - - - - - - - - A life cycle temporal boundary that marks the end of the life cycle of the organism. - - life-death temporal boundary - - - - - - - - - - - - - - - - - - - - - - - - - Obsolete Class - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - example to be eventually removed - - - - - - - - - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - - - - - - - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - - term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - core - - - - - - - - - placeholder removed - - - - - - - - - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - - - - - - - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - - - - - - - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - - - - - - - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - - - - - - - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - - - - - - - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - - - - - - - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - - -## Elucidation - -This is used when the statement/axiom is assumed to hold true 'eternally' - -## How to interpret (informal) - -First the "atemporal" FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. - -## Example - - Class: nucleus - SubClassOf: part_of some cell - - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) - -## Notes - -This interpretation is *not* the same as an at-all-times relation - - - axiom holds for all times - - - - - - - - - -## Elucidation - -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. - -## Example: - - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm - - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - - - - relation has no temporal argument - - - - - - - - Person:Alan Ruttenberg - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - - - - - - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/tmp/mirror-obi.owl b/src/ontology/tmp/mirror-obi.owl index 3478afb..7054a46 100644 --- a/src/ontology/tmp/mirror-obi.owl +++ b/src/ontology/tmp/mirror-obi.owl @@ -7,15 +7,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -82,7 +79,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2025-05-01 + 2026-05-08 @@ -104,32 +101,10 @@ - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - + editor preferred label editor preferred label editor preferred term editor preferred term @@ -138,7 +113,7 @@ The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - + editor preferred label editor preferred label editor preferred term editor preferred term @@ -155,7 +130,6 @@ A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - example of usage @@ -192,8 +166,11 @@ definition textual definition + A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. + English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition. 2012-04-05: Barry Smith @@ -216,7 +193,6 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition definition textual definition @@ -232,7 +208,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note @@ -247,7 +222,6 @@ We also have the outstanding issue of how to aim different definitions to differ 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - term editor @@ -263,9 +237,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - alternative term @@ -279,7 +251,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source @@ -304,7 +275,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg - curator note @@ -314,13 +284,14 @@ We also have the outstanding issue of how to aim different definitions to differ term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588 - An IRI or similar locator for a request or discussion of an ontology term. + A URL for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + @@ -360,7 +331,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - imported from @@ -509,7 +479,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - elucidation @@ -522,7 +491,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language - has associated axiom(nl) @@ -535,7 +503,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax - has associated axiom(fol) @@ -600,7 +567,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label @@ -720,11 +686,24 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + + 2025-06-02 + preferred label for community + + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) - A synonym type for describing abbreviations or initalisms + A synonym type for describing abbreviations or initialisms 2023-03-03 @@ -899,6 +878,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`. + Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf. + + + 2025-09-17 + has ontology hierarchical property + + + + @@ -912,12 +904,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1051,12 +1037,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1185,6 +1165,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + @@ -1194,12 +1180,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1295,17 +1275,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - label + label + A human readable name for this class. label + label @@ -1316,12 +1293,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + realized in @@ -1456,13 +1394,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1471,15 +1403,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - preceded by - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + preceded by @@ -1488,50 +1415,43 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + precedes - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in + + + + executed by + + + + + + + + intended to realize + + + + + + + + has plan - + - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + intended plan process type @@ -1539,10 +1459,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has measurement unit label - + has measurement unit label @@ -1551,9 +1469,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is about + A (currently) primitive relation that relates an information artifact to an entity. - is about @@ -1563,9 +1480,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - denotes + + A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - denotes @@ -1575,9 +1492,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is quality measurement of + m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - is quality measurement of @@ -1586,9 +1502,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - denoted by + inverse of the relation 'denotes' - denoted by @@ -1597,10 +1512,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has coordinate unit label - has coordinate unit label @@ -1610,9 +1522,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is duration of + relates a process to a time-measurement-datum that represents the duration of the process - is duration of @@ -1654,11 +1565,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has specified input see is_input_of example_of_usage - The inverse property of is specified input of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters @@ -1690,11 +1601,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified input of @@ -1743,10 +1654,10 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - + has specified output - The inverse property of is specified output of + The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter @@ -1910,10 +1821,10 @@ instance level relation [GOC:cjm] - + is specified output of - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified output of @@ -2011,7 +1922,7 @@ level of radioactivity is_proxy_for level of toxicity - + achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' @@ -2130,7 +2041,7 @@ level of radioactivity is_proxy_for level of toxicity - + objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. @@ -2255,15 +2166,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + - @@ -2377,15 +2288,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2394,16 +2297,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - has characteristic @@ -2412,15 +2306,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in participates in @@ -2429,16 +2315,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -2447,11 +2324,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as @@ -2461,10 +2333,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes @@ -2474,15 +2342,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this catalysis function is a function of this enzyme + function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of @@ -2491,14 +2353,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this red color is a quality of this apple + quality of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of @@ -2507,14 +2364,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this investigator role is a role of this person + role of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of @@ -2523,13 +2375,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + has function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function + has function @@ -2538,12 +2386,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this apple has quality this red color + has quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality + has quality @@ -2552,13 +2397,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) + has role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role + has role @@ -2567,11 +2408,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - + has disposition a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition @@ -2580,8 +2419,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + inverse of has disposition + disposition of @@ -2590,47 +2430,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - derives from - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - + derives from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from derives from - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - location of @@ -2640,97 +2451,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in + located in - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately preceded by @@ -2739,11 +2472,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - David Osumi-Sutherland - ends_at_start_of - meets - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + immediately precedes @@ -2752,14 +2482,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + has component w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - + has component - @@ -2767,11 +2493,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + capable of A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - has function realized in - capable of + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + capable of @@ -2779,9 +2506,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - surrounded by - x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y + surrounded by + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x surrounded by @@ -2796,15 +2522,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + inverse of surrounded by + surrounds + + + + - - - move to BFO? - Allen - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporal relation + temporally related to + + temporally related to @@ -2812,61 +2544,50 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + starts inverse of starts with - Chris Mungall - Allen + starts - + - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input - + - - - - has member is a mereological relation between a collection and an item. - SIO - - has member + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + has output - + - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true + + inverse of enables + enabled by - + - - DEPRECATED bearer of - true + + + has member + has member is a mereological relation between a collection and an item. + + has member @@ -2888,17 +2609,47 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - - has measurement value - - has measurement value + + has quantity + + + + + Number of protons in an atomic nucleus + has atomic number + + + + + + + + + has number of atomic nuclei + + + + + + + + has inchi string + + + + + + + + + + @@ -2972,518 +2723,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - + process - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - @@ -3491,226 +2736,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - disposition - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - + realizable entity - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - - specifically dependent continuant - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - @@ -3718,183 +2754,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - role - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - @@ -3902,105 +2763,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - site - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - @@ -4008,439 +2772,40 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - function - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - material - MaterialEntity + material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - material entity - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - + immaterial entity - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - + - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history + + + Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. + electron - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - @@ -4449,7 +2814,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ insulin - A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. + A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the β cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. insulin @@ -4459,7 +2824,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + water An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms @@ -4471,7 +2836,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ATP An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. @@ -4491,7 +2856,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ biotin - An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. + An organic heterobicyclic compound that consists of 2-oxohexahydro-1<em>H</em>-thieno[3,4-<em>d</em>]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin @@ -4501,9 +2866,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cholesterol - A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. + A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3β-hydroxy group. cholesterol @@ -4513,7 +2878,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ammonia An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. @@ -4525,7 +2890,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phospholipid A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. @@ -4537,7 +2902,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + nitrite The nitrogen oxoanion formed by loss of a proton from nitrous acid. @@ -4549,9 +2914,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + carbon dioxide - A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. + A one-carbon compound with formula CO<small><sub>2</sub></small> in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. carbon dioxide @@ -4563,7 +2928,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ peptide - Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. + Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide @@ -4573,7 +2938,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + globulin type One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. @@ -4585,7 +2950,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatinine A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. @@ -4597,9 +2962,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + mycophenolic acid - A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. + A member of the class of 2-benzofurans that is 2-benzofuran-1(3<em>H</em>)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2<i>E</i>)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by <em>Penicillium brevi-compactum, P. stoloniferum, P. echinulatum</em> and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. mycophenolic acid @@ -4609,7 +2974,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatine A glycine derivative having methyl and amidino groups attached to the nitrogen. @@ -4621,7 +2986,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bilirubin IXalpha A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. @@ -4645,9 +3010,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + progesterone - A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. + A C<small><sub>21</sub></small>-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. progesterone @@ -4657,7 +3022,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogensulfite hydrogensulfite @@ -4668,7 +3033,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + homocysteine A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. @@ -4680,7 +3045,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + glucose An aldohexose used as a source of energy and metabolic intermediate. @@ -4692,9 +3057,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + testosterone - An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. + An androstanoid having 17β-hydroxy and 3-oxo groups, together with unsaturation at C-4‒C-5.. testosterone @@ -4704,9 +3069,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methemoglobin - A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. + A hemoprotein that is the ferric (Fe<small><sup>3+</small></sup>) form of hemoglobin. methemoglobin @@ -4716,7 +3081,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogencarbonate The carbon oxoanion resulting from the removal of a proton from carbonic acid. @@ -4728,9 +3093,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. + A 17α-hydroxy-C<small><sub>21</sub></small>-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. cortisol @@ -4740,7 +3105,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5'-adenylyl sulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. @@ -4752,7 +3117,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + triglyceride Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. @@ -4764,7 +3129,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chloride A halide anion formed when chlorine picks up an electron to form an an anion. @@ -4776,7 +3141,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3-hydroxybutyric acid A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. @@ -4788,7 +3153,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bile salt A sodium salt of the conjugate of any bile acid with either glycine or taurine. @@ -4797,23 +3162,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - - molecular entity - - - - - + cytochalasin cytochalasin @@ -4824,7 +3176,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + estradiol A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. @@ -4836,21 +3188,35 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-ethyl-N-nitrosourea - A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. + A member of the class of <em>N</em>-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. N-ethyl-N-nitrosourea + + + + + hormone + Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. + + hormone + + + + - + + proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + Nuclear particle of charge number +1, spin ½ and rest mass of 1.007276470(12) u. proton @@ -4860,7 +3226,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + iron cation iron cation @@ -4871,7 +3237,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. @@ -4880,10 +3246,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + nitrogen atom + + nitrogen atom + + + + - + amikacin An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. @@ -4895,7 +3272,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. @@ -4907,7 +3284,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + uric acid An oxopurine that is the final oxidation product of purine metabolism. @@ -4919,7 +3296,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lead(0) lead(0) @@ -4930,9 +3307,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + vancomycin - A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. + A complex glycopeptide from <em>Streptomyces orientalis</em>. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria <em>Staphylococcus aureus</em> and <em>Clostridium difficile</em>. vancomycin @@ -4944,7 +3321,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ rac-lactic acid - A racemate comprising equimolar amounts of (R)- and (S)-lactic acid. + A racemate comprising equimolar amounts of (<i>R</i>)- and (<i>S</i>)-lactic acid. rac-lactic acid @@ -4954,7 +3331,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. @@ -4966,9 +3343,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dehydroepiandrosterone - An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. + An androstanoid that is androst-5-ene substituted by a β-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. dehydroepiandrosterone @@ -4978,7 +3355,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3,3',5'-triiodothyronine 3,3',5'-triiodothyronine @@ -4989,7 +3366,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tobramycin A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. @@ -5001,7 +3378,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium(1+) A monoatomic monocation obtained from sodium. @@ -5013,7 +3390,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + potassium(1+) A monoatomic monocation obtained from potassium. @@ -5025,7 +3402,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydroxyl hydroxyl @@ -5036,20 +3413,29 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + deuterium atom - The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). + The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek δευτερον, second). deuterium atom + + + + + Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. + neutron + + + + - + thyroxine An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. @@ -5061,7 +3447,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ruthenium atom ruthenium atom @@ -5069,6 +3455,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + bile acid + Any member of a group of hydroxy-5β-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5β-configuration. + + bile acid + + + + @@ -5090,7 +3488,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadodiamide hydrate The hydrate of gadodiamide. @@ -5102,7 +3500,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadoteridol A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5114,9 +3512,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phenol red - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. phenol red @@ -5126,7 +3524,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium citrate dihydrate The dihydrate of trisodium citrate. @@ -5138,7 +3536,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methyl group An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom. @@ -5147,14 +3545,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - - atom - A chemical entity constituting the smallest component of an element having the chemical properties of the element. - - atom + + + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 + atomic nucleus @@ -5162,7 +3566,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + elemental oxygen elemental oxygen @@ -5173,7 +3577,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rare earth metal atom rare earth metal atom @@ -5184,7 +3588,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rhodium atom A cobalt group element atom of atomic number 45. @@ -5196,7 +3600,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium atom gadolinium atom @@ -5207,7 +3611,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + terbium atom terbium atom @@ -5220,7 +3624,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ nucleic acid - A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), <small>D</small>-ribose or 2-deoxy-<small>D</small>-ribose and phosphoric acid. nucleic acid @@ -5242,7 +3646,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + amino acid A carboxylic acid containing one or more amino groups. @@ -5254,7 +3658,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer @@ -5267,7 +3671,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hemoglobin hemoglobin @@ -5278,7 +3682,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + fatty acid Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. @@ -5290,7 +3694,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium molecular entity gadolinium molecular entity @@ -5301,7 +3705,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phosphate ion A phosphorus oxoanion that is the conjugate base of phosphoric acid. @@ -5310,10 +3714,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + A particle smaller than an atom. + subatomic particle + + + + - + gadodiamide A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5325,9 +3740,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + folic acids - A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. + A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more <small>L</small>-glutamic acid units. folic acids @@ -5337,7 +3752,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium phosphate sodium phosphate @@ -5348,7 +3763,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5367,7 +3782,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5376,7 +3791,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ phosphorus-33 atom - The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. + The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin <small><sup>1</small></sup>/<small><sub>2</sub></small>. phosphorus-33 atom @@ -5417,6 +3832,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cytochrome P450 + + cytochrome P450 + + + + @@ -5456,7 +3882,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium cation calcium cation @@ -5467,7 +3893,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium ion calcium ion @@ -5478,7 +3904,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + magnesium cation Any magnesium ion that is positively charged. @@ -5510,7 +3936,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ digoxigenin - A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. + A hydroxy steroid that consists of 5β-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3β-, 12β- and 14β-positions. It has been isolated from the plant species of the genus <em>Digitalis</em>. digoxigenin @@ -5520,7 +3946,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA(4-) A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). @@ -5532,7 +3958,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + deoxyribonucleotide A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen. @@ -5544,9 +3970,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + digoxin - A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. + A cardenolide glycoside that is digitoxin β-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, <em>Digitalis lanata</em>, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. digoxin @@ -5567,7 +3993,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. @@ -5579,7 +4005,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + low-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). @@ -5591,7 +4017,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + high-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). @@ -5603,15 +4029,37 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chromium-51 - A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. + A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of γ rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. chromium-51 + + + + + 2'-(4-ethoxyphenyl)-5-(4-methylpiperazin-1-yl)-2,5'-bibenzimidazole + + 2'-(4-ethoxyphenyl)-5-(4-methylpiperazin-1-yl)-2,5'-bibenzimidazole + + + + + + + + + resorufin + + resorufin + + + + @@ -5667,7 +4115,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. @@ -5679,7 +4127,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dimethyl sulfate The dimethyl ester of sulfuric acid. @@ -5691,7 +4139,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + diethyl pyrocarbonate The diethyl ester of dicarbonic acid. @@ -5703,7 +4151,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 1,1-dihydroxy-3-ethoxy-2-butanone A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. @@ -5715,9 +4163,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide - A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. + A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two <em>N</em>-substituents. N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide @@ -5727,9 +4175,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-methylisatoic anhydride - A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. + A 3,1-benzoxazin-1,4-dione having an <em>N</em>-methyl substituent. N-methylisatoic anhydride @@ -5739,9 +4187,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + (S)-1-(4-bromoacetamidobenzyl)EDTA - A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. + A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (<i>S</i>)-configuration. (S)-1-(4-bromoacetamidobenzyl)EDTA @@ -5751,7 +4199,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA methidiumpropylamide A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. @@ -5763,19 +4211,31 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bromophenol blue - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. bromophenol blue + + + + + 1-methyl-7-nitroisatoic anhydride + A 3,1-benzoxazin-1,4-dione having an <em>N</em>-methyl substituent and a nitro group at the 7-position. + + 1-methyl-7-nitroisatoic anhydride + + + + - + tacrolimus hydrate A hydrate that is the monohydrate form of tacrolimus. @@ -5787,7 +4247,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + oxygen radical An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. @@ -5799,7 +4259,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lipoprotein A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. @@ -5811,7 +4271,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + thyroid stimulating hormone thyroid stimulating hormone @@ -5822,7 +4282,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Luteinizing hormone Luteinizing hormone @@ -5833,7 +4293,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Follicle stimulating hormone Follicle stimulating hormone @@ -5844,9 +4304,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 25-hydroxyvitamin D2 - A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. + A hydroxycalciol that is vitamin D<small><sub>2</sub></small> in which the hydrogen at position 25 has been replaced by a hydroxy group. 25-hydroxyvitamin D2 @@ -5856,9 +4316,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tris - A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. + A primary amino compound that is <em>tert</em>-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7—9; p<em>K</em><small><sub>a</sub></small> = 8.3 at 20 °C; p<em>K</em><small><sub>a</sub></small> = 7.82 at 37 °C. tris @@ -5960,7 +4420,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5980,24 +4440,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - cell line cell + + + + + + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture - + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. cell line cell - - - - - - - - - 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. - @@ -6005,9 +4459,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mortal cell line cell A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. - mortal cell line cell @@ -6017,9 +4469,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immortal cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. - immortal cell line cell @@ -6028,7 +4478,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -6041,11 +4491,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cell line A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). - cell line @@ -6067,9 +4515,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immortal cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. - immortal cell line @@ -6098,9 +4544,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mortal cell line A cell line is able to support only a limited number of passages in vitro. - mortal cell line @@ -6109,11 +4553,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - cell + PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell @@ -6153,26 +4597,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - primary cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. - primary cultured cell - - - - - obsolete native cell - OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - - obsolete native cell - - - - @@ -6196,9 +4626,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. - cultured cell @@ -6208,9 +4636,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sperm A mature male germ cell that develops from a spermatid. - sperm @@ -6220,9 +4646,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - fibroblast + + + + + + + + + + + + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. - fibroblast @@ -6232,9 +4668,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - epithelial cell + + + + + + + + + + + + + A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. - epithelial cell @@ -6244,21 +4691,27 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mesothelial cell A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement. - mesothelial cell + + + + + A cell found predominately in the blood. + blood cell + + + + - T cell A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. - T cell @@ -6267,22 +4720,52 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - mast cell + + + + + + + + + + + + + A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. - mast cell + + + + + + + + + + + + + + + + + A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system. + oligodendrocyte + + + + - hepatocyte The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. - hepatocyte @@ -6291,10 +4774,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - erythrocyte + A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. - erythrocyte @@ -6303,10 +4784,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - platelet + A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. - platelet @@ -6315,10 +4794,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - macrophage + A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. - macrophage @@ -6328,21 +4805,28 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - B cell A lymphocyte of B lineage that is capable of B cell mediated immunity. - B cell + + + + + A cell that initiates an electrical signal and passes that signal to another cell. + electrically signaling cell + + + + - - dendritic cell + + A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). - dendritic cell @@ -6351,10 +4835,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + - neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. - neuron @@ -6364,9 +4847,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - lymphocyte A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - lymphocyte @@ -6376,9 +4857,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - megakaryocyte A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release. - megakaryocyte @@ -6388,9 +4867,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - reticulocyte + + + + + + + + + + + + An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. - reticulocyte @@ -6400,9 +4889,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - band form neutrophil A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. - band form neutrophil @@ -6412,9 +4899,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - nucleate erythrocyte An erythrocyte having a nucleus. - nucleate erythrocyte @@ -6423,11 +4908,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - monocyte Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. - monocyte @@ -6437,16 +4919,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + - experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. - experimentally modified cell in vitro @@ -6456,9 +4935,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - natural killer cell A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. - natural killer cell @@ -6468,9 +4945,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD4-positive, alpha-beta T cell + A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. - CD4-positive, alpha-beta T cell @@ -6480,21 +4956,39 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD8-positive, alpha-beta T cell A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. - CD8-positive, alpha-beta T cell + + + + + A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration. + radial glial cell + + + + - leukocyte + + + + + + + + + + + + An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. - leukocyte @@ -6503,10 +4997,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - basophil + + + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. - basophil @@ -6515,10 +5020,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + - eosinophil + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. - eosinophil @@ -6527,10 +5043,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + - neutrophil + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. - neutrophil @@ -6540,9 +5067,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immature neutrophil Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking. - immature neutrophil @@ -6551,10 +5076,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - plasma cell + A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. - plasma cell @@ -6564,9 +5087,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - alpha-beta T cell A T cell that expresses an alpha-beta T cell receptor complex. - alpha-beta T cell @@ -6576,9 +5097,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD8-positive, alpha-beta cytotoxic T cell A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. - CD8-positive, alpha-beta cytotoxic T cell @@ -6588,9 +5107,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mature NK T cell A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. - mature NK T cell @@ -6600,9 +5117,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - promyelocyte + + + + + + + + + + + + A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. - promyelocyte @@ -6611,11 +5138,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - mononuclear cell + + + + + + + + + + + + + A leukocyte with a single non-segmented nucleus in the mature form. - - mononuclear cell + mononuclear leukocyte @@ -6624,9 +5161,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - malignant cell A neoplastic cell that is capable of entering a surrounding tissue - malignant cell @@ -6636,9 +5171,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - metamyelocyte A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. - metamyelocyte @@ -6648,9 +5181,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - myelocyte A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. - myelocyte @@ -6660,21 +5191,49 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - neural cell + + + + + + + + + + + + A cell that is part of the nervous system. - neural cell + + + + + An epithelial cell of the respiratory tract epithelium. These cells have an endodermal origin. + respiratory tract epithelial cell + + + + + + + + + A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + neural crest cell + + + + - segmented neutrophil of bone marrow A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface. - segmented neutrophil of bone marrow @@ -6684,22 +5243,303 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - peripheral blood mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. - peripheral blood mononuclear cell + + + + + obsolete elementary charge + true + + + + + + + + + + + + + + + + A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. + atom + + + + + + + + + + + + + + + A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. + This molecular entity is different than ChEBI's 'molecular entity'. + We would like to have cardinality restrictions on the logic, but there are some technical limitations. + molecule + + + + + + + + + obsolete macromolecular entity + true + + + + + + + + + + obsolete subcellular structure + true + + + + + + + + + A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. + gross anatomical part + + + + + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + obsolete geographical location + true + + + + + + + + + + + + + + + + + completely executed planned process + + + + + + + + + A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. + nucleic acid chain + + + + + + + + + + obsolete immaterial anatomical entity + true + + + + + + + + + obsolete gene product + true + + + + + + + + + + obsolete action specification + true + + + + - complex of molecules - A complex of two or more molecular entities that are not covalently bound. - - complex of molecules + + + + + + + A complex of two or more molecules that are not covalently bound. + complex of molecules + + + + + + + + + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + planned process + + + + + + + + + failed planned process + + + + + + + + + + + + + + + + + + + + + + + A completely executed planned process that intends to output material entities from input material entities + material processing + + + + + + + + + obsolete cellular membrane + true + + + + + + + + + obsolete physical information carrier + true + + + + + + + + + characteristic + + + + + + + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + + + + + + + + + + + + A processed material entity which is designed to be capable of a process. + device @@ -6740,6 +5580,83 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + A material part of an astronomical body. + geophysical entity + + + + + + + + + An environmental system which includes both living and non-living components. + ecosystem + + + + + + + + + A process in which includes the components of an environmental system as participants. + environmental system process + + + + + + + + + food material by consumer group + + food material by consumer group + + + + + + + + + food material + Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience + + food material + + + + + + + + + animal feed + Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs. + + animal feed + + + + + + + + + food material for animals + Food product for animal covers foods intended for consumption by domesticated animals. + + food material for animals + + + + @@ -6806,6 +5723,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neural crest cell migration + The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo. + + neural crest cell migration + + + + + + + + + neuron migration + The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature. + + neuron migration + + + + @@ -6891,6 +5832,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hematopoietic progenitor cell differentiation + The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. + + hematopoietic progenitor cell differentiation + + + + @@ -6984,6 +5937,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + renal system process + An organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). + + renal system process + + + + + + + + + heart process + A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. + + heart process + + + + @@ -6999,7 +5976,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + glomerular filtration The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein. @@ -7014,7 +5991,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -7096,10 +6075,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - L-alanine:2-oxoglutarate aminotransferase activity - Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate. + L-alanine:2-oxoglutarate transaminase activity + Catalysis of the reaction: L-alanine + 2-oxoglutarate = pyruvate + L-glutamate. - L-alanine:2-oxoglutarate aminotransferase activity + L-alanine:2-oxoglutarate transaminase activity @@ -7120,10 +6099,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - L-aspartate:2-oxoglutarate aminotransferase activity + L-aspartate:2-oxoglutarate transaminase activity Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate. - L-aspartate:2-oxoglutarate aminotransferase activity + L-aspartate:2-oxoglutarate transaminase activity @@ -7156,10 +6135,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - glutamate dehydrogenase [NAD(P)+] activity - Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+. + L-glutamate dehydrogenase [NAD(P)+] activity + Catalysis of the reaction: L-glutamate + NAD(P)+ + H2O = 2-oxoglutarate + NH4+ + NAD(P)H + H+. - glutamate dehydrogenase [NAD(P)+] activity + L-glutamate dehydrogenase [NAD(P)+] activity @@ -7169,7 +6148,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ glutathione transferase activity - Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group. + Catalysis of the reaction: RX + glutathione = an S-substituted glutathione + a halide anion + H+. glutathione transferase activity @@ -7205,7 +6184,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ RNA nuclease activity - Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. + Catalysis of the cleavage of phosphodiester bonds in chains of RNA. RNA nuclease activity @@ -7227,6 +6206,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). @@ -7296,6 +6284,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of DNA repair + Any process that modulates the frequency, rate or extent of DNA repair. + + regulation of DNA repair + + + + @@ -7320,6 +6320,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + apoptotic process + A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. + + apoptotic process + + + + @@ -7344,6 +6356,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + plasma membrane organization + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + + plasma membrane organization + + + + @@ -7368,6 +6392,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + female pregnancy + The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. + + female pregnancy + + + + + + + + + embryo implantation + Attachment of the blastocyst to the uterine lining. + + embryo implantation + + + + @@ -7392,14 +6440,32 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + growth factor activity + The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation. + + growth factor activity + + + + - + + + + + + biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + biological process biological_process @@ -7453,6 +6519,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + glial cell migration + The orderly movement of a glial cell, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system. + + glial cell migration + + + + @@ -7465,6 +6543,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + response to toxic substance + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. + + response to toxic substance + + + + @@ -7549,6 +6639,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cell migration + The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. + + cell migration + + + + + + + + + oxidoreductase activity + Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. + + oxidoreductase activity + + + + @@ -7585,6 +6699,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cytolysis + The rupture of cell membranes and the loss of cytoplasm. + + cytolysis + + + + @@ -7669,6 +6795,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neuron differentiation + The process in which a relatively unspecialized cell acquires specialized features of a neuron. + + neuron differentiation + + + + + + + + + neuron projection development + The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). + + neuron projection development + + + + @@ -8190,7 +7340,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + @@ -8200,6 +7351,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ protein-containing complex A ribosome is a protein complex. A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + This is not covalently bonded, which conflicts with changes to the parent definition. protein complex protein-containing complex @@ -8339,6 +7491,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of growth + Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. + + regulation of growth + + + + @@ -8375,6 +7539,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hormone biosynthetic process + The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone biosynthetic process + + + + + + + + + hormone catabolic process + The chemical reactions and pathways resulting in the breakdown of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone catabolic process + + + + @@ -8439,6 +7627,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + drinking behavior + The specific behavior of an organism relating to the intake of liquids, especially water. + + drinking behavior + + + + + + + + + neuron projection + A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. + + neuron projection + + + + @@ -8475,6 +7687,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Any constituent part of a virion, a complete fully infectious extracellular virus particle. + virion component + + + + @@ -8511,6 +7733,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + DNA-templated DNA replication maintenance of fidelity + A DNA metabolic process that prevents or corrects errors to ensure that DNA is replicated accurately. Errors can be corrected either by intrinsic DNA polymerase proofreading activity or via mismatch repair. + + DNA-templated DNA replication maintenance of fidelity + + + + @@ -8523,6 +7757,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + synapse + The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. + + synapse + + + + + + + + + luciferin monooxygenase activity + Catalysis of the generalized reaction: luciferin + O2 = oxidized luciferin + CO2 + light. There may be additional substrates and reactants involved in the reaction. The reaction results in light emission as luciferin returns to the ground state after enzymatic oxidation. + + luciferin monooxygenase activity + + + + @@ -8535,6 +7793,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oligodendrocyte differentiation + The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system. + + oligodendrocyte differentiation + + + + + + + + + anatomical structure development + The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. + + anatomical structure development + + + + @@ -8607,6 +7889,55 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + embryonic process involved in female pregnancy + A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother. + + embryonic process involved in female pregnancy + + + + + + + + + estrous cycle phase + The progression of physiological phases, occurring in the endometrium during the estrous cycle that recur at regular intervals during the reproductive years. The estrous cycle is an ovulation cycle where the endometrium is resorbed if pregnancy does not occur. + + estrous cycle phase + + + + + + + + + regulation of feeding behavior + Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food. + + regulation of feeding behavior + + + + + + + + + + establishment of endothelial barrier + The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition. + + establishment of endothelial barrier + + + + @@ -8835,6 +8166,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of synapse maturation + Any process that modulates the extent of synapse maturation, the process that organizes a synapse so that it attains its fully functional state. + + regulation of synapse maturation + + + + @@ -8967,6 +8310,49 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + synaptic signaling + Cell-cell signaling to, from or within a synapse. + + synaptic signaling + + + + + + + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. + Overlaps with some cellular components from GO + cellular anatomical entity + + + + + + + + + neuron projection arborization + The process in which the anatomical structures of a neuron projection are generated and organized into branches. A neuron projection is any process extending from a neural cell, such as axons or dendrites. + + neuron projection arborization + + + + @@ -8991,6 +8377,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + negative regulation of cell wall organization or biogenesis + Any process that stops, prevents or reduces the frequency, rate or extent of cell wall organization or biogenesis. + + negative regulation of cell wall organization or biogenesis + + + + + + + + + mitotic DNA replication maintenance of fidelity + Any maintenance of fidelity that is involved in mitotic cell cycle DNA replication. + + mitotic DNA replication maintenance of fidelity + + + + @@ -9015,13 +8425,23 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Severity + The intensity or degree of a manifestation. + + Severity + + + + - conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. - conditional specification @@ -9031,9 +8451,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - measurement unit label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - measurement unit label @@ -9043,9 +8461,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - objective specification A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - objective specification @@ -9055,21 +8471,27 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - narrative object A narrative object is an information content entity that is a set of propositions. - narrative object + + + + + A directive information entity that describes an action the bearer will take. + action specification + + + + - datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - datum label @@ -9079,10 +8501,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. - software @@ -9092,10 +8512,12 @@ interpreted by or directly executed by a processing unit. + data entity data item An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - + An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + data entity data item @@ -9105,9 +8527,7 @@ interpreted by or directly executed by a processing unit. - symbol An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - symbol @@ -9116,10 +8536,10 @@ interpreted by or directly executed by a processing unit. - + information content entity A generically dependent continuant that is about some thing. - + Pier: 'data, information or knowledge'. OR 'representation' information content entity @@ -9136,9 +8556,7 @@ interpreted by or directly executed by a processing unit. - scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - scalar measurement datum @@ -9148,9 +8566,7 @@ interpreted by or directly executed by a processing unit. - directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. - directive information entity @@ -9160,9 +8576,7 @@ interpreted by or directly executed by a processing unit. - dot plot A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - dot plot @@ -9172,9 +8586,7 @@ interpreted by or directly executed by a processing unit. - graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - graph @@ -9184,9 +8596,7 @@ interpreted by or directly executed by a processing unit. - rule A rule is an executable which guides, defines, restricts actions. - rule @@ -9196,9 +8606,7 @@ interpreted by or directly executed by a processing unit. - algorithm A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - algorithm @@ -9230,7 +8638,6 @@ interpreted by or directly executed by a processing unit. PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 - curation status specification @@ -9240,9 +8647,7 @@ interpreted by or directly executed by a processing unit. - density plot A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. - density plot @@ -9252,9 +8657,7 @@ interpreted by or directly executed by a processing unit. - report A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - report @@ -9264,10 +8667,8 @@ interpreted by or directly executed by a processing unit. - data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - data format specification @@ -9277,10 +8678,8 @@ Example: The ISO document specifying what encompasses an XML document; The instr - data set A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - - data set + homogenous data collection @@ -9289,9 +8688,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - image @@ -9313,9 +8710,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - plan specification A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - plan specification @@ -9331,9 +8726,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - measurement datum @@ -9356,9 +8749,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - conclusion textual entity A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. - conclusion textual entity @@ -9368,9 +8759,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - material information bearer A material entity in which a concretization of an information content entity inheres. - material information bearer @@ -9380,10 +8769,8 @@ Example: The ISO document specifying what encompasses an XML document; The instr - histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. - histogram @@ -9393,11 +8780,9 @@ distribution in terms of occurrence frequencies of different event classes. - heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. - heatmap @@ -9407,11 +8792,9 @@ two-dimensional map. - dendrogram A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. - dendrogram @@ -9421,9 +8804,7 @@ clustering algorithm. - scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - scatter plot @@ -9460,9 +8841,7 @@ clustering algorithm. - textual entity A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - textual entity @@ -9472,9 +8851,7 @@ clustering algorithm. - table A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions - table @@ -9484,9 +8861,7 @@ clustering algorithm. - figure An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - figure @@ -9496,9 +8871,7 @@ clustering algorithm. - document A collection of information content entities intended to be understood together as a whole - document @@ -9508,9 +8881,7 @@ clustering algorithm. - publication A document that is the output of a publishing process. - publication @@ -9520,9 +8891,13 @@ clustering algorithm. - publication about an investigation + + + + + + A publication that is about an investigation - publication about an investigation @@ -9532,9 +8907,7 @@ clustering algorithm. - one dimensional cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region - one dimensional cartesian spatial coordinate datum @@ -9544,9 +8917,13 @@ clustering algorithm. - length measurement datum + + + + + + A scalar measurement datum that is the result of measurement of length quality - length measurement datum @@ -9579,9 +8956,7 @@ clustering algorithm. - mass measurement datum A scalar measurement datum that is the result of measurement of mass quality - mass measurement datum @@ -9591,9 +8966,7 @@ clustering algorithm. - time measurement datum A scalar measurement datum that is the result of measuring a temporal interval - time measurement datum @@ -9603,9 +8976,7 @@ clustering algorithm. - postal address A textual entity that is used as directive to deliver something to a person, or organization - postal address @@ -9615,8 +8986,6 @@ clustering algorithm. - email address - email address @@ -9625,10 +8994,8 @@ clustering algorithm. - - documenting + A planned process in which a document is created or added to by including the specified input in it. - documenting @@ -9638,10 +9005,8 @@ clustering algorithm. - line graph A line graph is a type of graph created by connecting a series of data points together with a line. - line graph @@ -9650,10 +9015,8 @@ points together with a line. - - assigning a centrally registered identifier + A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - assigning a centrally registered identifier @@ -9663,9 +9026,7 @@ points together with a line. - centrally registered identifier symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - centrally registered identifier symbol @@ -9675,9 +9036,7 @@ points together with a line. - centrally registered identifier registry A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. - centrally registered identifier registry @@ -9687,9 +9046,7 @@ points together with a line. - software application A software application is software that can be directly executed by some processing unit. - software application @@ -10021,6 +9378,17 @@ No imports + + + + + A process in which at least one of the participants is a molecule. + This is meant to capture processes that are more fundamental than macromolecular activities + physico-chemical process + + + + @@ -10415,7 +9783,7 @@ No imports - + Viruses Viruses @@ -10560,10 +9928,19 @@ No imports + + + + + cellular organism + + + + - + Treponema pallidum Treponema pallidum @@ -10585,8 +9962,9 @@ No imports - + Bacteria + bacteria eubacteria Bacteria @@ -10597,7 +9975,7 @@ No imports - + Archaea Archaea @@ -10611,6 +9989,7 @@ No imports Riboviria RNA viruses + RNA viruses and retroviruses RNA viruses and viroids Riboviria @@ -10644,9 +10023,8 @@ No imports - + Eukaryota - eucaryotes eukaryotes Eukaryota @@ -10659,6 +10037,7 @@ No imports Orthoherpesviridae + Herpesviridae Orthoherpesviridae @@ -10734,6 +10113,7 @@ No imports Metazoa + animals metazoans multicellular animals @@ -10753,6 +10133,17 @@ No imports + + + + + Pseudomonadati + + Pseudomonadati + + + + @@ -10828,7 +10219,7 @@ No imports Ascomycota - ascomycetes + ascomycete fungi sac fungi Ascomycota @@ -10853,6 +10244,7 @@ No imports Saccharomyces cerevisiae + Saccharomyces boulardii Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast @@ -10982,7 +10374,7 @@ No imports - + Orientia tsutsugamushi Orientia tsutsugamushi @@ -11051,6 +10443,7 @@ No imports Rodentia rodent + rodents Rodentia @@ -11060,7 +10453,7 @@ No imports - + biological attribute biological attribute @@ -11223,30 +10616,21 @@ No imports - - - - - - - - - - - - - planned process + + obsolete planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + obsolete planned process + true @@ -11529,7 +10913,7 @@ objectives is a planned process. - + drug role @@ -11549,7 +10933,7 @@ objectives is a planned process. - + @@ -11584,7 +10968,7 @@ objectives is a planned process. - + physical document a book is a physical document @@ -11615,24 +10999,16 @@ objectives is a planned process. - - - - - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + obsolete processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material + PERSON: Alan Ruttenberg + + + obsolete processed material + true @@ -11919,7 +11295,7 @@ objectives is a planned process. - + polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. @@ -11934,7 +11310,7 @@ objectives is a planned process. - + @@ -12041,7 +11417,21 @@ objectives is a planned process. - + + + + + + + + + + + + + + + @@ -12127,7 +11517,7 @@ objectives is a planned process. - + @@ -12190,7 +11580,7 @@ objectives is a planned process. - + culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 @@ -12332,38 +11722,21 @@ In regard to the statement that reagents are 'distinct' from the speci - - - - - - - - - - - - - - - - - - - - - material processing + + obsolete material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material - PERSON: Bjoern Peters + PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra - material transformation - OBI branch derived - material processing + OBI branch derived + + + obsolete material processing + true @@ -12478,7 +11851,7 @@ editor = PRS - + @@ -12867,7 +12240,7 @@ specimen can later be subject. - + @@ -13602,7 +12975,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13690,7 +13063,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13986,7 +13359,7 @@ for now. - + @@ -14028,10 +13401,16 @@ for now. + + + + + + plan The plan of researcher X to perform an experiment according to a protocol. - A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived @@ -14193,8 +13572,8 @@ for now. - - + + @@ -14273,7 +13652,7 @@ for now. - + @@ -14372,14 +13751,14 @@ for now. - + - + @@ -14442,7 +13821,7 @@ need to add mobile phase as role - + @@ -14515,7 +13894,6 @@ need to add mobile phase as role - @@ -14629,7 +14007,7 @@ Proposal is to obsolete. - + @@ -14791,7 +14169,7 @@ Proposal is to obsolete. - + @@ -15143,7 +14521,7 @@ Proposal is to obsolete. - + @@ -15207,7 +14585,7 @@ Proposal is to obsolete. - + @@ -15468,7 +14846,7 @@ Proposal is to obsolete. - + @@ -15687,7 +15065,7 @@ activity) - + @@ -15708,7 +15086,7 @@ activity) - + @@ -16081,7 +15459,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16243,7 +15621,6 @@ that has_part some material entity is a material entity. If we add as equivalent genotyping assay - High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. Philippe Rocca-Serra @@ -16258,7 +15635,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16327,7 +15704,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16627,7 +16004,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16737,7 +16114,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16747,7 +16124,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + manufacturing @@ -16950,7 +16327,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16963,7 +16340,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. @@ -17152,7 +16529,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR sample holder An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. @@ -17366,7 +16743,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR tube washing system An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. @@ -17382,7 +16759,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR console A component of an NMR instrument that controls the activities of the other components. @@ -17689,7 +17066,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR magnet A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. @@ -17748,7 +17125,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -17759,7 +17136,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -17772,33 +17149,20 @@ that has_part some material entity is a material entity. If we add as equivalent - - - - - - - - - - - - - - - - + + + - - + + - - + + clinical chemistry assay Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. - An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. + An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a specimen collected from an organism in order to determine a phenotype of that organism. Philippe Rocca-Serra chemical pathology detection of analyte in blood sample @@ -17841,7 +17205,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18201,7 +17565,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18433,7 +17797,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + autosampler An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. @@ -18802,13 +18166,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + scattered molecular aggregate @@ -19699,15 +19063,6 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - @@ -19775,26 +19130,55 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - + + + + hematology assay Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 - An assay that studies blood and blood producing organs using a variety of techniques and instruments + An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments Philippe Rocca-Serra blood analysis haematology @@ -20229,7 +19613,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20272,11 +19656,11 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + device setting @@ -20375,7 +19759,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20383,7 +19767,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20850,7 +20234,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + whole organism preparation @@ -21278,7 +20662,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21288,13 +20672,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + animal feeding @@ -21454,7 +20838,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21469,7 +20853,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21741,14 +21125,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + @@ -21811,7 +21195,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21879,7 +21263,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21905,7 +21289,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22057,7 +21441,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22081,7 +21465,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22211,7 +21595,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. @@ -22306,7 +21690,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + host role @@ -22526,7 +21910,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. @@ -22580,7 +21964,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -22605,7 +21989,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs @@ -22630,13 +22014,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - - - + cloning vector @@ -22783,7 +22165,6 @@ the role 'adjuvant role' inheres in some 'material entity' a - nucleic acid restriction enzyme digest A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site @@ -23255,6 +22636,7 @@ the role 'adjuvant role' inheres in some 'material entity' a + @@ -23489,11 +22871,11 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23565,7 +22947,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23598,7 +22980,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23689,14 +23071,14 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23765,7 +23147,6 @@ http://en.wikipedia.org/wiki/Survival_rate - amplified DNA Amplied DNA created by PCR @@ -23780,7 +23161,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23813,24 +23194,15 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - - - - - - - - - - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule - a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. + a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues placeholder for SO BP et al - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule + true @@ -23884,7 +23256,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + Berichrom(r) Antithrombin III (A) Kit For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution @@ -23921,7 +23293,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + fucoidan Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). @@ -23935,7 +23307,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24193,7 +23565,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24214,7 +23586,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + pill A dose of medicine or placebo in the form of a small pellet. @@ -24273,7 +23645,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24281,7 +23653,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + measurement device A ruler, a microarray scanner, a Geiger counter. @@ -24406,7 +23778,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + material maintenance A planned process with the objective to maintain some or all of the characteristics of an input material over time. @@ -24418,6 +23790,7 @@ http://en.wikipedia.org/wiki/Survival_rate + @@ -24446,7 +23819,7 @@ placeholder - + @@ -24474,7 +23847,7 @@ placeholder - + @@ -24495,7 +23868,7 @@ placeholder - + @@ -24577,23 +23950,14 @@ placeholder - - - - - - - - - - - - - primary structure of RNA molecule + + obsolete primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters - primary structure of RNA molecule + + obsolete primary structure of RNA molecule + true @@ -25144,7 +24508,7 @@ placeholder - + @@ -25467,7 +24831,7 @@ Person: Chris Stoeckert - + @@ -25478,7 +24842,7 @@ Person: Chris Stoeckert - + @@ -25884,7 +25248,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26031,7 +25395,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26055,7 +25419,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - + @@ -26773,8 +26137,8 @@ Updated both textual and logical definition. Both input and output material of f - + labeled specimen A specimen that has been modified in order to be able to detect it in future experiments @@ -26794,7 +26158,7 @@ Updated both textual and logical definition. Both input and output material of f - + infectious agent is a material entity bearing the disposition to infect an organism @@ -26903,7 +26267,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26955,7 +26319,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26963,7 +26327,7 @@ Updated both textual and logical definition. Both input and output material of f - + material separation device flow cytometer @@ -27045,7 +26409,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27122,7 +26486,7 @@ Updated both textual and logical definition. Both input and output material of f - + training process e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility @@ -27225,7 +26589,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27238,7 +26602,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27351,7 +26715,7 @@ Biochimie. 2010 Feb 18. - + service provider role @@ -27521,14 +26885,14 @@ Biochimie. 2010 Feb 18. - + - + processed specimen @@ -27593,7 +26957,7 @@ Biochimie. 2010 Feb 18. - + @@ -27813,7 +27177,7 @@ Biochimie. 2010 Feb 18. - + @@ -27844,7 +27208,7 @@ Biochimie. 2010 Feb 18. - + @@ -27852,7 +27216,7 @@ Biochimie. 2010 Feb 18. - + container A device that can be used to restrict the location of material entities over time @@ -27866,50 +27230,21 @@ Biochimie. 2010 Feb 18. - - - - - - - - - - - - - - - - - - - - - - - - - device + + obsolete device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. - device + + + obsolete device + true @@ -27989,11 +27324,11 @@ In the examples above, a reagent is an operational component of a device, but th - + - + @@ -28004,7 +27339,7 @@ In the examples above, a reagent is an operational component of a device, but th sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + A data item that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data @@ -28111,7 +27446,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28531,7 +27866,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28853,7 +28188,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -28945,7 +28280,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. @@ -29332,7 +28667,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -29349,7 +28684,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30083,7 +29418,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30091,7 +29426,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) @@ -30109,7 +29444,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30117,7 +29452,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + perturbation device A homogenizer is a perturbation device. @@ -30137,7 +29472,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30153,7 +29488,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + environmental control device A growth chamber is an environmental control device. @@ -30446,7 +29781,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30532,7 +29867,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30629,7 +29964,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30731,7 +30066,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30751,7 +30086,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30797,7 +30132,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30823,7 +30158,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30883,7 +30218,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31032,7 +30367,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31052,7 +30387,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31283,7 +30618,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31355,7 +30690,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31457,7 +30792,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31477,7 +30812,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31651,7 +30986,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31719,7 +31054,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31864,7 +31199,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31918,7 +31253,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31978,7 +31313,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32046,7 +31381,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32066,7 +31401,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32126,7 +31461,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32365,7 +31700,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32418,7 +31753,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + individual organism identifier @@ -32577,7 +31912,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32676,7 +32011,7 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - + genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. @@ -32819,7 +32154,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -32830,7 +32165,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -33150,7 +32485,7 @@ All subtype will be defined by textual definition now. - + @@ -33166,11 +32501,11 @@ All subtype will be defined by textual definition now. - + - + service @@ -33320,15 +32655,6 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - @@ -33468,13 +32794,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + @@ -33486,7 +32812,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms @@ -37726,7 +37052,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -38335,7 +37661,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -40990,32 +40316,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - + genetic characteristics information @@ -43395,7 +42696,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -43424,7 +42725,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44305,7 +43606,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44361,7 +43662,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -46020,10 +45321,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + @@ -46044,30 +45345,20 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - + + + - - + + + + + - - - - - - - - - - - - - - - - + + @@ -46727,7 +46018,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + material processing service @@ -47182,7 +46473,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + DNA sequence data @@ -49290,7 +48581,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + purified material A mixture of peptide molecules that has been run through an HPLC column to remove 65 @@ -57712,7 +57003,7 @@ is realized in a specimen collection process. - + @@ -58378,7 +57669,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59378,7 +58669,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59730,7 +59021,7 @@ PMID: 23587118. - + @@ -59816,11 +59107,11 @@ When harvesting blood from a human, isolating T cells, and then limited dilution - + - + reagent @@ -60824,7 +60115,7 @@ The following are NOT conclusions based on data: data themselves; results from p - + cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. @@ -61926,7 +61217,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. @@ -62006,7 +61297,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -62142,7 +61433,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay @@ -62298,7 +61589,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - + @@ -62520,7 +61811,7 @@ PMID: 23587118. - + freezing A planned process with the objective to bring some material entity to a temperature below its freezing point. @@ -62683,7 +61974,7 @@ PMID: 23587118. - + @@ -62718,7 +62009,7 @@ PMID: 23587118. - + @@ -62966,7 +62257,7 @@ PMID: 23587118. - + @@ -63205,7 +62496,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63213,7 +62504,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63276,7 +62567,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63287,7 +62578,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64575,6 +63866,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + @@ -64689,54 +64004,6 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - histone modification identification by ChIP-Seq assay - - An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. - Chris Stoeckert - Jie Zheng - histone modification ChIP-Seq - Penn group - histone modification identification by ChIP-Seq assay - - - - - - - - - @@ -64745,39 +64012,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -64785,20 +64023,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - + @@ -64815,7 +64040,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64825,43 +64050,32 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - + - + - transcription factor binding site identification by ChIP-chip assay + histone modification identification by ChIP-Seq assay - A transcription factor binding site assay that utilizes ChIP-chip technology. + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. Chris Stoeckert Jie Zheng - TF Binding ChIP-chip + histone modification ChIP-Seq Penn group - transcription factor binding site identification by ChIP-chip assay + histone modification identification by ChIP-Seq assay - + - + - + @@ -64873,7 +64087,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64881,7 +64095,132 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transcription factor binding site identification by ChIP-chip assay + + A transcription factor binding site assay that utilizes ChIP-chip technology. + Chris Stoeckert + Jie Zheng + TF Binding ChIP-chip + Penn group + transcription factor binding site identification by ChIP-chip assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -65665,7 +65004,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -65695,7 +65034,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -67343,11 +66682,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + @@ -68066,14 +67405,14 @@ https://www.doi.org/ - high performance liquid chromotography assay + high performance liquid chromatography assay On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. ImmPort HPLC PMID:9491555 - high performance liquid chromotography assay + high performance liquid chromatography assay @@ -70590,7 +69929,7 @@ https://www.doi.org/ - + microtome blade A device that is the part of a microtome used to slice specimens to a desired thickness. @@ -70705,7 +70044,7 @@ https://www.doi.org/ - + determination if assay will provide reliable results A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. @@ -71707,7 +71046,7 @@ https://www.doi.org/ - + delivery form for hormonal replacement therapy A processed material used for delivery of hormones in hormone replacement therapy. @@ -72310,7 +71649,7 @@ https://www.doi.org/ - + @@ -72321,7 +71660,7 @@ https://www.doi.org/ - + @@ -72884,11 +72223,11 @@ https://www.doi.org/ - + - + @@ -72909,11 +72248,11 @@ https://www.doi.org/ - + - + @@ -73264,7 +72603,7 @@ https://www.doi.org/ - + pipette A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. @@ -74913,7 +74252,7 @@ https://www.doi.org/ - + esophagus muscularis mucosa specimen A specimen that is derived from esophagus muscularis mucosa. @@ -75151,7 +74490,7 @@ https://www.doi.org/ - + coronary artery specimen A specimen that is derived from coronary artery. @@ -75480,7 +74819,7 @@ https://www.doi.org/ - + minor salivary gland specimen A specimen that is derived from minor salivary gland. @@ -75621,7 +74960,7 @@ https://www.doi.org/ - + sigmoid colon specimen A specimen that is derived from sigmoid colon. @@ -76336,7 +75675,7 @@ https://www.doi.org/ - + @@ -76358,7 +75697,7 @@ https://www.doi.org/ - + machine learning A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. @@ -78586,19 +77925,14 @@ https://www.doi.org/ - - - - - - - 1 - - - - - + + + + 1 + + + individual organism specimen A specimen composed of an individual organism to be studied in an investigation. @@ -78660,7 +77994,7 @@ https://www.doi.org/ - + @@ -78668,7 +78002,7 @@ https://www.doi.org/ - + @@ -78691,7 +78025,7 @@ https://www.doi.org/ - + @@ -78713,7 +78047,7 @@ https://www.doi.org/ - + @@ -81919,7 +81253,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + @@ -81927,7 +81261,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + molecular label @@ -82001,7 +81335,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + passage process A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. @@ -82125,7 +81459,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + cDNA library cDNA library lacks the non-coding and regulatory elements found in genomic DNA @@ -82893,7 +82227,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + personal protective device Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. PPE is equipment worn by a worker to minimize exposure to specific hazards. @@ -83079,7 +82413,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + apron A garment which is worn over other clothing and covers mainly the front of the body. @@ -83185,7 +82519,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + transparent partition A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. @@ -83333,7 +82667,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + specimen collection device A device used to collect a specimen. @@ -83402,7 +82736,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + cotton swab A device which is a cotton pad mounted on one or both ends of a stick. @@ -83466,7 +82800,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. @@ -83838,7 +83172,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + arthropod trap A device designed to catch arthropods. @@ -83897,7 +83231,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -83957,7 +83291,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + dipper for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. @@ -85421,11 +84755,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -85591,7 +84925,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + device for collection of resting adult arthropods A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. @@ -85607,7 +84941,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + well net for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. @@ -86312,8 +85646,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + @@ -86701,7 +86034,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -86709,7 +86042,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87016,7 +86349,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87037,7 +86370,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + hand-held sweep net A device that consists of a network of mesh and is designed to capture adult arthropods. @@ -87414,7 +86747,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + common name of organism @@ -87502,7 +86835,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87513,7 +86846,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -88421,7 +87754,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -90922,7 +90255,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre leukapheresis - A blood harvesting process in which white blood cells are separated from a blood specimen. + A blood specimen collection in which white blood cells are separated from a blood specimen. Hector Guzman-Orozco https://en.wikipedia.org/wiki/Leukapheresis leukapheresis @@ -91529,7 +90862,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood assay datum - A data item that is the specified output of a blood assay. + A data entity that is the specified output of a blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91582,7 +90915,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre feces assay datum - A data item that is the specified output of a feces assay. + A data entity that is the specified output of a feces assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91635,7 +90968,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre urine assay datum - A data item that is the specified output of a urine assay. + A data entity that is the specified output of a urine assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91688,7 +91021,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre induced sputum assay datum - A data item that is the specified output of a induced sputum assay. + A data entity that is the specified output of a induced sputum assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91760,7 +91093,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre cerebrospinal fluid assay datum - A data item that is the specified output of a cerebrospinal fluid assay. + A data entity that is the specified output of a cerebrospinal fluid assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91944,7 +91277,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre umbilical cord blood assay datum - A data item that is the specified output of an umbilical cord blood assay. + A data entity that is the specified output of an umbilical cord blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -92822,7 +92155,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + mosquito membrane feeding device A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. @@ -93723,7 +93056,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -93731,7 +93064,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -94577,7 +93910,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre milk assay datum - A data item that is the specified output of a milk assay. + A data entity that is the specified output of a milk assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1515 @@ -94652,7 +93985,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf @@ -95568,7 +94901,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre antigen specific antibodies assay datum - A data item that is the specified output of an antigen specific antibodies assay. + A data entity that is the specified output of an antigen specific antibodies assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 @@ -96267,7 +95600,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -97825,7 +97158,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -98314,7 +97647,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100728,7 +100061,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100736,7 +100069,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100759,7 +100092,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100850,7 +100183,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100858,7 +100191,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100881,7 +100214,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100972,7 +100305,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100980,7 +100313,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -101003,7 +100336,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -102898,22 +102231,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - + + + + + + + + + + albumin-free serum A blood serum specimen that contains no albumin. @@ -102928,14 +102256,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -102948,7 +102276,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasting @@ -102988,7 +102316,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasted @@ -103266,15 +102594,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - @@ -103357,7 +102676,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - lavage fluid specimen The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. @@ -103791,7 +103109,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103833,7 +103151,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103874,7 +103192,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103942,7 +103260,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103966,7 +103284,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104022,7 +103340,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104033,7 +103351,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104080,7 +103398,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104091,7 +103409,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104138,7 +103456,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104149,7 +103467,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104196,7 +103514,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104207,7 +103525,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104254,7 +103572,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104265,7 +103583,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104312,7 +103630,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104323,7 +103641,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104370,7 +103688,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104381,7 +103699,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104428,7 +103746,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104439,7 +103757,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104486,7 +103804,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104497,7 +103815,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104550,7 +103868,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104561,7 +103879,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104614,7 +103932,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104625,7 +103943,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104770,7 +104088,7611 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + + + + + + + + + + + + cell based DNA damage assay + + A cytometry assay that measures DNA damage in cells. + Jennifer Fostel + cell based DNA damage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell count assay + + A cytometry assay to determine the number of natural killer cells in a specimen + Jennifer Fostel + natural killer cell count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell percentage assay + + A cytometry assay that measures the percentage of natural killer cells in a specimen. + Jennifer Fostel + natural killer cell percentage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sperm count assay + + A cytometry assay to count the number of mature sperm in a specimen. + Jennifer Fostel + sperm count assay + + + + + + + + + survey administration assay + + An assay that obtains data from one or more participants by using a survey or questionnaire + Jennifer Fostel + survey administration assay + + + + + + + + + maximum data transformation + + A data transformation that has as its output the greatest value in the input data set. + Sebastian Duesing + maximum data transformation + + + + + + + + + minimum data transformation + + A data transformation that has as its output the least value in the input data set. + Sebastian Duesing + minimum data transformation + + + + + + + + + + + + + + + + + + + + + + + + + clinical history collection assay + A clinician asking a patient about the patient's smoking status. + + A clinical assay that produces a data item indicating whether an organism has ever had a particular disease, lifestyle factor, immune exposure, or medical procedure. + Sebastian Duesing + HCC + clinical history collection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + disease severity assay + Measuring bone mineral density to determine the severity of osteoporosis. + + An assay that measures the severity of a disease in an organism. + Sebastian Duesing + HCC + disease severity assay + + + + + + + + + + + + + + + genetic characteristic assay + Determining a patient's HLA type. + + An assay that produces information about a genetic characteristic of an organism. + Sebastian Duesing + HCC + genetic characteristic assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood type assay + Identifying a person's ABO blood type. + + An assay that classifies an organism's blood within one or more blood group classification systems by identifying antigens present in the blood. + Sebastian Duesing + https://medlineplus.gov/ency/article/003345.htm + blood type assay + + + + + + + + + manual muscle testing 8 score + + A clinical data item that quantifies the muscle function of a person based on the person's ability to hold a series of eight body positions that target different muscle groups. + Sebastian Duesing + MMT-8 + https://www.niehs.nih.gov/sites/default/files/research/resources/assets/docs/mmt8_grading_and_testing_procedures_for_the_abbreviated_8_muscle_groups_508.pdf + manual muscle testing 8 score + + + + + + + + + childhood myositis assessment scale score + + A clinical data item that quantifies the degree of muscle function in a child with myositis based on performance of 14 tasks associated with muscular strength and endurance. + Sebastian Duesing + CMAS + https://pubmed.ncbi.nlm.nih.gov/10524696/ + childhood myositis assessment scale score + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + capillary electrophoresis mass spectrometry assay + + A mass spectrometry assay where a sample mixture is first separated by capillary electrophoresis before being analysed by mass spectrometry. + Sebastian Duesing + CE-MS + Thomas Payne + https://en.wikipedia.org/wiki/Capillary_electrophoresis–mass_spectrometry + https://github.com/obi-ontology/obi/issues/1904 + Thomas Payne + capillary electrophoresis mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite outgrowth assay + + A cell differentiation assay that detects neurite outgrowth and/or branching + The UBERON term for neurite is Neuron projection (GO:0043005; A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.). Multiplexed fluorescent imaging can be used to detect nuclei in neuronal cell bodies using Hoechst dye and neurites using anti-beta III-tubulin antibody staining. Commonly measured are neurite length, number and/or number of branch points (arborization). + Jennifer Fostel + neurite outgrowth assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuronal differentiation assay + + A cell differentiation assay that measures differentiation of neurons. + Jennifer Fostel + neuronal differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligodendrocyte differentiation assay + + A cell differentiation assay that measures differentiation of oligodendrocytes. + Jennifer Fostel + oligodendrocyte differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + regulation of synapse maturation assay + + A cell differentiation assay that measures synapse formation and maturation using antibodies to protein found in synaptic puncta. + Synaptic puncta is this context is a small (0.5 to 2 um) distinct localized cluster of proteins involved in synaptic transmission. + Jennifer Fostel + regulation of synapse maturation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ames assay + + A cell based DNA damage assay that uses several constructed bacterial strains to detect mutations. + The bacterial strains were originally constructed by Bruce Ames. Each carries a mutation in a gene involved in histidine synthesis. The cell requires histidine for growth but cannot produce it. The assay measures the creation of mutations that result in a return of function so that the cells can grow on a histidine-free medium. + Jennifer Fostel + Ames assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + micronucleus assay + + A cell based DNA damage assay in eukaryotic cells that detects cytoplasmic micronuclei. + The GO term "micronucleus" (GO:0031040) applies to protozoa but does not pertain to this case. Here micronucleus is a chromosome or fragment of a chromosome bounded by nuclear membrane that did not segregate properly at mitosis. + Jennifer Fostel + micronucleus assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PIG-a assay + + A cell based DNA damage assay in eukaryotic cells that detects loss of function through mutation of the X-linked (single-copy) Pig-a gene. + The Pig-A gene encodes a product involved in biosynthesis of cell surface anchor glycosylphosphatidylinositol (GPI). + Jennifer Fostel + PIG-a assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin + + A cell viability assay using the NAD(P)H-aided conversion of resazurin to resorufin by metabolically active cells. + Resazurin is the active ingredient in alamar blue; has a blue color and is non-fluorescent. Resorufin has pink color and is fluorescent. Detection of resorufin can be by absorbance or fluorescence. + Jennifer Fostel + Alamar Blue viability assay + cell viability assay based on detection of resorufin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay using caspase abundance to detect apoptosis + + A cell death assay that uses fluorescence imaging-based detection of caspases involved in apoptosis + Caspases 3 and 7 are frequently used as indicators of apoptosis. + Jennifer Fostel + cell death assay using caspase abundance to detect apoptosis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay + + A cell viability assay which measures the number or proportion of dead cells in a population. + Jennifer Fostel + cell death assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + A cell viability assay based on detection of resorufin that uses fluorescence to quantify resorufin + Resazurin (active ingredient in alamar blue and CellTiter blue reagents) has a blue color and is not fluorescent. Resorufin is pink and fluorescent. This assay uses the commercial reagent CellTiter Blue (Promega) containing resazurin and fluorescence to detect resorufin. + Jennifer Fostel + CellTiter Blue viability assay + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release + + A cell death assay that measures the release of intracellular LDH. + Jennifer Fostel + cell death assay detecting lactate dehydrogenase (LDH) release + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + A cell death assay detecting lactate dehydrogenase (LDH) release by absorbance of substrate + In this assay reagents are added so that LDH produces reduced nicotinamide adenine dinucleotide (NADH) when it catalyzes the oxidation of lactate to pyruvate, and the NADH converts a tetrazolium salt to a colored formazan product in the presence of an electron acceptor. This formazan product is detected by absorbance quality. + Jennifer Fostel + Cytotox 96 assay + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ovulation assessment in rodent assay + + A histological assay that measures the number of corpora lutea (UBERON:0002512) in the ovary of an organism; corpora lutea develop from the postovulatory follicle. + Jennifer Fostel + Corpus luteum count + ovulation assessment in rodent assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + macroscopic examination of material anatomical entity assay + + An assay that performs a macroscopic assessment of a material anatomical entity using the sense of sight. + Jennifer Fostel + macroscopic examination of material anatomical entity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pathological macroscopic examination of specimen assay + + A macroscopic examination of material anatomical entity assay performed on a post-mortem anatomical specimen. + one objective of this assay is to provide information about the character and extent of changes present and to inform on the cause of death. + Jennifer Fostel + Gross pathology assessment + pathological macroscopic examination of specimen assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle assay based on tissue morphology + + A histological assay that evaluates cells in the vaginal endometrium to assess the estrous cycle phase the subject was in at the time of specimen collection. + Jennifer Fostel + estrous cycle assay based on tissue morphology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo + + An organism development assay performed with a late embryo stage subject. + one objective of this assay is to assess anatomical structures and identify developmental phenotype + Jennifer Fostel + fetal examination + organism development assay in late embryo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pregnancy assessment based on tissue morphology assay + + A histological assay that measures the number of implantation sites in an organism. + An implantation site in this context is the site in the endometrium where the fertilized egg attaches and embeds itself to begin development + Jennifer Fostel + implantation site count + pregnancy assessment based on tissue morphology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay using vital dye + + A cell death assay that uses the Trypan blue vital dye to stain cells which have lost membrane integrity. + Living cells exclude Trypan blue + Jennifer Fostel + cell death assay using vital dye + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite length assay + + A cytometry assay that uses a distance measurement assay to determine the length of a neurite. + A neurite is a neuronal process greater than 10 um extending from a neuron. + Jennifer Fostel + neurite length assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite degree of arborization assay + + A cytometry assay that measures the degree of arborization, or branching, in neuronal processes + Jennifer Fostel + neurite branch point count + neurite degree of arborization assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite count assay + + A cytometry assay that measures the number of neurites in a cultured specimen. + A neurite is a neuronal process greater than 10 um extending from a neuron. + Jennifer Fostel + neurite count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron count assay + + A cytometry assay that measures the number of neurons in a sample + Jennifer Fostel + neuron count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell-body-associated presynaptic puncta count assay + + A regulation of synapse maturation assay that determines the number of synaptic puncta in the cell body compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. + Jennifer Fostel + cell-body-associated presynaptic puncta count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + dendrite-associated presynaptic puncta count assay + + A regulation of synapse maturation assay that determines the number of synaptic puncta in the dendritic compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. + Jennifer Fostel + dendrite-associated presynaptic puncta count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + synapse per neuron assay + + A regulation of synapse maturation assay that determines the number of synaptic puncta in a culture and normalizes it by the number of neurons in the culture. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. + Jennifer Fostel + synapse per neuron assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + absorbance quality detection assay + + An assay that measures the absorbance quality of the evaluant + the unit of this assay is absorbance unit (UO:0000269) + Jennifer Fostel + absorbance quality detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + hormone assay + + The analyte assay that measures the abundance of a hormone in a specimen. + Jennifer Fostel + hormone assay + + + + + + + + + chemiluminescent assay + + An analyte assay that detects a substance by measuring the release of light triggered by a chemical reaction. + SD + CLIA + HCC + HCC + chemiluminescent assay + + + + + + + + + electrochemiluminescence assay + + A chemiluminescent assay that detects a substance by measuring the release of light triggered by an electrochemical reaction. + SD + ECL + Meso Scale Discovery ECL + HCC + HCC + electrochemiluminescence assay + + + + + + + + + + + + + + + + + + + + + + proteomics by mass spectrometry assay + + A mass spectrometry assay that identifies and measures proteins. + SD + HCC + HCC + proteomics by mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + metabolomics by mass spectrometry assay + + A mass spectrometry assay that identifies and measures metabolites. + SD + HCC + HCC + metabolomics by mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + cellular indexing of transcriptomes and epitopes by sequencing + + An assay performed on single cells that simultaneously measures transcript expression via single-cell RNA sequencing and profiles surface proteins via sequencing of DNA-barcodes attached to antibodies recognizing particular surface proteins from individual cells. + SD + CITE-Seq + HCC + HCC + cellular indexing of transcriptomes and epitopes by sequencing + + + + + + + + + immune receptor repertoire profiling assay + + An assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors or T cell receptors within an input sample. + SD + HCC + HCC + immune receptor repertoire profiling assay + + + + + + + + + + + + + + + + + + + + antibody-dependent complement deposition assay + + An assay measuring antibody-dependent complement-dependent cytotoxicity. + SD + ADCD + HCC + HCC + antibody-dependent complement deposition assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial flagellin detection in plasma assay + + An analyte assay measuring bacterial flagellin in a plasma sample. + SD + HCC + HCC + bacterial flagellin detection in plasma assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial flagellin detection in feces assay + + An analyte assay measuring bacterial flagellin in a feces sample. + SD + HCC + HCC + bacterial flagellin detection in feces assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial lipopolysaccharide detection in plasma assay + + An analyte assay measuring bacterial lipopolysaccharide in a plasma sample. + SD + LPS + HCC + HCC + bacterial lipopolysaccharide detection in plasma assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial lipopolysaccharide detection in feces assay + + An analyte assay measuring bacterial lipopolysaccharide in a feces sample. + SD + LPS + HCC + HCC + bacterial lipopolysaccharide detection in feces assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + adenosine deaminase activity assay + + An analyte assay measuring adenosine deaminase activity in a sample. + SD + ADA + HCC + HCC + adenosine deaminase activity assay + + + + + + + + + pathogen neutralization assay + + An assay that measures neutralization of a pathogen. + SD + HCC + pathogen neutralization assay + + + + + + + + + bacterial neutralization assay + + A pathogen neutralization assay measuring neutralization of bacteria. + SD + HCC + bacterial neutralization assay + + + + + + + + + viral plaque assay + + An analyte assay measuring the number of discrete viral plaques. + SD + PMID:Ê25407402 + HCC + viral plaque assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + analyte detection by flow based bead assay + + An analyte assay that uses beads to measure the concentration of an analyte with a flow cytometer. + SD + HCC + HCC + analyte detection by flow based bead assay + + + + + + + + + bacterial lipopolysaccharide + + A molecule that is a component of the outermost membrane of the cell envelope of gram-negative bacteria and which consists of three parts: an outer core polysaccharide termed the O-antigen, an inner core oligosaccharide, and Lipid A, all covalently linked. + RV + SD + https://en.wikipedia.org/wiki/Lipopolysaccharide + Temporary term created for HCC & intended to be replaced with a term from a different ontology once one can be NTRed. + bacterial lipopolysaccharide + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine clarity assay + + A histological assay with urine evaluant that measures opacity of the urine + Jennifer Fostel + urine opacity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine color assay + + A histological assay with urine evaluant that measures color. + Jennifer Fostel + urine color assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine histological assay + + A histological assay with urine sediment as evaluant. + Frequently this assay detects the presence of cells, casts, crystals, bacteria and parasites. + Jennifer Fostel + urine histological assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + color detection assay + + An assay that measures the color of the evaluant + generally detected by sight, as a color indicator. + Jennifer Fostel + color detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + opacity determination assay + + An assay that measures the opacity of the evaluant + Jennifer Fostel + opacity determination assay + + + + + + + + + electrocardiograph + + An instrument for recording the changes of electrical potential occurring during the heartbeat used especially in diagnosing abnormalities of heart action. + Jennifer Fostel + https://www.merriam-webster.com/dictionary/electrocardiograph + electrocardiograph + + + + + + + + + biotelemeter + + A measurement device that also transmits the measurement information from a biological material to a distant station. + Jennifer Fostel + biotelemeter + + + + + + + + + multi-electrode array plate + + A measurement device consisting of grid of tightly spaced microscopic electrodes that can detect the electrical signals of cells in close proximity. + Multielectrode arrays can be embedded in the bottom of a well and cells can be cultured over the electrodes for passive, noninvasive monitoring of electrical activity. + Jennifer Fostel + multi-electrode array plate + + + + + + + + + Transepithelial Electrical Resistance (TEER) device + + A measurement device that measures monolayer barrier integrity via measurement of membrane potential and electrical resistance across a cell monolayer in culture. + Jennifer Fostel + Transepithelial Electrical Resistance (TEER) device + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle count assay + + An estrous cycle assay based on tissue morphology that determines the number of estrous cycles observed in a defined time. + Jennifer Fostel + estrous cycle count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle duration assay + + An estrous cycle assay based on tissue morphology that determines the average length of a full estrous cycle observed in a defined time. + Jennifer Fostel + estrous cycle duration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo based on examination of surface structure + + An organism development assay in late embryo that evaluates only the external surface structure of the organism + Jennifer Fostel + external fetal exam + organism development assay in late embryo based on examination of surface structure + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo based on examination of skeletal system + + An organism development assay in late embryo that evaluates the skeletal system of the organism + Jennifer Fostel + skeletal fetal exam + organism development assay in late embryo based on examination of skeletal system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo based on examination of anatomical system + + An organism development assay in late embryo that evaluates the anatomical system of the organism + Jennifer Fostel + visceral fetal exam + organism development assay in late embryo based on examination of anatomical system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + distance measurement assay + + An assay that measures the space between two entities. + Distance is a measure of the amount of space between two points. + Jennifer Fostel + distance measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + length measurement assay + + An assay that measures the distance between two points. + Typically length is a property of an object, the distance from end to end often in the largest dimension. + Jennifer Fostel + length measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + crown rump length + + A length measurement assay that measures the length of a neonate or fetus from crown of head to base of torso (rump) + Jennifer Fostel + crown rump length + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + path length assay + the distance traveled by a rodent in a maze + + An assay that measures the distance traveled in a defined period of time. + The total distance traveled by an entity in a given time; the sum of all segments in the path traveled if it is not straight. + Jennifer Fostel + path length assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell migration assay + + A distance measurement assay in which the migration of cells in culture is monitored by measuring the distance between the start position and the cell's location when observed. + This is the distance between the start and end points of cultured cells + Jennifer Fostel + cell migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligodendrocyte migration assay + + A cell migration assay that measures migration of an oligodendrocyte + Jennifer Fostel + oligodendrocyte migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + radial glial migration assay + + A cell migration assay that measures migration of a radial glia cell + Jennifer Fostel + radial glial migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron migration assay + + A cell migration assay that measures migration of a neuron + Jennifer Fostel + neuron migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neural crest cell migration assay + + A cell migration assay that measures migration of a neural crest cell + Jennifer Fostel + neural crest cell migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + acidity quality assay + + An assay that measures the acidity of a specimen on the pH scale. + The measurement of pH is the negative logarithm to base ten of the hydrogen ion activity in a solution, this measures the degree of acidity or alkalinity. + Jennifer Fostel + acidity quality assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specific gravity assay + + An assay that measures the specific gravity of a sample. + Specific gravity is the ratio of the density of the specimen to the ratio of water or other standard. + Jennifer Fostel + specific gravity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + speed measurement assay + + An assay to determine the speed of an evaluant. + Speed is a physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position (PATO). + Jennifer Fostel + speed measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + velocity measurement assay + + An assay to measure the velocity of an evaluant + Velocity is a physical quality inhering in a bearer by virtue of the bearer's rate of change of the position (PATO). + Jennifer Fostel + velocity measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + luminescence detection assay + + An assay that measures the luminescence of the evaluant + the unit of this assay is relative luminescence unit (UO:0000313) + Jennifer Fostel + luminescence detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay using luciferase to detect ATP in the cell + + A cell viability assay that uses an ATP bioluminescence assay to detect ATP in the living cell + one reagent is CellTiter Glo (Promega) which contains luciferase and luciferin. Luciferase uses ATP in the living cell to convert luciferin to oxyluciferin and light. + Jennifer Fostel + cell viability assay using luciferase to detect ATP in the cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + population count assay + + An assay that measures the number of elements in a portion of a population + Not a synonym of organism detection assay (OBI:0002738); "A population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + Jennifer Fostel + population count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + hemolysis assay + + A hematology assay that measures the fragility of red blood cells by observing spillage of hemoglobin from burst cells. + Jennifer Fostel + hemolysis assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mean firing rate + + An electrophysiology assay that measures action potential events in neurons during a time period. + Jennifer Fostel + neuron action potential rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron burst rate assay + + An electrophysiology assay that measures the number of action potential bursts in neurons during a time period. + A burst is temporal arrangement of action potentials that occur close together in time followed by a period of quiescence. + Jennifer Fostel + neuron burst rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron interburst interval assay + + An electrophysiology assay that measures the elapsed time between consecutive action potential bursts in neurons. + A burst is temporal arrangement of action potentials that occur close together in time followed by a period of quiescence, the interburst interval. + Jennifer Fostel + neuron interburst interval assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron burst duration assay + + An electrophysiology assay that measures the time elapsed between the first action potential in a neuron burst and the last in that burst. + Jennifer Fostel + neuron burst duration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + interspike interval within a burst + + An electrophysiology assay that measures the time elapsed between the peaks of consecutive action potential spikes in a neuron burst. + Jennifer Fostel + action potential interval assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + rate of action potentials in neuron burst assay + + An electrophysiology assay that measures the number of action potential spikes occurring within a neuron burst + singleton spikes in the same time period unrelated to a neuron burst are not included in the count. + Jennifer Fostel + rate of action potentials in neuron burst assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body mass assay + + A mass measurement assay with evaluant an individual organism. + Jennifer Fostel + body mass assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body mass change assay + + A body mass assay that measures the change in body mass for a subject over a period of time. + Jennifer Fostel + body mass change assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + terminal body weight assay + + A body weight assay with evaluant individual organism specimen with quality dead. + Jennifer Fostel + body weight assay at death + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tissue mass assay + + A mass measurement assay with evaluant tissue or bodily fluid specimen. + Jennifer Fostel + tissue mass assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tissue mass percent of body mass assay + + A mass measurement assay with evaluant tissue expressed as a percentage of the body weight of the organism from which the specimen was derived. + Jennifer Fostel + tissue mass percent of body mass assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + developmental marker age of attainment assessment + the age of the rat at testis descent, the age of a human child at first menses. + + An age determination assay which determines the age of the subject at the time of the change from a state where it did not have a developmental stage marker to one in which it does. + Jennifer Fostel + developmental marker age of attainment assessment + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytochrome P450 assay + + A protein assay that measures the abundance of cytochrome P450 in a specimen. + Jennifer Fostel + cytochrome P450 assay + + + + + + + + + + + + + + + + + + + + growth factor assay + + An analyte assay to measure the abundance of one or more growth factors in a volume of sample. + A growth factor is a signalling role of a chemical substance in which it stimulates a biological system to proliferate, divide, differentiate, migrate, and so forth. + Jennifer Fostel + growth factor assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Hoechst dye assay + + A fluorescence imaging-based cell morphology assay that uses Hoechst dye 33342 + Hoechst dye binds to DNA and can be used to visualize nuclei. Often used to quantify cells, identify position over time, identify the cell body and other assays. + Jennifer Fostel + Hoechst dye assay + + + + + + + + + + + + + + + + + + + + hypersensitivity assay + + An immune response assay to assess the hypersensitivity response in an organism or cell culture. + Jennifer Fostel + hypersensitivity assay + + + + + + + + + super-resolution microscopy assay + + A type of light microscopy assay where the images are taken with a resolution higher than the diffraction limit. + Lachlan Whitehead + Marek Cmero + super resolution microscopy assay + http://purl.obolibrary.org/obo/MI_2213 + super-resolution microscopy assay + + + + + + + + + + + + + + + multi-photon microscope + + A microscope that uses simultaneous absorption of multiple photons to excite fluorescent molecules. + PERSON: Lachlan Whitehead + PERSON: Marek Cmero + PERSON: Pradeep Rajasekhar + MPLSM + multiphoton laser scanning microscope + two-photon excitation microscope + doi:10.1364/AOP.7.000276 + multiphoton microscope + + + + + + + + + + + + + + + light sheet microscope + + A microscope that uses illumination and detection objectives to image a sample illuminated with a thin sheet of laser light. + PERSON: Lachlan Whitehead + PERSON: Marek Cmero + light-sheet microscope + lightsheet microscope + doi:10.1016/B978-0-12-420138-5.00011-2 + light sheet microscope + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1M7 RNA structure mapping assay + PMID: 29551268 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methyl-7-nitroisatoic anhydride as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 1M7 probe + 1M7 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + NAI RNA structure mapping assay + PMID: 37674078 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-methylnicotinic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using NAI probe + NAI RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + NAI-N3 RNA structure mapping assay + PMID: 29804836 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-(azidomethyl)nicotinic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using NAI-N3 probe + NAI-N3 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 2A3 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-aminopyridine-3-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 2A3 probe + 2A3 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + I5 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using indoline-5-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using I5 probe + I5 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 1M4 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methylimidazole-4-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 1M4 probe + 1M4 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 6A3 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 6-aminopyridine-3-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 6A3 probe + 6A3 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + B5 RNA structure mapping assay + PMID:33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using benzotriazole-5-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using B5 probe + B5 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + NIC RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using nicotinic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using NIC probe + NIC RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + BzCN RNA structure mapping assay + PMID: 33453165 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using benzoyl cyanide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using BzCN probe + BzCN RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 1M6 RNA structure mapping assay + PMID: 30341219 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methyl-6-nitroisatoic anhydride as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 1M6 probe + 1M6 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 5NIA RNA structure mapping assay + PMID: 36062555 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 5-nitroisatoic anhydride as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 5NIA probe + 5NIA RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell count assay + + An assay that measures the number of cells in a portion of a cell culture or tissue or bodily fluid + OBI:2100330 count bodily fluid cell count assay / OBI:2100345 bodily fluid cell count assay + Jennifer Fostel + cell count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + differential leukocyte count assay + + A hematology assay that measures the percentage of classes of leukocytes in a sample. + Jennifer Fostel + differential leukocyte count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + electrocardiogram assay + + An electrophysiology assay that measures heart activity using electrodes placed to detect electrical signals from the heart. + related to electrocardiography (MAXO:0010203): A procedure that displays the electrical activity of the heart. + Jennifer Fostel + electrocardiogram assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + telemeter sensor detection assay + + An assay which uses an implanted telemeter to measure physiological data in a living organism and transmit the measures via radio waves to a recording device. + different types of telemeters can measure blood pressure, gross activity, heart rate, ECG, glucose and other physiological parameters. + Jennifer Fostel + telemeter sensor detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MEA assay + + A multi-unit recording assay using a multi-electrode array (MEA) on the surface of a well on a cell culture plate. + When cells capable of electrical signaling are cultured in the well the MEA grid can detect electrical signaling by the cells. + Jennifer Fostel + multi-electrode array assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transepithelial / transendothelial electrical resistance (TEER) assay + An example would be a TEER assay to measure the integrity of a cell monolayer with apical surface exposed to air and basal surface in culture medium; this mimics the airway epithelium. + + An extracellular electrophysiology recording assay to measure the integrity of a cell monolayer + the assay measures electrical resistance by manually placing two chopstick-style electrodes on each side of a confluent cell layer. A low frequency current is applied and the resistance of the barrier is measured. + Jennifer Fostel + transepithelial / transendothelial electrical resistance (TEER) assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + number of active electrodes + + A multi-electrode array assay that measures the number of electrodes in a well where the mean rate of action potentials is at least 5 spikes per minute. + Jennifer Fostel + count of multi-electrode plate electrodes detecting action potential assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + number of bursting electrodes + + A multi-electrode array assay that measures the number of electrodes in a well where the burst rate is at least 0.5 bursts per minute. + A burst is temporal arrangement of action potentials that occur close together in time followed by a period of quiescence. + Jennifer Fostel + count of multi-electrode plate electrodes detecting neuron burst assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neural network spike rate assay + + An multi-electrode assay that measures the number of events when multiple electrodes simultaneously detect an action potential during a time period. + In a microelectrode array assay, the number of instances during a 15-minute recording when 5 or more electrodes in a well participate in an action potential burst at the same time. + Jennifer Fostel + neural network spike rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neural network spike duration assay + + A multi-electrode assay that measures the mean duration of events when multiple electrodes detect an action potential + In a microelectrode array (MEA) assay, the time interval before and after the network spike peak when half as many electrodes are spiking as at the peak of the network spike . + Jennifer Fostel + neural network spike duration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + network spike peak + + A multi-electrode array assay that measures the average number of electrodes detecting a network spike, measured at the peak of a network spike. + a network spike is defined in this context as an event when multiple electrodes detect an action potential + Jennifer Fostel + count of multi-electrode plate electrodes detecting spike peak assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mean interspike interval in network spike + + A multi-electrode assay that measures the average interval between network spikes, events where multiple electrodes simultaneously detect an action potential. + The time interval between the peaks of consecutive network spikes in a microelectrode array (MEA). A network spike is an event where multiple electrodes simultaneously detect an action potential. + Jennifer Fostel + mean interspike interval in network spike + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -104778,35 +111700,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - - - - - - - - - - - cell based DNA damage assay + bile acid concentration assay - A cytometry assay that measures DNA damage in cells. + An analyte assay that measures the abundance of bile acid in a volume of sample. + The major component of bile acids are cholic and chenodeoxycholic acid. Jennifer Fostel - cell based DNA damage assay + bile acid concentration assay - + - - + + @@ -104818,7 +111730,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104829,7 +111741,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104841,30 +111753,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - natural killer cell count assay - - A cytometry assay to determine the number of natural killer cells in a specimen - Jennifer Fostel - natural killer cell count assay - - - - - - - - @@ -104873,10 +111761,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -104884,17 +111772,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + @@ -104905,24 +111783,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - natural killer cell percentage assay + urea nitrogen assay - A cytometry assay that measures the percentage of natural killer cells in a specimen. + An analyte assay that measures the abundance of urea nitrogen. + urea nitrogen is the nitrogen component of urea found in a biological specimen Jennifer Fostel - natural killer cell percentage assay + urea nitrogen assay - + - - + + @@ -104934,7 +111813,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104945,7 +111824,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104957,35 +111836,80 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + + + + + + + + + - + - sperm count assay + urea nitrogen concentration assay - A cytometry assay to count the number of mature sperm in a specimen. + A urea nitrogen assay that measures the abundance of urea nitrogen in a specimen + urea nitrogen is the nitrogen component of urea found in a biological specimen Jennifer Fostel - sperm count assay + urea nitrogen concentration assay - + - - - survey administration assay - - An assay that obtains data from one or more participants by using a survey or questionnaire - Jennifer Fostel - survey administration assay + + + randomized clinical trial + + A clinical trial in which the participants are divided by chance into separate groups that compare different treatments or other interventions. Using chance to divide people into groups means that the groups will be similar and that the effects of the treatments they receive can be compared more fairly. At the time of the trial, it is not known which treatment is best. + Sebastian Duesing + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/randomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + randomized clinical trial + + + + + + + + + non-randomized clinical trial + + A clinical trial in which the participants are not assigned by chance to different treatment groups. Participants may choose which group they want to be in, or they may be assigned to the groups by the researchers. + Sebastian Duesing + nonrandomized clinical trial + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/nonrandomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + non-randomized clinical trial @@ -105032,7 +111956,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + Epstein Barr virus transformed B cell PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. @@ -105047,7 +111971,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + chimera An organism which contains cells or tissues with a different genotype @@ -105081,7 +112005,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -105155,31 +112078,22 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - organism - animal - fungus - plant - virus + + obsolete organism + animal + fungus + plant + virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism + WEB: http://en.wikipedia.org/wiki/Organism + + + obsolete organism + true @@ -105340,7 +112254,7 @@ This issue is outside the scope of OBI. - + @@ -105350,7 +112264,7 @@ This issue is outside the scope of OBI. - + xenograft @@ -105369,7 +112283,7 @@ This issue is outside the scope of OBI. - + @@ -105484,7 +112398,7 @@ Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39- - + screening library PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] @@ -105514,7 +112428,6 @@ change biomaterial to material in definition - synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme @@ -105533,7 +112446,7 @@ DS: Is this synthetic an oxymoron to the biomaterial? - + @@ -105653,7 +112566,21 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - + + + + + + + + + + + + + + + @@ -105685,7 +112612,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. - A planned process that produces output data from input data. + A completely executed planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone @@ -107840,7 +114767,7 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - + @@ -109676,28 +116603,23 @@ determinations of compounds. - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. @@ -109784,7 +116706,7 @@ determinations of compounds. - + @@ -109812,7 +116734,7 @@ determinations of compounds. - + @@ -109836,7 +116758,7 @@ determinations of compounds. - + @@ -109959,15 +116881,16 @@ determinations of compounds. - comet assay + DNA damage comet assay PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. - An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis + A cell based DNA damage assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis Philippe Rocca-Serra SCGE assay + comet assay single cell gel electrophoresis assay PMID:7686265 - comet assay + DNA damage comet assay @@ -110069,7 +116992,6 @@ determinations of compounds. - denatured polymer Is a polymer which has lost secondary or tertiary structure @@ -110094,7 +117016,7 @@ determinations of compounds. - + decapitated organism Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 @@ -110188,7 +117110,6 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - methylated polymer Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 @@ -110207,7 +117128,7 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 - + @@ -110215,8 +117136,8 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 + - genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 @@ -110402,7 +117323,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110423,7 +117344,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110456,7 +117377,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110489,11 +117410,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + - + @@ -110538,7 +117459,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110687,7 +117608,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + intentional overdosing @@ -110753,7 +117674,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110774,7 +117695,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110806,14 +117727,14 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + - + @@ -110876,7 +117797,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110904,7 +117825,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -110931,7 +117852,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + validation PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. @@ -111017,7 +117938,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -111235,7 +118156,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112165,7 +119086,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112199,7 +119120,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + particle delivery vessel FC 500 particle delivery vessel @@ -112285,7 +119206,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112307,7 +119228,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112549,7 +119470,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112640,7 +119561,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112711,7 +119632,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112830,7 +119751,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113199,7 +120120,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113374,7 +120295,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113449,7 +120370,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -114107,7 +121028,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114136,14 +121057,14 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114159,7 +121080,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114213,7 +121134,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114230,13 +121151,13 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114316,7 +121237,7 @@ Relates to the creation of a class 'selection rule' - + exposure of material to environment Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. @@ -114436,7 +121357,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114463,11 +121384,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + @@ -114479,7 +121400,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114675,7 +121596,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114698,7 +121619,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114892,7 +121813,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114914,7 +121835,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114977,7 +121898,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115074,7 +121995,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115096,7 +122017,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115152,7 +122073,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115226,7 +122147,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115266,7 +122187,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115287,17 +122208,17 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + - + @@ -115383,7 +122304,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115779,7 +122700,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115874,7 +122795,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115995,7 +122916,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116110,8 +123031,8 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ + - @@ -116139,7 +123060,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116167,7 +123088,7 @@ Isolation of proliferation factor of immature T-cell clone in concanavalin A-sti - + @@ -116235,7 +123156,7 @@ addition of has_role restriction - + @@ -116266,7 +123187,7 @@ old defintion: A mixture (collection) of cell components created by rupturing of - + @@ -116320,7 +123241,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - @@ -116350,7 +123270,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + assay bead Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. @@ -116675,7 +123595,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + Immunization in vivo @@ -116767,7 +123687,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116883,7 +123803,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116928,7 +123848,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116936,7 +123856,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + host of immune response A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. @@ -117204,7 +124124,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - lymph node cell specimen @@ -118000,19 +124919,20 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - blood harvesting + blood specimen collection - A material separation where blood is taken from an organism. + A specimen collection in which blood is collected from an organism. IEDB + blood harvesting IEDB - blood harvesting + blood specimen collection @@ -118200,7 +125120,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - splenocyte specimen @@ -122002,7 +128921,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + calcium cation assay An analyte assay that measures the abundance of calcium cation @@ -147892,18 +154811,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - phenotype - A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. - - phenotype - - - - @@ -147960,7 +154867,7 @@ realizes some 'host of immune response role' - + treatment A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process @@ -148010,7 +154917,7 @@ realizes some 'host of immune response role' health care provider role - A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. + A health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. health care provider role @@ -148044,7 +154951,7 @@ realizes some 'host of immune response role' - + parasite organism An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. @@ -148068,7 +154975,7 @@ realizes some 'host of immune response role' - + quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities @@ -148077,6 +154984,18 @@ realizes some 'host of immune response role' + + + + + speed + A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position. + + speed + + + + @@ -148089,6 +155008,19 @@ realizes some 'host of immune response role' + + + + + + color + A composite chromatic quality composed of hue, saturation and intensity parts. + + color + + + + @@ -148125,6 +155057,18 @@ realizes some 'host of immune response role' + + + + + distance + A quality that is the extent of space between two entities. + + distance + + + + @@ -148305,6 +155249,18 @@ realizes some 'host of immune response role' + + + + + opacity + An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. + + opacity + + + + @@ -148317,6 +155273,18 @@ realizes some 'host of immune response role' + + + + + mass density + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. + + mass density + + + + @@ -148404,7 +155372,7 @@ realizes some 'host of immune response role' - + physical object quality A quality which inheres in a continuant. @@ -148413,6 +155381,30 @@ realizes some 'host of immune response role' + + + + + full-spectrum EM radiation quality + An EM radiation quality that is independent of the EM wavelength range. + + full-spectrum EM radiation quality + + + + + + + + + absorption quality + A scalar EM radiation quality which obtains by the capacity of the bearer to retain radiation. + + absorption quality + + + + @@ -148749,6 +155741,18 @@ realizes some 'host of immune response role' + + + + + conductivity + A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium. + + conductivity + + + + @@ -148810,6 +155814,18 @@ realizes some 'host of immune response role' + + + + + electrical conductivity + A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity. + + electrical conductivity + + + + @@ -148834,6 +155850,18 @@ realizes some 'host of immune response role' + + + + + acidity + A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions). + + acidity + + + + @@ -148918,6 +155946,16 @@ realizes some 'host of immune response role' + + + + + A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. + electric charge + + + + @@ -148978,6 +156016,18 @@ realizes some 'host of immune response role' + + + + + velocity + A physical quality inhering in a bearer by virtue of the bearer's rate of change of the position. + + velocity + + + + @@ -149026,12 +156076,40 @@ realizes some 'host of immune response role' + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + collection of organisms + + + + + + + + + An anatomical entity that is or was part of a plant. + plant anatomical entity + + + + + protein antithrombin III is a protein + An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein @@ -149087,6 +156165,18 @@ realizes some 'host of immune response role' + + + + + adenosine deaminase + A protein that is a translation product of the human ADA gene or a 1:1 ortholog thereof. + + adenosine deaminase + + + + @@ -149279,6 +156369,16 @@ realizes some 'host of immune response role' + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + amino acid chain + + + + @@ -149412,6 +156512,30 @@ realizes some 'host of immune response role' + + + + + luciferase-like monooxygenase + A protein that is a translation product of the Escherichia coli K-12 yhbW gene or a 1:1 ortholog thereof. + + luciferase-like monooxygenase + + + + + + + + + bacterial protein + A protein that is encoded in the genome of some Bacteria <prokaryote>. + + bacterial protein + + + + @@ -149484,6 +156608,18 @@ realizes some 'host of immune response role' + + + + + modified histone + A histone that contains one or more amino acid modifications. + + modified histone + + + + @@ -149519,7 +156655,7 @@ realizes some 'host of immune response role' - + region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule @@ -149654,10 +156790,26 @@ realizes some 'host of immune response role' - - uterine cervix + + + + + + + + + + + + + + + + + + + Lower, narrow portion of the uterus where it joins with the top end of the vagina. - uterine cervix @@ -149666,10 +156818,8 @@ realizes some 'host of immune response role' - - pituitary gland + The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. - pituitary gland @@ -149678,10 +156828,14 @@ realizes some 'host of immune response role' - - peripheral nervous system + + + + + + + A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. - peripheral nervous system @@ -149690,10 +156844,26 @@ realizes some 'host of immune response role' - - lymph node + + + + + + + + + + + + + + + + + + + Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. - lymph node @@ -149702,22 +156872,50 @@ realizes some 'host of immune response role' - - urethra + + + + + + + The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. - urethra + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + anatomical structure + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + organ + + + + - life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. - life cycle stage @@ -149726,10 +156924,26 @@ realizes some 'host of immune response role' - - cloaca + + + + + + + + + + + + + + + + + + + Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. - cloaca @@ -149738,10 +156952,20 @@ realizes some 'host of immune response role' - - mouth + + + + + + + + + + + + + The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - mouth @@ -149751,9 +156975,7 @@ realizes some 'host of immune response role' - amniotic fluid Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. - amniotic fluid @@ -149763,9 +156985,13 @@ realizes some 'host of immune response role' - blood + + + + + + A fluid that is composed of blood plasma and erythrocytes. - blood @@ -149774,10 +157000,26 @@ realizes some 'host of immune response role' - - amnion + + + + + + + + + + + + + + + + + + + The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected. - amnion @@ -149786,10 +157028,14 @@ realizes some 'host of immune response role' - - breast + + + + + + + The upper ventral region of the torso of an organism. - breast @@ -149799,21 +157045,33 @@ realizes some 'host of immune response role' - cervical mucus A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. - cervical mucus + + + + + An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. + late embryo + + + + - - throat + + + + + + + In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. - throat @@ -149823,9 +157081,7 @@ realizes some 'host of immune response role' - renal medulla The inner portion of the kidney consisting of the renal pyramids. - renal medulla @@ -149835,9 +157091,7 @@ realizes some 'host of immune response role' - organism substance Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. - organism substance @@ -149846,22 +157100,57 @@ realizes some 'host of immune response role' + + + + + + + + + + - material anatomical entity + Anatomical entity that has mass. - material anatomical entity + + + + + + Anatomical entity that has no mass. + immaterial anatomical entity + + + + + + + + + + + + + + + Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. + anatomical system + + + + - - testis + + A gonad of a male animal. A gonad produces and releases sperm. - testis @@ -149870,10 +157159,8 @@ realizes some 'host of immune response role' - - anatomical cluster + Anatomical group whose component anatomical structures lie in close proximity to each other. - anatomical cluster @@ -149882,10 +157169,8 @@ realizes some 'host of immune response role' - - tissue + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. - tissue @@ -149894,10 +157179,14 @@ realizes some 'host of immune response role' - - multi-tissue structure + + + + + + + Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. - multi-tissue structure @@ -149907,9 +157196,13 @@ realizes some 'host of immune response role' - epithelium + + + + + + Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - epithelium @@ -149918,10 +157211,20 @@ realizes some 'host of immune response role' - - stomach + + + + + + + + + + + + + An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. - stomach @@ -149930,10 +157233,14 @@ realizes some 'host of immune response role' - - aorta + + + + + + + The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. - aorta @@ -149942,10 +157249,8 @@ realizes some 'host of immune response role' - - heart + A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. - heart @@ -149954,10 +157259,8 @@ realizes some 'host of immune response role' - - brain + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. - brain @@ -149966,10 +157269,14 @@ realizes some 'host of immune response role' - - cerebral cortex + + + + + + + The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. - cerebral cortex @@ -149978,10 +157285,8 @@ realizes some 'host of immune response role' - - eye + An organ that detects light. - eye @@ -149990,10 +157295,8 @@ realizes some 'host of immune response role' - - leg + The portion of the hindlimb that contains both the stylopod and zeugopod. - leg @@ -150002,10 +157305,8 @@ realizes some 'host of immune response role' - - ovary + The gonad of a female organism which contains germ cells. - ovary @@ -150014,10 +157315,20 @@ realizes some 'host of immune response role' - - uterus + + + + + + + + + + + + + The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. - uterus @@ -150026,10 +157337,20 @@ realizes some 'host of immune response role' - - vagina + + + + + + + + + + + + + A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. - vagina @@ -150039,9 +157360,20 @@ realizes some 'host of immune response role' - skin epidermis + + + + + + + + + + + + + The outer epithelial layer of the skin that is superficial to the dermis. - skin epidermis @@ -150050,10 +157382,9 @@ realizes some 'host of immune response role' - - respiratory system + + Functional system which consists of structures involved in respiration. - respiratory system @@ -150062,10 +157393,8 @@ realizes some 'host of immune response role' - - adipose tissue + Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. - adipose tissue @@ -150074,10 +157403,26 @@ realizes some 'host of immune response role' - - strand of hair + + + + + + + + + + + + + + + + + + + A filament, mostly protein, that grows from follicles found in the dermis[WP]. - strand of hair @@ -150086,22 +157431,54 @@ realizes some 'host of immune response role' - - rectum + + + + + + + + + + + + + + + + + + + The terminal portion of the intestinal tube, terminating with the anus. - rectum + + + + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + - pleural fluid Transudate contained in the pleural cavity. - pleural fluid @@ -150111,9 +157488,7 @@ realizes some 'host of immune response role' - urine Excretion that is the output of a kidney. - urine @@ -150123,9 +157498,7 @@ realizes some 'host of immune response role' - sweat Secretion produced by a sweat gland. - sweat @@ -150135,9 +157508,7 @@ realizes some 'host of immune response role' - synovial fluid Joint fluid is a transudate of plasma that is actively secreted by synovial cells. - synovial fluid @@ -150146,10 +157517,14 @@ realizes some 'host of immune response role' - - diaphragm + + + + + + + A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. - diaphragm @@ -150158,10 +157533,8 @@ realizes some 'host of immune response role' - - skeletal muscle tissue + Muscle tissue that consists primarily of skeletal muscle fibers. - skeletal muscle tissue @@ -150170,10 +157543,20 @@ realizes some 'host of immune response role' - - colon + + + + + + + + + + + + + A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. - colon @@ -150182,10 +157565,26 @@ realizes some 'host of immune response role' - - sigmoid colon + + + + + + + + + + + + + + + + + + + The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. - sigmoid colon @@ -150194,10 +157593,14 @@ realizes some 'host of immune response role' - - cortex of kidney + + + + + + + Outer cortical portion of the kidney, between the renal capsule and the renal medulla. - cortex of kidney @@ -150206,10 +157609,14 @@ realizes some 'host of immune response role' - - urinary bladder + + + + + + + Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. - urinary bladder @@ -150218,10 +157625,14 @@ realizes some 'host of immune response role' - - pancreas + + + + + + + An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. - pancreas @@ -150231,9 +157642,7 @@ realizes some 'host of immune response role' - peritoneal fluid Transudate contained in the peritoneal cavity. - peritoneal fluid @@ -150242,10 +157651,26 @@ realizes some 'host of immune response role' - - tibial nerve + + + + + + + + + + + + + + + + + + + The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]. - tibial nerve @@ -150255,21 +157680,39 @@ realizes some 'host of immune response role' - cerebrospinal fluid A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. - cerebrospinal fluid + + + + + + + + + + + + + + + + + Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. + skeletal system + + + + - - arm + The part of the forelimb extending from the shoulder to the autopod[cjm]. - arm @@ -150278,10 +157721,14 @@ realizes some 'host of immune response role' - - knee joint + + + + + + + The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. - knee joint @@ -150290,10 +157737,14 @@ realizes some 'host of immune response role' - - ankle joint + + + + + + + A joint that connects the hindlimb autopod and zeugopod skeletons. - ankle joint @@ -150303,9 +157754,7 @@ realizes some 'host of immune response role' - common carotid artery plus branches A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. - common carotid artery plus branches @@ -150314,10 +157763,20 @@ realizes some 'host of immune response role' - - digestive tract + + + + + + + + + + + + + A tube extending from the mouth to the anus. - digestive tract @@ -150326,10 +157785,14 @@ realizes some 'host of immune response role' - - upper respiratory tract + + + + + + + The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. - upper respiratory tract @@ -150338,10 +157801,14 @@ realizes some 'host of immune response role' - - lower respiratory tract + + + + + + + The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. - lower respiratory tract @@ -150350,10 +157817,14 @@ realizes some 'host of immune response role' - - cheek + + + + + + + A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. - cheek @@ -150362,10 +157833,8 @@ realizes some 'host of immune response role' - - facial muscle + A muscle innervated by a facial nerve. - facial muscle @@ -150375,9 +157844,13 @@ realizes some 'host of immune response role' - coronary artery + + + + + + An artery that supplies the myocardium. - coronary artery @@ -150386,10 +157859,14 @@ realizes some 'host of immune response role' - - artery + + + + + + + An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. - artery @@ -150398,10 +157875,14 @@ realizes some 'host of immune response role' - - vein + + + + + + + Any of the tubular branching vessels that carry blood from the capillaries toward the heart. - vein @@ -150410,10 +157891,14 @@ realizes some 'host of immune response role' - - tongue + + + + + + + A muscular organ in the floor of the mouth. - tongue @@ -150422,10 +157907,20 @@ realizes some 'host of immune response role' - - nasopharynx + + + + + + + + + + + + + The section of the pharynx that lies above the soft palate. - nasopharynx @@ -150434,10 +157929,20 @@ realizes some 'host of immune response role' - - oropharynx + + + + + + + + + + + + + The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. - oropharynx @@ -150447,9 +157952,19 @@ realizes some 'host of immune response role' - vitreous humor + + + + + + + + + + + + A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina. - vitreous humor @@ -150458,10 +157973,14 @@ realizes some 'host of immune response role' - - conjunctiva + + + + + + + The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball. - conjunctiva @@ -150470,10 +157989,32 @@ realizes some 'host of immune response role' - - nasal cavity mucosa + + + + + + + + + + + + + + + + + + + + + + + + + The mucous membrane that lines the nasal cavity[MP]. - nasal cavity mucosa @@ -150482,10 +158023,20 @@ realizes some 'host of immune response role' - - minor salivary gland + + + + + + + + + + + + + One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. - minor salivary gland @@ -150495,9 +158046,7 @@ realizes some 'host of immune response role' - saliva A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. - saliva @@ -150506,10 +158055,20 @@ realizes some 'host of immune response role' - - caudate nucleus + + + + + + + + + + + + + Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. - caudate nucleus @@ -150518,10 +158077,20 @@ realizes some 'host of immune response role' - - putamen + + + + + + + + + + + + + Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion. - putamen @@ -150531,9 +158100,19 @@ realizes some 'host of immune response role' - telencephalon + + + + + + + + + + + + Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. - telencephalon @@ -150543,9 +158122,7 @@ realizes some 'host of immune response role' - milk An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. - milk @@ -150555,9 +158132,7 @@ realizes some 'host of immune response role' - semen Organism substance that is composed of sperm cells suspended in seminal fluid. - semen @@ -150567,21 +158142,45 @@ realizes some 'host of immune response role' - bile Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. - bile + + + + + + + + + + + + + + + + + A vessel through which blood circulates in the body. + blood vessel + + + + - - placenta + + + + + + + Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. - placenta @@ -150591,9 +158190,7 @@ realizes some 'host of immune response role' - feces Portion of semisolid bodily waste discharged through the anus[MW,modified]. - feces @@ -150602,10 +158199,14 @@ realizes some 'host of immune response role' - - areola + + + + + + + Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. - areola @@ -150615,9 +158216,19 @@ realizes some 'host of immune response role' - cerebellum + + + + + + + + + + + + Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. - cerebellum @@ -150626,10 +158237,8 @@ realizes some 'host of immune response role' - - thyroid gland + A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. - thyroid gland @@ -150638,10 +158247,14 @@ realizes some 'host of immune response role' - - lung + + + + + + + Respiration organ that develops as an outpocketing of the esophagus. - lung @@ -150650,10 +158263,26 @@ realizes some 'host of immune response role' - - dermis + + + + + + + + + + + + + + + + + + + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. - dermis @@ -150662,10 +158291,26 @@ realizes some 'host of immune response role' - - hypodermis + + + + + + + + + + + + + + + + + + + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. - hypodermis @@ -150674,10 +158319,14 @@ realizes some 'host of immune response role' - - skin of body + + + + + + + The organ covering the body that consists of the dermis and epidermis. - skin of body @@ -150686,10 +158335,8 @@ realizes some 'host of immune response role' - - spleen + The organ that functions to filter blood and to store red corpuscles and platelets. - spleen @@ -150698,10 +158345,8 @@ realizes some 'host of immune response role' - - liver + An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. - liver @@ -150710,10 +158355,20 @@ realizes some 'host of immune response role' - - ileum + + + + + + + + + + + + + The portion of the small intestine that extends from the jejunum to the colon. - ileum @@ -150722,10 +158377,26 @@ realizes some 'host of immune response role' - - integument + + + + + + + + + + + + + + + + + + + The dermis, epidermis and hypodermis. - integument @@ -150735,9 +158406,19 @@ realizes some 'host of immune response role' - peritoneum + + + + + + + + + + + + A serous membrane that lines the peritoneal cavity[VHOG,modified]. - peritoneum @@ -150746,10 +158427,8 @@ realizes some 'host of immune response role' - - prostate gland + The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. - prostate gland @@ -150758,10 +158437,8 @@ realizes some 'host of immune response role' - - adrenal gland + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. - adrenal gland @@ -150771,21 +158448,55 @@ realizes some 'host of immune response role' - bone marrow + + + + + + + + + + + + The soft tissue that fills the cavities of bones. - bone marrow + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. + connective tissue + + + + + + + + + Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. + muscle tissue + + + + - - forelimb zeugopod + + + + + + + The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants. - forelimb zeugopod @@ -150794,10 +158505,8 @@ realizes some 'host of immune response role' - - manual digit + A digit that is part of a manus (hand). - manual digit @@ -150807,9 +158516,13 @@ realizes some 'host of immune response role' - lymph + + + + + + Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. - lymph @@ -150819,9 +158532,7 @@ realizes some 'host of immune response role' - pericardial fluid Transudate contained in the pericardial cavity.[FMA]. - pericardial fluid @@ -150830,10 +158541,8 @@ realizes some 'host of immune response role' - - tail + An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. - tail @@ -150842,10 +158551,14 @@ realizes some 'host of immune response role' - - lymphoid system + + + + + + + The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. - lymphoid system @@ -150854,22 +158567,68 @@ realizes some 'host of immune response role' - - esophagus mucosa + + + + + + + + + + + + + + + + + + + A mucosa that is part of a esophagus [Automatically generated definition]. - esophagus mucosa + + + + + + + + + + + A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID]. + corpus luteum + + + + + + + + + An organ that functions as a secretory or excretory organ. + gland + + + + - - left cerebral hemisphere + + + + + + + A cerebral hemisphere that is in the left side of a brain. - left cerebral hemisphere @@ -150878,22 +158637,40 @@ realizes some 'host of immune response role' - - right cerebral hemisphere + + + + + + + A cerebral hemisphere that is in the right side of a brain. - right cerebral hemisphere + + + + + Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. + surface structure + + + + - - trachea + + + + + + + The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. - trachea @@ -150902,10 +158679,20 @@ realizes some 'host of immune response role' - - cranium + + + + + + + + + + + + + Upper portion of the skull that excludes the mandible (when present in the organism). - cranium @@ -150914,10 +158701,14 @@ realizes some 'host of immune response role' - - omentum + + + + + + + A fold of peritoneum originating at the stomach and supporting the viscera. - omentum @@ -150926,10 +158717,20 @@ realizes some 'host of immune response role' - - esophagus muscularis mucosa + + + + + + + + + + + + + A muscularis mucosa that is part of a esophagus. - esophagus muscularis mucosa @@ -150938,10 +158739,38 @@ realizes some 'host of immune response role' - - mucosa of nasopharynx + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a nasopharynx [Automatically generated definition]. - mucosa of nasopharynx @@ -150950,10 +158779,44 @@ realizes some 'host of immune response role' - - mucosa of oropharynx + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a oropharynx [Automatically generated definition]. - mucosa of oropharynx @@ -150962,10 +158825,26 @@ realizes some 'host of immune response role' - - middle nasal concha + + + + + + + + + + + + + + + + + + + The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. - middle nasal concha @@ -150975,9 +158854,7 @@ realizes some 'host of immune response role' - bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. - bodily fluid @@ -150987,9 +158864,7 @@ realizes some 'host of immune response role' - respiratory system fluid/secretion A portion of organism substance that secreted_by a respiratory system. - respiratory system fluid/secretion @@ -150999,9 +158874,7 @@ realizes some 'host of immune response role' - atrium auricular region A small conical pouch projections located on the upper anterior portion of each atrium of the heart. - atrium auricular region @@ -151011,8 +158884,6 @@ realizes some 'host of immune response role' - digestive system secreted substance - digestive system secreted substance @@ -151022,9 +158893,13 @@ realizes some 'host of immune response role' - chorionic villus + + + + + + One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. - chorionic villus @@ -151034,9 +158909,13 @@ realizes some 'host of immune response role' - meconium + + + + + + A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. - meconium @@ -151046,9 +158925,7 @@ realizes some 'host of immune response role' - sputum Matter ejected from the lungs, bronchi, and trachea, through the mouth. - sputum @@ -151058,9 +158935,7 @@ realizes some 'host of immune response role' - tibial artery The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. - tibial artery @@ -151069,10 +158944,8 @@ realizes some 'host of immune response role' - - esophagogastric junction + The junction between the esophagus and the stomach epithelium. - esophagogastric junction @@ -151081,22 +158954,62 @@ realizes some 'host of immune response role' - - tendon of biceps brachii + + + + + + + + + + + + + A tendon that attaches_to a biceps brachii. - tendon of biceps brachii + + + + + A body of a multi-cellular organism that is no longer living. + carcass + + + + + + + + + An organism containing a developing embryo, fetus, or unborn offspring within the body. + gravid organism + + + + - omental fat pad + + + + + + + + + + + + Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon. - omental fat pad @@ -151105,10 +159018,14 @@ realizes some 'host of immune response role' - - brachioradialis + + + + + + + Brachioradialis is a muscle of the forearm that acts to flex the forearm at the elbow. It is also capable of both pronation and supination, depending on the position of the forearm. It is attached to the distal styloid process of the radius by way of the brachioradialis tendon, and to the lateral supracondylar ridge of the humerus. - brachioradialis @@ -151118,9 +159035,13 @@ realizes some 'host of immune response role' - umbilical cord blood + + + + + + Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. - umbilical cord blood @@ -151130,9 +159051,7 @@ realizes some 'host of immune response role' - arterial blood A blood that is part of a artery. - arterial blood @@ -151142,9 +159061,7 @@ realizes some 'host of immune response role' - venous blood A blood that is part of a vein. - venous blood @@ -151154,9 +159071,7 @@ realizes some 'host of immune response role' - capillary blood A blood that is part of a capillary. - capillary blood @@ -151165,10 +159080,26 @@ realizes some 'host of immune response role' - - suprapubic skin + + + + + + + + + + + + + + + + + + + Area of skin in the hypoastric region of the abdomen. - suprapubic skin @@ -151177,10 +159108,14 @@ realizes some 'host of immune response role' - - anterior nasal wall + + + + + + + Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule. - anterior nasal wall @@ -151190,9 +159125,7 @@ realizes some 'host of immune response role' - placental blood Blood located in the placenta. - placental blood @@ -151264,6 +159197,17 @@ realizes some 'host of immune response role' + + + + + speed/velocity unit + + speed/velocity unit + + + + @@ -151319,13 +159263,35 @@ realizes some 'host of immune response role' + + + + + phenotype + A phenotypic effect related to http://www.w3.org/2002/07/owl#Thing. + + phenotype + + + + + + + + + increased number of material anatomical entity in the urine + The presence of an increased number of material anatomical entity in the urine. + + increased number of material anatomical entity in the urine + + + + - - vaccine + Material entity that is manufactured to realize the vaccine function. - vaccine @@ -151335,9 +159301,7 @@ realizes some 'host of immune response role' - vaccination - A process of administering a vaccine in vivo to a recipient (e.g., human) with the intent to invoke a protective or therapeutic adaptive immune response. - + Process of administering a vaccine in vivo to a recipient (e.g., a human), with the intent to invoke a protective or therapeutic adaptive immune response. vaccination @@ -151390,8 +159354,11 @@ realizes some 'host of immune response role' failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. + Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg + + failed exploratory term @@ -151415,7 +159382,7 @@ realizes some 'host of immune response role' organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release + The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. PERSON:Alan Ruttenberg organizational term @@ -151488,6 +159455,10 @@ realizes some 'host of immune response role' placeholder removed + The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. + This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. + + placeholder removed @@ -151498,7 +159469,10 @@ realizes some 'host of immune response role' terms merged - An editor note should explain what were the merged terms and the reason for the merge. + The term has been combined with one or more other terms to create a more encompassing (merged) term. + The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. + + terms merged @@ -151509,7 +159483,10 @@ realizes some 'host of immune response role' term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + The term has been replaced by a term imported from another ontology. + This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. + + term imported @@ -151520,7 +159497,10 @@ realizes some 'host of immune response role' term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + The term has been split into two or more new terms. + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001. + + term split @@ -154934,10 +162914,12 @@ realizes some 'host of immune response role' The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 + + out of scope @@ -155625,12 +163607,6 @@ realizes some 'host of immune response role' microgram per liter - - - - - - @@ -155642,25 +163618,6 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - Person:Alan Ruttenberg - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - - - - - - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - geographic location A reference to a place on the Earth, by its name or by its geographical location. @@ -155678,48 +163635,16 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + @@ -155742,195 +163667,6 @@ realizes some 'host of immune response role' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/tmp/mirror-ro.owl b/src/ontology/tmp/mirror-ro.owl deleted file mode 100644 index a3d3910..0000000 --- a/src/ontology/tmp/mirror-ro.owl +++ /dev/null @@ -1,17884 +0,0 @@ - - - - - The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - - OBO Relations Ontology - 2025-03-05 - https://github.com/oborel/obo-relations/ - - - - - - - - - - - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - editor preferred term - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - example of usage - example of usage - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - has curation status - - - - - - - - definition - - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition - definition - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - term editor - - - - - - - - alternative label - - A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. - OBO Operations committee - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - - - - - - - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source - - - - - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - curator note - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - imported from - - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - imported from - - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - elucidation - - - - - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - - - - - term replaced by - - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - Add as annotation triples in the granting ontology - term replaced by - - - - - - - - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } - Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. - - - - defined by construct - - - - - - - - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation - - - - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: ?X DisjointWith: RO_0002162 some ?Y - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> -PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> -CONSTRUCT { - in_taxon: a owl:ObjectProperty . - ?x owl:disjointWith [ - a owl:Restriction ; - owl:onProperty in_taxon: ; - owl:someValuesFrom ?taxon - ] . - ?x rdfs:subClassOf [ - a owl:Restriction ; - owl:onProperty in_taxon: ; - owl:someValuesFrom [ - a owl:Class ; - owl:complementOf ?taxon - ] - ] . -} -WHERE { - ?x never_in_taxon: ?taxon . -} - never in taxon - - - - - - - - - - A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. - non-overlapping with - shares no parts with - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) - PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> -PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> -CONSTRUCT { - part_of: a owl:ObjectProperty . - [ - a owl:Restriction ; - owl:onProperty part_of: ; - owl:someValuesFrom ?x ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty part_of: ; - owl:someValuesFrom ?y - ] - ] -} -WHERE { - ?x mutually_spatially_disjoint_with: ?y . -} - mutually spatially disjoint with - - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - - - - - - - - An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. - taxonomic class assertion - - - - - - - - - - S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] - ambiguous for taxon - - - - - - - - - - S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - - - This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost - dubious for taxon - - - - - - - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> -PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> -CONSTRUCT { - in_taxon: a owl:ObjectProperty . - ?witness rdfs:label ?label . - ?witness rdfs:subClassOf ?x . - ?witness rdfs:subClassOf [ - a owl:Restriction ; - owl:onProperty in_taxon: ; - owl:someValuesFrom ?taxon - ] . -} -WHERE { - ?x present_in_taxon: ?taxon . - BIND(IRI(CONCAT( - "http://purl.obolibrary.org/obo/RO_0002175#", - MD5(STR(?x)), - "-", - MD5(STR(?taxon)) - )) as ?witness) - BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) -} - The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. - present in taxon - - - - - - - - - - defined by inverse - - - - - - - - - An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. - logical macro assertion - http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ - - - - - - - - An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. - annotation property cardinality - - - - - - - - - - A logical macro assertion whose domain is an IRI for a class - The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL - logical macro assertion on a class - - - - - - - - - A logical macro assertion whose domain is an IRI for a property - logical macro assertion on a property - - - - - - - - - Used to annotate object properties to describe a logical meta-property or characteristic of the object property. - logical macro assertion on an object property - - - - - - - - - logical macro assertion on an annotation property - - - - - - - - - An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. - dispositional interpretation - - - - - - - - - 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' - A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. - shares no connection with - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) - has no connections with - - - - - - - - - inherited annotation property - - - - - - - - Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) - curator guidance link - - - - - - - - - brain always_present_in_taxon 'Vertebrata' - forelimb always_present_in_taxon Euarchontoglires - S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S - This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. - never lost in - always present in taxon - - - - - - - - - This property was originally created for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. - temporal logical macro assertion on a class - - - - - - - - - measurement property has unit - - - - - - - - - has start time value - http://purl.obolibrary.org/obo/ro/docs/temporal-durations/ - - - - - - - - - has end time value - - - - - - - - - - Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. - start, days post fertilization - - - - - - - - - - Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. - end, days post fertilization - - - - - - - - - - Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. - start, years post birth - - - - - - - - - - Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 - end, years post birth - - - - - - - - - - Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. - start, months post birth - - - - - - - - - - Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 - end, months post birth - - - - - - - - - - Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. - month of gestation - - - - - - - - - - A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process - has developmental stage marker - - - - - - - - - - Count of number of days intervening between the start of the stage and the time of coitum. - For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) - start, days post coitum - - - - - - - - - - Count of number of days intervening between the end of the stage and the time of coitum. - end, days post coitum - - - - - - - - - - start, weeks post birth - - - - - - - - - - end, weeks post birth - - - - - - - - - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p - is asymmetric relational form of process class - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p - is symmetric relational form of process class - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process - is relational form of process class - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y - The general property hierarchy is: - - "directly P" SubPropertyOf "P" - Transitive(P) - -Where we have an annotation assertion - - "directly P" "is direct form of" "P" - If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - - is direct form of - - - - - - - - - - relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y - - is indirect form of - - - - - - - - - - logical macro assertion on an axiom - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. - is relational form of a class - - - - - - - - - A shortcut relationship that holds between two entities based on their identity criteria - logical macro assertion involving identity - - - - - - - - - A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. - in approximate one to one relationship with - - - - - - - - - x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y - The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" - is approximately equivalent to - - - - - - - - - 'anterior end of organism' is-opposite-of 'posterior end of organism' - 'increase in temperature' is-opposite-of 'decrease in temperature' - x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - is opposite of - - - - - - - - - x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - is indistinguishable from - - - - - - - - - evidential logical macro assertion on an axiom - - - - - - - - - A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. - axiom has evidence - - - - - - - - - A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. - axiom contradicted by evidence - - - - - - - - - In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. - this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. - If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion - is representative IRI for equivalence set - OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member - - - - - - - - - true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - - nominally disjoint with - - - - - - - - - Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" - - 2018-03-13T23:59:29Z - is directional form of - - - - - - - - - - 2018-03-14T00:03:16Z - is positive form of - - - - - - - - - - 2018-03-14T00:03:24Z - is negative form of - - - - - - - - - part-of is homeomorphic for independent continuants. - R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. - - 2018-10-21T19:46:34Z - R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. - is homeomorphic for - - - - - - - - - - - 2020-09-22T11:05:29Z - valid_for_go_annotation_extension - - - - - - - - - - - 2020-09-22T11:05:18Z - valid_for_go_gp2term - - - - - - - - - - - 2020-09-22T11:04:12Z - valid_for_go_ontology - - - - - - - - - - - 2020-09-22T11:05:45Z - valid_for_gocam - - - - - - - - - - eco subset - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - subset_property - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - has broad synonym - has_broad_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - - - - - - - - - disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string - An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. - - - 2024-03-18 - database_cross_reference - has cross-reference - - - - - - - - An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - has exact synonym - has_exact_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - - - - - - - - - An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 - has narrow synonym - has_narrow_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 - - - - - - - - - has_obo_format_version - - - - - - - - An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 - has related synonym - has_related_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 - - - - - - - - - - - - - - - in_subset - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is defined by - - - - - is defined by - This is an experimental annotation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - - - - - - part of - - - http://www.obofoundry.org/ro/#OBO_REL:part_of - https://wiki.geneontology.org/Part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - - - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - accidentally included in BFO 1.2 proposal - - should have been BFO_0000062 - obsolete preceded by - true - - - - - - - - - - - - - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - precedes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - https://wiki.geneontology.org/Occurs_in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. - derives from part of - - - - - - - - - A has part relationship between a whole and a part, where the number of parts present in the whole is higher than in comparable entities. - This relation is present in ENVO to support compositional classes such as "X-enriched soil". These will later be formalized, and a different relation from RO may be chosen. - has increased levels of - - - - - - - - - - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple - a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. - characteristic of - - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - has characteristic - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes. - is concretized as - - - - - - - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - inverse of has disposition - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - disposition of - - - - - - - - - OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. - - - - Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). - obsolete in neural circuit with - true - - - - - - - - - OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. - - - - Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). - obsolete upstream in neural circuit with - true - - - - - - - - - OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. - - - - Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). - obsolete downstream in neural circuit with - true - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. - - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - location of - - - - - - - - contained in - Containment is location not involving parthood, and arises only where some immaterial continuant is involved. - Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - contained_in - obsolete contained in - - true - - - - - - - - contains - obsolete contains - - true - - - - - - - - - - - penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - is allergic trigger for - - - - - - - - - - - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - is autoimmune trigger for - - - - - - - - - - penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - has allergic trigger - - - - - - - - - - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - has autoimmune trigger - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - - located in - https://wiki.geneontology.org/Located_in - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - - 2D boundary of - - - - - - - - - - May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 - - - aligned with - - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - A relation that holds between two neurons that are electrically coupled via gap junctions. - - - electrically_synapsed_to - - - - - - - - - - - The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - - tracheates - - - - - - - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - innervated_by - - - - - - - - - - - - has synaptic terminal of - - - - - - - - - - - - - - - - - - - - - X outer_layer_of Y iff: -. X :continuant that bearer_of some PATO:laminar -. X part_of Y -. exists Z :surface -. X has_boundary Z -. Z boundary_of Y - -has_boundary: http://purl.obolibrary.org/obo/RO_0002002 -boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. - bounding layer of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. - Note from NCEAS meeting: consider changing primary label - - - Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. - coincident with - - - - - - - - - - A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. - - x 'cell expresses' y iff: -cell(x) -AND gene(y) -AND exists some 'transcription, DNA templated (GO_0006351)'(t) -AND t occurs_in x -AND t has_input y - cell expresses - - - - - - - - - - - x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - - regulates in other organism - - regulates in another organism - - - - - - - - - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - - - regulates transport of - - - - - - - - - - - - A part of relation that applies only between occurrents. - occurrent part of - - - - - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - - 2017-05-24T09:30:46Z - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - has positive regulatory component activity - - - - - - - - - - - 2017-05-24T09:36:08Z - A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. - has necessary component activity - - - - - - - - - - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - - 2017-05-24T09:49:21Z - has component process - - - - - - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - - 2017-07-19T17:30:36Z - has ligand - - - - - - - - - Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - - 2017-07-20T17:11:08Z - transports - - - - - - - - - A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - - 2017-07-20T17:19:37Z - occurs across - - - - - - - - - - - 2017-09-17T13:52:24Z - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - directly regulated by - - - - - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - - - - - - - - - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - - 2017-09-17T13:52:38Z - directly negatively regulated by - - - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - - - - - - - - - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - - 2017-09-17T13:52:47Z - directly positively regulated by - - - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - - - - - - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - - - - - - - - - - - - A relationship that holds between two images, A and B, where: -A depicts X; -B depicts Y; -X and Y are both of type T' -C is a 2 layer image consiting of layers A and B; -A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. -Note: A and B may be 2D or 3D. -Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - - 2017-12-07T12:58:06Z - in register with - - - - - A relationship that holds between two images, A and B, where: -A depicts X; -B depicts Y; -X and Y are both of type T' -C is a 2 layer image consiting of layers A and B; -A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. -Note: A and B may be 2D or 3D. -Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - - - - - - - - - - David Osumi-Sutherland - <= - - Primitive instance level timing relation between events - before or simultaneous with - - - - - - - - - - - x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - - t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with - - - - - - - - - - David Osumi-Sutherland - - t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) - before - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which ends - - - - - - - - - - - - di - Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - encompasses - - - - - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - ends after - - - - - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - immediately preceded by - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which starts - - - - - - - - - - - - - - David Osumi-Sutherland - - starts before - - - - - - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - immediately precedes - - - - - - - - - - - David Osumi-Sutherland - io - - X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) - starts during - - - - - - - - - - - David Osumi-Sutherland - d - during - - - - - X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) - happens during - https://wiki.geneontology.org/Happens_during - - - - - - - - - David Osumi-Sutherland - o - overlaps - - X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). - ends during - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and a material anatomical entity that its soma is part of. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - - has soma location - - - - - - - - - - - - - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - fasciculates with - - - - - - - - - - - - - - - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( - <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - - axon synapses in - - - - - - - - - - - - - - - - - - - - - - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - synapsed by - - - - - - - - - - - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - - has plasma membrane part - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - - - BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_Ib_bouton_to - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - - - BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_Is_bouton_to - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - - - BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_II_bouton_to - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_II_bouton - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_Ib_bouton - - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in - http://purl.obolibrary.org/obo/BFO_0000051 some ( - http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( - http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - - has postsynaptic terminal in - - - - - - - - - - - has neurotransmitter - releases neurotransmitter - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_Is_bouton - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - - has presynaptic terminal in - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type III bouton. - BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_III_bouton_to - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type III bouton. - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_III_bouton - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - N1 synapsed_to some N2 -Expands to: -N1 SubclassOf ( - has_part some ( - ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( - ‘synapse ; GO:0045202’ that has_part some ( - ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) - synapsed to - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( - http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( - <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - - dendrite synapsed in - - - - - - - - - - - - - - - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in - <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - - has synaptic terminal in - - - - - - - - - - - - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - - - - - overlaps - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - - has fasciculating neuron projection - - - - - - - - - - - - - - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. -T innervates some R -Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - innervates - - - - - - - - - - - - - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - continuous with - FMA:85972 - - - - - - - - - - x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x - We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) - (iff - (proper_overlaps ?x ?y) - (and - (overlaps ?x ?y) - (not (part_of ?x ?y)) - (not (part_of ?y ?x))))) - - - partially overlaps - - - - - - - - - - - - d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. - ancestral_stucture_of - evolutionarily_descended_from - derived by descent from - - - - - - - - - - - inverse of derived by descent from - - has derived by descendant - - - - - - - - - - - - - - - - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - VBO calls this homologous_to - shares ancestor with - - - - - - - - - - - - serially homologous to - - - - - - - - - lactation SubClassOf 'only in taxon' some 'Mammalia' - - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. - The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. - - 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - only in taxon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - life cycle stage of - - Connects a biological entity to its taxon of origin. - in taxon - - - - - - - - - - - A is spatially_disjoint_from B if and only if they have no parts in common - There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy - BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - - - spatially disjoint from - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - - - - - - - - - - - - - - - - - - - - - - - - - - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - connected to - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - - - - - - - - - - - - - - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - connects - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - - - - - - - - - - - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - attached to part of - - - - - - - - - true - - - - - - - - - Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - supplies - - - - - - - - - Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - drains - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - has component - - - - - - - - - - - - - - - - - - - - - - A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - - - has phenotype - - - - - - - - - - inverse of has phenotype - - - - phenotype of - - - - - - - - - - - - - - - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - This is the transitive form of the develops from relation - develops from - - - - - - - - - - - - - inverse of develops from - - - - - develops into - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" - We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. - - gene product of - - - - - - - - - - - - - - - every HOTAIR lncRNA is the gene product of some HOXC gene - every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene - - x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y - - has gene product - - - - - - - - - - - - - - - - - - - - - - - - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - - expressed in - - - - - - - - - - - - - - - - - - - - - - - - - - - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - has developmental precursor - TODO - add child relations from DOS - directly develops from - - - - - - - - - - A parasite that kills or sterilizes its host - parasitoid of - - - - - - - - - inverse of parasitoid of - - has parasitoid - - - - - - - - - - inverse of directly develops from - developmental precursor of - - directly develops into - - - - - - - - - - - - - - - - - - - - - - - - - p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - - - - regulates - - - - - - - - - - - - - - - p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) - - - - - negatively regulates - - - - - - - - - - - - - - - - - - - - p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - - - - - positively regulates - - - - - - - - - - - - - - - - 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) - heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') - - x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. - Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) - TODO: add homeomorphy axiom - This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - - has prototype - - - - - - - - - - - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - - capable of - - - - - - - - - - - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in - capable of part of - - - - - - - - - - true - - - - - - - - OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role - - agent in - - Obsoleted as the inverse property was obsoleted. - obsolete actively participates in - true - - - - - - - - OBSOLETE x has participant y if and only if x realizes some active role that inheres in y - - has agent - - obsolete has active participant - true - - - - - - - - - - - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - surrounded by - - - - - - - - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - - x adjacent to y if and only if x and y share a boundary. - This relation acts as a join point with BSPO - - - - - - adjacent to - - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - - - - - - - - - - inverse of surrounded by - - - - surrounds - - - - - - - - - - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporally related to - - - - - - - - - - - - inverse of starts with - - Chris Mungall - Allen - - starts - - - - - - - - - - - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by - - starts with - - - - - - - - - - - - - - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - develops from part of - - - - - - - - - - - - - - - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - develops in - - - - - - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - obligate parasite of - - - - - - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - facultative parasite of - - - - - - - - - - - - inverse of ends with - - Chris Mungall - - ends - - - - - - - - - - - - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by - - ends with - - - - - - - - - - - - - - - - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in - - has start location - - - - - - - - - - - - - - - - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in - - has end location - - - - - - - - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes - - - - - has input - https://wiki.geneontology.org/Has_input - - - - - - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces - - - - - has output - https://wiki.geneontology.org/Has_output - - - - - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - stem parasite of - - - - - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - root parasite of - - - - - - - - - A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. - hemiparasite of - - - - - - - - - X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). - -If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. - - has component participant - - - - - - - - - A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. - ExO:0000001 - has exposure receptor - - - - - - - - - A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. - ExO:0000000 - has exposure stressor - - - - - - - - - A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor - ExO:0000055 - has exposure route - - - - - - - - - A broad relationship between an exposure event or process and the course takes from the source to the target. - http://purl.obolibrary.org/obo/ExO_0000004 - has exposure transport path - - - - - - - - - - Any relationship between an exposure event or process and any other entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. - related via exposure to - - - - - - - - - g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. - over-expressed in - - - - - - - - - g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. - under-expressed in - - - - - - - - - - - - Any portion of roundup 'has active ingredient' some glyphosate - A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. - has active substance - has active pharmaceutical ingredient - has active ingredient - - - - - - - - - inverse of has active ingredient - - active ingredient in - - - - - - - - - - - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. - b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - connecting branch of - - - - - - - - - - inverse of connecting branch of - - - has connecting branch - - - - - - - - - - - - - - - - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - - x has developmental contribution from y iff x has some part z such that z develops from y - - has developmental contribution from - - - - - - - - - - - - - - - inverse of has developmental contribution from - - - developmentally contributes to - - - - - - - - - - - - - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - developmentally induced by - - - - - - - - - - - Inverse of developmentally induced by - - developmentally induces - - - - - - - - - - - - - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p - false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one - This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by - - - - - - - - - c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) - has biological role - - - - - - - - - c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) - has application role - - - - - - - - - c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) - has chemical role - - - - - - - - - - - - - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. - c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. - - acts upstream of - - - - - - - - - - - - - - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. - c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. - affects - - acts upstream of or within - https://wiki.geneontology.org/Acts_upstream_of_or_within - - - - - - - - - - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else - This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - developmentally replaces - - - - - - - - - - Inverse of developmentally preceded by - - developmentally succeeded by - - - - - - - - - - - - - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - - part of developmental precursor of - - - - - - - - - - - x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x - Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. - - ubiquitously expressed in - - - - - - - - - - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - - expresses - - - - - - - - - - inverse of ubiquiotously expressed in - - - ubiquitously expresses - - - - - - - - - - - - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). - This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - - results in developmental progression of - - - - - - - - - - - every flower development (GO:0009908) results in development of some flower (PO:0009046) - - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml - - - - results in development of - - - - - - - - - - - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 - - - - results in formation of anatomical entity - - - - - - - - - - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 - - - - results in morphogenesis of - - - - - - - - - - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 - - - - results in maturation of - - - - - - - - - foramen ovale closure SubClassOf results in disappearance of foramen ovale - - - May be merged into parent relation - results in disappearance of - - - - - - - - - every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - - - May be merged into parent relation - results in developmental regression of - - - - - - - - - - Inverse of 'is substance that treats' - - - is treated by substance - - - - - - - - - - - Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' -where -'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview - - x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - - adapted for living in - - A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. - has habitat - - - - - - - - - - p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - - - - holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y - causally upstream of, positive effect - - - - - - - - - - - p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - - - - - causally upstream of, negative effect - - - - - - - - - - A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - - - - - 2017-06-05T17:35:04Z - has exposure stimulus - - - - - - - - - - evolutionary variant of - - - - - - - - - - Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - - regulates localization of - - - - transports or maintains localization of - - - - - - - - - - - - - - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. - Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - - characteristic of part of - - - - - - - - - - true - - - - - - - - - - - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. - The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 - - - - results in acquisition of features of - - - - - - - - A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. - evolutionarily related to - - - - - - - - A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) - Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions - - ecologically related to - - - - - - - - - - An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - - adapted for - - confers advantage in - - - - - - - - A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - - mereotopologically related to - - - - - - - - A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development - developmentally related to - - - - - - - - - - - Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) - a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - - In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - - colocalizes with - - - - - - - - - - ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. - Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. - eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex - We would like to say - -if and only if - exists c', p' - c part_of c' and c' capable_of p - and - c capable_of p' and p' part_of p -then - c contributes_to p - -However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - - In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. - - contributes to - https://wiki.geneontology.org/Contributes_to - - - - - - - - - - - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity - c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - - enables - https://wiki.geneontology.org/Enables - - - - - - - - A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - functionally related to - - - - - - - - - - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false - part of structure that is capable of - - - - - - - - - true - - - - - - - - - - holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism - genomically related to - - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of - involved in - https://wiki.geneontology.org/Involved_in - - - - - - - - - - - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid - p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) - regulates levels of - - - - - - - - - - inverse of enables - - - enabled by - https://wiki.geneontology.org/Enabled_by - - - - - - - - - - - - inverse of regulates - - regulated by (processual) - - regulated by - - - - - - - - - inverse of negatively regulates - - - negatively regulated by - - - - - - - - - inverse of positively regulates - - - positively regulated by - - - - - - - - - - A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. - related via localization to - - - - - - - - - - - - - This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - - - - - has target start location - - - - - - - - - - - - - This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - - - - - has target end location - - - - - - - - - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - - - imports - - - - - - - - - Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - - results in transport along - - - - - - - - - - Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - - - results in transport across - - - - - - - - - - 'pollen tube growth' results_in growth_of some 'pollen tube' - - results in growth of - - - - - - - - - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - - results in transport to from or in - - - - - - - - - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - - - exports - - - - - - - - - - an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. - p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - - - - - results in commitment to - - - - - - - - - - p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - - - - - results in determination of - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - inverse of has input - - - - input of - - - - - - - - - - inverse of has output - - - - output of - - - - - - - - - - formed as result of - - - - - - - - - - A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - - results in structural organization of - - - - - - - - - - The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - - - - - results in specification of - - - - - - - - - p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - - results in developmental induction of - - - - - - - - - - http://neurolex.org/wiki/Property:DendriteLocation - has dendrite location - - - - - - - - - - - a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - - attached to - - - - - - - - - - - m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - has muscle origin - - - - - - - We need to import uberon muscle to create a stricter domain constraint - - - - - - - - - - - m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - has muscle insertion - - - - - - - We need to import uberon muscle into RO to use as a stricter domain constraint - - - - - - - - - false - - x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat - - - has fused element - A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. - derived from ancestral fusion of - - - - - - - - - - - - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - - in branching relationship with - - https://github.com/obophenotype/uberon/issues/170 - - - - - - - - - - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - - tributary of - - http://en.wikipedia.org/wiki/Tributary - - - - - - - - - - Deschutes River distributary_of Little Lava Lake - - x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - - branch of - distributary channel of - http://en.wikipedia.org/wiki/Distributary - - This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes - distributary of - - - - - - - - - - - - - - - - - x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - - anastomoses with - - anabranch of - - - - - - - - - - - - - - - A lump of clay and a statue - x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios - spatially coextensive with - - - - - - - - - - - - - - - - - - - - - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S - x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - - branching part of - - FMA:85994 - - - - - - - - - - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. - - x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - - - main stem of - - - - - - - - - - - x proper_distributary_of y iff x distributary_of y and x does not flow back into y - - - proper distributary of - - - - - - - - - - x proper_tributary_of y iff x tributary_of y and x does not originate from y - - - proper tributary of - - - - - - - - - - - - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - - has developmental potential involving - - - - - - - - - - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - has potential to developmentally contribute to - - - - - - - - - - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - - has potential to developmentally induce - - - - - - - - - - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - This relation has a stronger meaning than merely indicating that X may develop into Y, in that the capability of developing into Y is always present, even if X does not always actually develop into Y. In particular, this means that if Y is restricted to a given taxon T, X is necessarily likewise restricted. - has potential to develop into - - - - - - - - - - - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - - has potential to directly develop into - - - - - - - - - - - - - 'protein catabolic process' SubClassOf has_direct_input some protein - - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - directly consumes - This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' - has direct input - - - - - - - - - - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect input - true - - - - - - - - translation SubClassOf has_direct_output some protein - - p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. - - directly produces - obsolete has direct output - true - - - - - - - - - - - - - - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - - - - - - - - - inverse of upstream of - - causally downstream of - - - - - - - - - - - - - immediately causally downstream of - - - - - - - - - This term was obsoleted because it has the same meaning as 'directly positively regulates'. - obsolete directly activates - true - - - - - - - - - - - - - - - - - - - - - - - - - - - p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - - indirectly positively regulates - https://wiki.geneontology.org/Indirectly_positively_regulates - - - - - - - - - This term was obsoleted because it has the same meaning as 'directly negatively regulates'. - obsolete directly inhibits - true - - - - - - - - - - - - - - - - - - - - - - - p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - - indirectly negatively regulates - https://wiki.geneontology.org/Indirectly_negatively_regulates - - - - - - - - relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. - This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. - -To define causal relations in an activity-flow type network, we make use of 3 primitives: - - * Temporal: how do the intervals of the two occurrents relate? - * Is the causal relation regulatory? - * Is the influence positive or negative? - -The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. - -For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. - -For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. - -Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causally related to - - - - - relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. - https://en.wikipedia.org/wiki/Causality - - - - - - - - - - - p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - - - - causally upstream of - - - - - - - - - - p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - - immediately causally upstream of - - - - - - - - - - - - - - p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - - directly provides input for - - directly provides input for (process to process) - provides input for - https://wiki.geneontology.org/Provides_input_for - - - - - - - - - - - - - transitive form of directly_provides_input_for - - This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. - transitively provides input for (process to process) - transitively provides input for - - - - - - - - - - - - - - - p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. - We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) - affects - causally upstream of or within - - - - - - - - false - - This is an exploratory relation - differs in - https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions - - - - - - - - - - - - - - - - - - differs in attribute of - - - - - - - - - - - differs in attribute - - - - - - - - - - inverse of causally upstream of or within - - - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - - involved in regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - - involved in positive regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - - - involved in negative regulation of - - - - - - - - - - - c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p - OWL does not allow defining object properties via a Union - - involved in or reguates - involved in or involved in regulation of - - - - - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in - enables activity in - is active in - https://wiki.geneontology.org/Is_active_in - - - - - - - - - true - - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - - - - - - - - - - p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - contributes to morphology of - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. - in pairwise interaction with - - interacts with - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 - - - - - - - - - - An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - - genetically interacts with - - http://purl.obolibrary.org/obo/MI_0208 - - - - - - - - - - An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with - molecularly interacts with - - http://purl.obolibrary.org/obo/MI_0915 - - - - - - - - - - - - - An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - - interacts with on organism level - - biotically interacts with - - http://eol.org/schema/terms/interactsWith - - - - - - - - - lions trophically interact with the zebras that they eat - An interaction relationship in which the partners are related via a feeding relationship. - - - trophically interacts with - - - - - - - - - - - A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] - Baleen whale preys on krill - An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - - - - is subject of predation interaction with - preys upon - - preys on - http://eol.org/schema/terms/preysUpon - http://www.inaturalist.org/observations/2942824 - - - - - - - - - - - - - - - - - whales symbiotically interact with the barnacles that attach to them - A biotic interaction in which the two organisms live together in more or less intimate association. - - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - - symbiotically interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - commensually interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - mutualistically interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - This relation groups a pair of inverse relations, parasite of and parasitized by - - interacts with via parasite-host interaction - - - - - - - - - - - - - - - - - - Pediculus humanus capitis parasite of human - A parasite-host relationship where an organism benefits at the expense of another. - - parasitizes - direct parasite of - - parasite of - http://eol.org/schema/terms/parasitizes - - - - - - - - - - Inverse of parasite of - - has parasite - parasitised by - directly parasitized by - - parasitized by - http://eol.org/schema/terms/hasParasite - - - - - - - - - Porifiera attaches to substrate - A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - - semibiotically interacts with - - participates in a abiotic-biotic interaction with - - - - - - - - - - - - - - - Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. - phosphorylates - - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - - molecularly controls - directly regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits - molecularly decreases activity of - directly negatively regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates - molecularly increases activity of - directly positively regulates activity of - - - - - - - - - all dengue disease transmitted by some mosquito - A relationship that holds between a disease and organism - Add domain and range constraints - - transmitted by - - - - - - - - - - A relation that holds between a disease or an organism and a phenotype - - has symptom - - - - - - - - - - The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) - - host of - - - - - - - - - X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - - - has host - http://eol.org/schema/terms/hasHost - - - - - - - - - - Bees pollinate Flowers - This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - - is subject of pollination interaction with - - pollinates - http://eol.org/schema/terms/pollinates - - - - - - - - - - has polinator - is target of pollination interaction with - - pollinated by - http://eol.org/schema/terms/hasPollinator - - - - - - - - - - Inverse of provides nutrients for - - Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. - - acquires nutrients from - - - - - - - - - inverse of preys on - - has predator - is target of predation interaction with - - - preyed upon by - http://eol.org/schema/terms/HasPredator - http://polytraits.lifewatchgreece.eu/terms/PRED - - - - - - - - - - Anopheles is a vector for Plasmodium - - a is a vector for b if a carries and transmits an infectious pathogen b into another living organism - - is vector for - - - - - - - - - - - has vector - - - - - - - - - - Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target - partner in - - - - - - - - - - Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. - subject participant in - - - - - - - - - - Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. - target participant in - - - - - - - - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property (not for use in curation) - - - - - - - - - - is symbiosis - - - - - - - - - - is commensalism - - - - - - - - - - is mutualism - - - - - - - - - - is parasitism - - - - - - - - - A biotic interaction where a material entity provides nutrition for an organism. - - - provides nutrients for - - - - - - - - - A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. - - is subject of eating interaction with - - eats - - - - - - - - - Inverse of eats - - eaten by - is target of eating interaction with - - is eaten by - - - - - - - - - - A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and -the a supports either the existence of b, or the truth value of b. - - - is evidence for - - - - - - - - - - - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' - x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - - composed primarily of - - - - - - - - - - - ABal nucleus child nucleus of ABa nucleus (in C elegans) - c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - - This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. - child nucleus of - - - - - - - - - A child nucleus relationship in which the cells are part of a hermaphroditic organism - - child nucleus of in hermaphrodite - - - - - - - - - A child nucleus relationship in which the cells are part of a male organism - - child nucleus of in male - - - - - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - - - has part that occurs in - - - - - - - - - true - - - - - - - - - - - - - - An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y - Axiomatization to GO to be added later - - ubiquitinates - - - - - - - - - - is kinase activity - - - - - - - - - - is ubiquitination - - - - - - - - - - See notes for inverse relation - - receives input from - - - - - - - - - This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - - sends output to - - - - - - - - - - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. - relation between physical entity and a process or stage - - - - - - - - - - - - - - - - - - x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - existence starts during - - - - - - - - - x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - existence starts with - - - - - - - - - x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence overlaps - - - - - - - - - - x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - exists during - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts and ends during - - - - - - - - - - - - - - - - - - x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during - - - - - - - - - x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends with - - - - - - - - - - x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - transformation of - - - - - - - - - - x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - immediate transformation of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts during or after - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during or before - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - - causal agent in process - - - - - - - - - - - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between processes - - - - - - - - - depends on - - - - - - - - - - q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 - This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. - - - towards - - - - - - - - - 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate - p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - - has intermediate product - - has intermediate - - - - - - - - - - - The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between entities - - - - - - - - - - - - - - A coral reef environment is determined by a particular coral reef - s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. - The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - - - determined by (system to material entity) - - - - determined by - - - - - - - - - inverse of determined by - - determines (material entity to system) - - - determines - - - - - - - - - - - - - - - - s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - - - determined by part of - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - - - - - x is transcribed from y if and only if x is synthesized from template y - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - transcribed from - - - - - - - - - inverse of transcribed from - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - transcribed to - - - - - - - - - - - - - - - - - - - - - - - - - - x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - ribosomal translation of - - - - - - - - - - - - - - - - - - - - - - - - - inverse of ribosomal translation of - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - ribosomally translates to - - - - - - - - - - A relation that holds between two entities that have the property of being sequences or having sequences. - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. - The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. - - sequentially related to - - - - - - - - - Every UTR is adjacent to a CDS of the same transcript - Two consecutive DNA residues are sequentially adjacent - Two exons on a processed transcript that were previously connected by an intron are adjacent - x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - sequentially adjacent to - - - - - - - - - - - Every CDS has as a start sequence the start codon for that transcript - x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - - started by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has start sequence - - - - - - - - - - inverse of has start sequence - - starts - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - - is start sequence of - - - - - - - - - - - Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) - x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - - ended by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has end sequence - - - - - - - - - - inverse of has end sequence - - ends - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - - is end sequence of - - - - - - - - - x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. - In the SO paper, this was defined as an instance-type relation - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - is consecutive sequence of - - - - - - - - - - Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. - x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - - - is sequentially aligned with - - - - - - - - - - - The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) - x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - - - bounds sequence of - - - - - - - - - - inverse of bounds sequence of - - - - is bound by sequence of - - - - - - - - - - - - - x has subsequence y iff all of the sequence parts of y are sequence parts of x - - contains - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has subsequence - - - - - - - - - - - - inverse of has subsequence - - contained by - - - is subsequence of - - - - - - - - - - - - - - - x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. - - - overlaps sequence of - - - - - - - - - - x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - - disconnected from - - does not overlap sequence of - - - - - - - - - - inverse of downstream of sequence of - - - is upstream of sequence of - - - - - - - - - - - x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - - - is downstream of sequence of - - - - - - - - - - A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript - x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - - - - is immediately downstream of sequence of - - - - - - - - - - A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript - inverse of immediately downstream of - - - is immediately upstream of sequence of - - - - - - - - - - - - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' - A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - has skeleton - - - - - - This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. - - - - - - - - - - p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - - results in ending of - - - - - - - - - - - - - - x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y - Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - - http://eol.org/schema/terms/hyperparasitoidOf - https://en.wikipedia.org/wiki/Hyperparasite - hyperparasitoid of - epiparasite of - - hyperparasite of - - - - - - - - - - - - - inverse of hyperparasite of - - has epiparasite - has hyperparasite - hyperparasitoidized by - - - hyperparasitized by - - - - - - - - - - A relationship between organisms where one organism is influenced by the biochemicals produced by another. - - http://en.wikipedia.org/wiki/Allelopathy - - Allelopathy is a phenomenon in which one organism releases chemicals to positively or negatively influence the growth, survival or reproduction of other organisms in its vicinity. - allelopath of - http://eol.org/schema/terms/allelopathyYes - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172429/ - x is an allelopath of y if x produces one or more biochemicals that influence the growth, survival, and reproduction of y - - - - - - - - - - Inverse of has pathogen - - - pathogen of - - - - - - - - - A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member - - - has pathogen - - - - - - - - - inverse of is evidence for - - - - - x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. - has evidence - - - - - - - - - - - - causally influenced by (entity-centric) - causally influenced by - - - - - - - - - - interaction relation helper property - - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - - molecular interaction relation helper property - - - - - - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - - - - results in movement of - - - - - - - - - - - - - - - - - - - - - The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) - causally influences - - - - - - - - - - - A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. - biomechanically related to - - - - - - - - - m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - has muscle antagonist - - - - - - - - - - - inverse of branching part of - - - - has branching part - - - - - - - - - - - x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - - conduit for - - - - - - - - - - x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - - lumen of - - - - - - - - - - s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - - luminal space of - - - - - - - - - - A relation that holds between an attribute or a qualifier and another attribute. - - - This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. - - has modifier - - - - - - - - - - - - - participates in a biotic-biotic interaction with - - - - - - - - - - - - inverse of has skeleton - - - skeleton of - - - - - - - - - - p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - - - - - directly regulates - - - - - - - - - holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y). - existence starts at end of - - - - - - - - - - - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' - s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - - has part structure that is capable of - - - - - - - - - - p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. - results in closure of - - - - - - - - - p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p - results in breakdown of - - - - - - - - - results in synthesis of - - - - - - - - - - - - - results in assembly of - - - - - - - - - p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. - results in catabolism of - - - - - - - - - - results in disassembly of - - - - - - - - - - results in remodeling of - - - - - - - - - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c - results in organization of - - - - - - - - - holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y). - existence ends at start of - - - - - - - - - - - A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - - causal relation between material entity and a process - - - - - - - - - - - - - pyrethroid -> growth - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - - capable of negatively regulating - - - - - - - - - - - - - renin -> arteriolar smooth muscle contraction - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - - capable of positively regulating - - - - - - - - - pazopanib -> pathological angiogenesis - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. - treats - - The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. - capable of inhibiting or preventing pathological process - - - - - treats - Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship - - - - - - - - - benzene -> cancer [CHEBI] - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. - causes disease - - capable of upregulating or causing pathological process - - - - - - - - - c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. - treats - - is substance that treats - - - - - - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - is marker for - - - - - - - - - Inverse of 'causal agent in process' - - process has causal agent - - - - - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - obsolete related via dependence to - true - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - correlated with - - - - - - - - - An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. - A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. - In the Gene Ontology association model, this corresponds to the With/From field - is evidence with support from - - - - - - - - - Inverse of is-model-of - has model - - - - - - - - Do not use this relation directly. It is a grouping relation. - related via evidence or inference to - - - - - - - - - - visits - https://github.com/oborel/obo-relations/issues/74 - - - - - - - - - visited by - - - - - - - - - - visits flowers of - - - - - - - - - has flowers visited by - - - - - - - - - - - lays eggs in - - - - - - - - - - has eggs laid in by - - - - - - - - - - https://github.com/jhpoelen/eol-globi-data/issues/143 - kills - - - - - - - - - is killed by - - - - - - - - - - p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - - - - - directly positively regulates - https://wiki.geneontology.org/Directly_positively_regulates - - - - - - - - - - p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) - - - - - directly negatively regulates - https://wiki.geneontology.org/Directly_negatively_regulates - - - - - - - - - - A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host - - ectoparasite of - - - - - - - - - inverse of ectoparasite of - - has ectoparasite - - - - - - - - - - - A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system - lives inside of - endoparasite of - - - - - - - - - has endoparasite - - - - - - - - - - A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite - mesoparasite of - - - - - - - - - inverse of mesoparasite of - - has mesoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. - - intercellular endoparasite of - - - - - - - - - inverse of intercellular endoparasite of - - has intercellular endoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits host cells. - - intracellular endoparasite of - - - - - - - - - inverse of intracellular endoparasite of - - has intracellular endoparasite - - - - - - - - - - Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. - - co-roosts with - - - - - - - - - - An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. - A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. - - - - A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. - reservoir host of - - - - - - - - - An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. - inverse of reservoir host of - - has reservoir host - - - - - - - - - - - - - - - - - - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - - - Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. - produces - - - - - - - - - - - a produced_by b iff some process that occurs_in b has_output a. - - - produced by - - - - - - - - - - - Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - - represses expression of - - - - - - - - - - - Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - - increases expression of - - - - - - - - - - A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - - is used to study - The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. - has role in modeling - - - - - - - - - The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. - -An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. - Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - causes or contributes to condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. - causes condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. - contributes to condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. - contributes to expressivity of condition - contributes to severity of condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. - contributes to penetrance of condition - contributes to frequency of condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. - is preventative for condition - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - ameliorates condition - - - - - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - correlated with condition - - - - - - - - - A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. - exacerbates condition - - - - - - - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. - condition ameliorated by - - - - - - - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. - condition exacerbated by - - - - - - - - - - - - - - - - - - - - Do not use this relation directly. It is intended as a grouping for a more specific relations - - 2017-11-05T02:38:20Z - condition has genetic basis in - - - - - - - - - - - 2017-11-05T02:45:20Z - has material basis in gain of function germline mutation in - - - - - - - - - - - - - 2017-11-05T02:45:37Z - has material basis in loss of function germline mutation in - - - - - - - - - - - 2017-11-05T02:45:54Z - has material basis in germline mutation in - - - - - - - - - - - - 2017-11-05T02:46:07Z - has material basis in somatic mutation in - - - - - - - - - - - - 2017-11-05T02:46:26Z - has major susceptibility factor - - - - - - - - - - - 2017-11-05T02:46:57Z - has partial material basis in germline mutation in - - - - - - - - - p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - - 2018-12-13T11:26:17Z - - has primary input or output - - - - - - - - - - p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - - 2018-12-13T11:26:32Z - - has primary output - - - - - p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - - GOC:dph - GOC:kva - GOC:pt - PMID:27812932 - - - - - - - - - - p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - - 2018-12-13T11:26:56Z - - has primary input - - - - - p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - - GOC:dph - GOC:kva - GOC:pt - PMID:27812932 - - - - - - - - - - Do not use this relation directly. It is intended as a grouping for a more specific relations - - 2017-11-05T02:53:08Z - is genetic basis for condition - - - - - - - - - Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - - 2017-11-05T02:55:51Z - is causal gain of function germline mutation of in - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - - 2017-11-05T02:56:06Z - is causal loss of function germline mutation of in - - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - - 2017-11-05T02:56:40Z - is causal germline mutation in - - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - - 2017-11-05T02:57:07Z - is causal somatic mutation in - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - - 2017-11-05T02:57:43Z - is causal susceptibility factor for - - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - - 2017-11-05T02:58:43Z - is causal germline mutation partially giving rise to - - - - - - - - - - - - 2017-11-05T03:20:01Z - realizable has basis in - - - - - - - - - - 2017-11-05T03:20:29Z - is basis for realizable - - - - - - - - - - - - 2017-11-05T03:26:47Z - disease has basis in - - - - - - - - - - A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. - disease has basis in dysfunction of (disease to anatomical structure) - - 2017-11-05T03:29:32Z - disease has basis in dysfunction of - - - - - - - - - - A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. - disease has basis in disruption of (disease to process) - - 2017-11-05T03:37:52Z - disease has basis in disruption of - - - - - - - - - - - - - - - - - - - A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - - 2017-11-05T03:46:07Z - disease has basis in feature - - - - - - - - - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - - 2017-11-05T03:50:54Z - causal relationship with disease as subject - - - - - - - - - - - - - - - - - - - A relationship between a disease and a process where the disease process disrupts the execution of the process. - disease causes disruption of (disease to process) - - 2017-11-05T03:51:09Z - disease causes disruption of - - - - - - - - - - - - - - - disease causes dysfunction of (disease to anatomical entity) - - 2017-11-05T03:58:20Z - disease causes dysfunction of - - - - - - - - - - - - - - - - - - - A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. - TODO: complete range axiom once more of CARO has been mireoted in to this ontology - This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - - 2017-11-05T04:06:02Z - disease has location - - - - - - - - - - - - - - - - - - - A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - - 2017-12-26T19:37:31Z - disease has inflammation site - - - - - - - - - - - - - - - A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - - 2017-12-26T19:45:49Z - realized in response to stimulus - - - - - - - - - - - - - - - - - - A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - - 2017-12-26T19:50:53Z - disease has feature - - - - - - - - - - A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - - 2017-12-26T19:58:44Z - disease arises from alteration in structure - - - - - - - - - - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - - 2018-01-25T23:20:13Z - enables subfunction - - - - - - - - - - - - - - - 2018-01-26T23:49:30Z - - acts upstream of or within, positive effect - https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect - - - - - - - - - - - - - - - 2018-01-26T23:49:51Z - - acts upstream of or within, negative effect - https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect - - - - - - - - - - - - - - c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - - - 2018-01-26T23:53:14Z - - acts upstream of, positive effect - https://wiki.geneontology.org/Acts_upstream_of,_positive_effect - - - - - - - - - - - - - - c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - - - 2018-01-26T23:53:22Z - - acts upstream of, negative effect - https://wiki.geneontology.org/Acts_upstream_of,_negative_effect - - - - - - - - - - - 2018-03-13T23:55:05Z - causally upstream of or within, negative effect - https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect - - - - - - - - - - - 2018-03-13T23:55:19Z - causally upstream of or within, positive effect - - - - - - - - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true - - - - - - - - DEPRECATED bearer of - true - - - - - - - - A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. - - has driver - - - - - - - - - - A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes. - - has disease driver - - - - - - - - - - - An interaction relationship wherein a plant or algae is living on the outside surface of another plant. - https://en.wikipedia.org/wiki/Epiphyte - epiphyte of - - - - - - - - - inverse of epiphyte of - - has epiphyte - - - - - - - - - - A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material - https://en.wikipedia.org/wiki/Kleptoparasitism - kleptoparasite of - - - - - - - - - inverse of kleptoparasite of - - kleptoparasitized by - - - - - - - - - - - An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. - creates habitat for - - - - - - - - - - - - An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. - ecologically co-occurs with - - - - - - - - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - lays eggs on - - - - - - - - - inverse of lays eggs on - has eggs laid on by - - - - - - - - - - - Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) - x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. - - 2023-01-18T14:28:21Z - - A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. - has roost - - - - - - - - - frog symbiotrophically interacts with the pitcher plant it lives inside of - A trophic interaction in which one organism acquires nutrients through a symbiotic relationship with another organism - - 2023-07-17T14:39:56Z - - symbiotrophically interacts with - - - - - - - - - tapeworm is trophic parasite of the cow it lives inside of - A symbiotrophic interaction in which one organism acquires nutrients through a parasitic relationship with another organism - - 2023-07-17T14:41:07Z - - trophic parasite of - - - - - - - - - - - muffin 'has substance added' some 'baking soda' - - "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - - has substance added - - - - - - - - - - - 'egg white' 'has substance removed' some 'egg yolk' - - "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. - - has substance removed - - - - - - - - - - - sardines 'immersed in' some 'oil and mustard' - - "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. - - immersed in - - - - - - - - - - sardine has consumer some homo sapiens - - 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. - - has consumer - - - - - - - - - - bread 'has primary substance added' some 'flour' - - 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. - - has primary substance added - - - - - - - - - - - A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material. - A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. - - 2023-05-23T15:24:15Z - assay measures characteristic - - - - - - - - - - Inverse of 'assay measures characteristic' - - 2023-05-23T15:29:50Z - characteristic measured by assay - - - - - - - - - - - - - - - A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. - An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) - Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. - r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - - - - - triggered by process - realized in response to - https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit - - - - - triggered by process - - - - - - - - - - - - - - - - Genetic information generically depend on molecules of DNA. - The novel *War and Peace* generically depends on this copy of the novel. - The pattern shared by chess boards generically depends on any chess board. - The score of a symphony g-depends on a copy of the score. - This pdf file generically depends on this server. - A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. - [072-ISO] - g-depends on - generically depends on - - - - - - - - - - - - - - Molecules of DNA are carriers of genetic information. - This copy of *War and Peace* is carrier of the novel written by Tolstoy. - This hard drive is carrier of these data items. - *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* - [072-ISO] - is carrier of - - - - - - - - - - - The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - - regulates activity of - - - - - - - - - - - The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - - regulates quantity of - - - - - - - - - - - The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - - indirectly regulates activity of - - - - - - - - - - - The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. - -For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - - decreases by repression quantity of - - - - - - - - - - - The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. - -For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - - increases by expression quantity of - - - - - - - - - - - The entity A has an activity that directly positively regulates the quantity of B. - - directly positively regulates quantity of - - - - - - - - - - - The entity A has an activity that directly negatively regulates the quantity of B. - - directly negatively regulates quantity of - - - - - - - - - - - The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - - indirectly activates - indirectly positively regulates activity of - - - - - - - - - - - AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) - An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - - destabilizes quantity of - - - - - - - - - - - AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) - An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - - stabilizes quantity of - - - - - - - - - The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - - indirectly inhibits - indirectly negatively regulates activity of - - - - - - - - - The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - - directly regulates quantity of - - - - - - - - - The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - - indirectly regulates quantity of - - - - - - - - - The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - - indirectly negatively regulates quantity of - - - - - - - - - The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - - indirectly positively regulates quantity of - - - - - - - - - - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - - 2020-04-22T20:27:26Z - has small molecule regulator - - - - - - - - - - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - - 2020-04-22T20:28:37Z - has small molecule activator - - - - - - - - - - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - - 2020-04-22T20:28:54Z - has small molecule inhibitor - - - - - - - - - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - - 2020-06-08T17:21:33Z - - - - acts on population of - - - - - - - - - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - - 2020-06-24T13:15:17Z - is small molecule regulator of - - - - - - - - - - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - - 2020-06-24T13:15:26Z - is small molecule activator of - https://wiki.geneontology.org/Is_small_molecule_activator_of - - - - - - - - - - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - - 2020-06-24T13:15:35Z - is small molecule inhibitor of - https://wiki.geneontology.org/Is_small_molecule_inhibitor_of - - - - - - - - - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - - 2020-08-27T08:13:59Z - results in adhesion of - - - - - - - - - - 2021-02-26T07:28:29Z - - - - results in fusion of - - - - - - - - - p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - - 2022-09-26T06:01:01Z - - - constitutively upstream of - https://wiki.geneontology.org/Constitutively_upstream_of - - - - - - - - - p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - - 2022-09-26T06:06:20Z - - - removes input for - https://wiki.geneontology.org/Removes_input_for - - - - - - - - - p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - - 2022-09-26T06:07:17Z - indirectly causally upstream of - - - - - - - - - - p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - - 2022-09-26T06:08:01Z - indirectly regulates - - - - - - - - - x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - - - 2023-10-12T10:02:28Z - positively regulates in other organism - - positively regulates in another organism - - - - - - - - - x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - - - 2023-10-12T10:02:42Z - negatively regulates in other organism - - negatively regulates in another organism - - - - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - - 2020-07-17T09:26:52Z - has synaptic input or output in - has synaptic IO in region - - - - - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - - 2020-07-17T09:42:23Z - receives synaptic input in region - - - - - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - - 2020-07-17T09:45:06Z - sends synaptic output to region - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - - 2020-07-17T09:52:19Z - has synaptic IO throughout - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - - 2020-07-17T09:55:36Z - receives synaptic input throughout - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - - 2020-07-17T09:57:27Z - sends synaptic output throughout - - - - - - - - - - - - - - Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - - 2020-07-20T12:10:09Z - has sensory dendrite location - has sensory terminal in - has sensory terminal location - has sensory dendrite in - - - - - - - - - - A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - - 2021-05-26T08:40:18Z - receives synaptic input from neuron - - - - - - - - - A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - - 2021-05-26T08:41:07Z - Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. - sends synaptic output to cell - - - - - - - - - - - - - An optic lobe intrinsic neuron has its synapses restricted to optic lobe neuropil. - A relationship between a neuron and a region, where all of the functionally relevant input and output synapses are in that region. - - 2023-08-17T12:17:24Z - intrinsic to - This relation may still be used if a very small number of synapses fall slightly outside the boundaries of the region, but any class using this relation should not have another restriction using this relation to another non-overlapping region. - synapses restricted to region - - - - - - - - - A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - - disease has infectious agent - - - - - - - - - - - - - - transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) - A relation between a material entity and some data in which the data is taken as exemplifying the material entity. - C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. - - This relation is not meant to capture the relation between occurrents and data. - has exemplar data - - - - - - - - - - exemplar data of - - - - - - - - - - A relation between a group and another group it is part of but does not fully constitute. - X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - - This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. - subcluster of - - - - - - - - - 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1'). - transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3. - A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. - C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. - This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. - - has marker gene combination - has marker signature set - has characterizing marker set - - - - - - - - - - q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - different in magnitude relative to - - - - - q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - - - - q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. - increased in magnitude relative to - - - - - q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - - - - q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. - decreased in magnitude relative to - - - - - q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - similar in magnitude relative to - - - - - q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - has relative magnitude - - - - - - - - s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. - Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. - has cross section - - - - - s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. - There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. - reciprocal of - - - - - q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - - - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') - A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - - has high plasma membrane amount - - - - - A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - PMID:19243617 - - - - - - - - - - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') - A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - - has low plasma membrane amount - - - - - A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - PMID:19243617 - - - - - - - - Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z - has phenotype or disease - https://github.com/oborel/obo-relations/issues/478 - - - - - - - - - A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z - has disease - https://github.com/oborel/obo-relations/issues/478 - - - - - - - - - X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. - ExO:0000083 - - 2021-12-14T20:41:45Z - has exposure medium - - - - - - - - - - - - A diagnostic testing device utilizes a specimen. - X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 - - - 2021-11-08T12:00:00Z - utilizes - device utilizes material - - - - - - - - - - A relation between entities in which one increases or decreases as the other does the same. - directly correlated with - - positively correlated with - - - - - - - - - - - A relation between entities in which one increases as the other decreases. - inversely correlated with - - negatively correlated with - - - - - - - - - - anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. - A relation between a container and measurement datum that specifies the actual amount of material in the container. - - - contains measured amount - - - - - - - - - - anticoagulant-containing test tube has maximum capacity 10 ml. - A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume. - - - has maximum capacity - - - - - - - - - biobank organization owns a specimen - hospital owns a laboratory facility - A primitive relation that holds between entities x and y in which y is at x's full disposal. - - - - This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal. - 2023-03-29T16:57:03Z - owns - - - - - - - - freezer is owned by a biobank organization - Inverse of the owns relation. - - - - 2023-03-29T17:06:06Z - - is owned by - - - - - - - - - - A thorax specimen was collected during the larval stage. - An oyster was collected during low tide. - A relation between a material entity and an occurrent in which the material entity is collected during the existence of the occurrent. - - 2023-09-13T04:12:32Z - collected during - - - - - - - - - Helper relation for OWL definition of RO:0018002 myristoylates - - is myristoyltransferase activity - - - - - - - - - - - - - - - A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input - - - myristoylates - - - - - - - - inverse of myristoylates - - myristoylated by - - - - - - - - - mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) - a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - - is agonist of - - - - - - - - - - pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) - a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - - is inverse agonist of - - - - - - - - - - tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) - a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - - is antagonist of - - - - - - - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical. - - chemical relationship - - - - - - - - - - pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) - A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B. - - - is direct conjugate base of - - - - - - - - - - neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) - A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B. - - - is direct conjugate acid of - - - - - - - - - - - - (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. - A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. - -This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. - - obo:chebi#is_conjugate_base_of - is deprotonated form of - - - - - - - - - - - (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. - A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. - -This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. - - obo:chebi#is_conjugate_acid_of - is protonated form of - - - - - - - - - - - phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol. - A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. - -While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. - -This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. - -This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. - - 2023-02-28T18:53:32Z - is MMP with - is matched molecular pair with - is matched small molecular pair with - - - - - A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. - -While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. - -This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. - -This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. - - - - - - - - - - - - - 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. - Two chemicals are tautomers if they can be readily interconverted. - -This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms. - - 2023-03-18T23:49:31Z - obo:chebi#is_tautomer_of - is desmotrope of - is tautomer of - - - - - - 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. - - - - - - - - - - - carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) - Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. - - 2023-03-18T23:49:31Z - obo:chebi#is_substituent_group_from - is substitutent group from - - - - - - carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) - - - - - - - - - - - hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) - Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. - -For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship. - - 2023-03-18T23:49:31Z - obo:chebi#has_functional_parent - has functional parent - - - - - - hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) - - - - - - - - - - - - dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. - Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. - -A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers). - - 2023-03-18T23:49:31Z - obo:chebi#is_enantiomer_of - is optical isomer of - is enantiomer of - - - - - - dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. - - - - - - - - - - - pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. - Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. - - 2023-03-18T23:49:31Z - obo:chebi#has_parent_hydride - has parent hydride - - - - - - pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. - - - - - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. - - regulates characteristic - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. - - positively regulates characteristic - - - - - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. - - negatively regulates characteristic - - - - - - - - - Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - - confers susceptibility to condition - - - - - - - - - - - brachial artery vessel supplies blood to brachialis muscle - x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. - - 2024-02-01T10:09:22Z - vessel supplies blood to - - - - - - - - - - - cystic vein vessel drains blood from gallbladder - x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. - - 2024-02-01T10:09:41Z - vessel drains blood from - - - - - - - - - - - - alveolar capillary directly supplies and drains some alveolus - x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. - - 2024-02-01T10:09:59Z - directly supplies and drains - - - - - - - - - This property only applies to neurons - - 2024-10-23T14:34:52Z - is neuron - - - - - - - - - This property only applies to anatomical entities. - - 2024-10-29T09:55:07Z - is anatomical entity - - - - - - - - - - - A relationship between a ratio or proportion and its dividend. - - has dividend - has numerator - - - - - - - - - - - A relationship between a ratio or proportion and its divisor. - - has divisor - has denominator - - - - - - - - - inverse of allelopath of - - has allelopath - https://en.wikipedia.org/wiki/Allelopathy - - - - - - - - This relation groups relations between diseases and any other kind of entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - - 2018-09-26T00:00:32Z - disease relationship - - - - - - - - - p has anatomical participant c iff p has participant c, and c is an anatomical entity - - 2018-09-26T01:08:58Z - results in changes to anatomical or cellular structure - - - - - - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - TODO: Add homeomorphy axiom - - - - - ECO:0000041 - SO:similar_to - sameness - similar to - correspondence - resemblance - in similarity relationship with - - - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - BGEE:curator - - - - - correspondence - - - - - - - - - - - - - Similarity that results from common evolutionary origin. - - - homologous to - This broad definition encompasses all the working definitions proposed so far in the literature. - in homology relationship with - - - - - - Similarity that results from common evolutionary origin. - - - - - - - - - - - - - - Similarity that results from independent evolution. - - - homoplasous to - analogy - in homoplasy relationship with - - - - - - Similarity that results from independent evolution. - - - - - - - - - - - - - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - - ECO:0000075 - homocracous to - Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. - in homocracy relationship with - - - - - - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - - - - - - - - - - - - - Homoplasy that involves different underlying mechanisms or structures. - - - analogy - Convergence usually implies a notion of adaptation. - in convergence relationship with - - - - - - Homoplasy that involves different underlying mechanisms or structures. - - - - - - - - - - - - Homoplasy that involves homologous underlying mechanisms or structures. - - - parallel evolution - Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. - in parallelism relationship with - - - - - - Homoplasy that involves homologous underlying mechanisms or structures. - - - - - - - - - - - - Homology that is defined by similarity with regard to selected structural parameters. - - - ECO:0000071 - MI:2163 - structural homologous to - idealistic homology - in structural homology relationship with - - - - - - Homology that is defined by similarity with regard to selected structural parameters. - - - - ISBN:0123195837 - - - - - - - - - - Homology that is defined by common descent. - - - homology - ECO:0000080 - RO_proposed_relation:homologous_to - SO:0000330 - SO:0000853 - SO:0000857 - SO:homologous_to - TAO:homologous_to - cladistic homology - historical homologous to - phylogenetic homology - taxic homology - true homology - in historical homology relationship with - - - - - - Homology that is defined by common descent. - - - ISBN:0123195837 - - - - - - - - - - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - - ECO:0000067 - biological homologous to - transformational homology - Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. - in biological homology relationship with - - - - - - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - - - - - - - - - - - - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - - atavism - rudiment - reversion - in reversal relationship with - - - - - - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - - - - - - - - - - - Structural homology that is detected by similarity in content and organization between chromosomes. - - - MeSH:Synteny - SO:0000860 - SO:0005858 - syntenic homologous to - synteny - in syntenic homology relationship with - - - - - - Structural homology that is detected by similarity in content and organization between chromosomes. - - MeSH:Synteny - - - - - - - - - - - Historical homology that involves genes that diverged after a duplication event. - - - SO:0000854 - SO:0000859 - SO:paralogous_to - paralogous to - in paralogy relationship with - - - - - - Historical homology that involves genes that diverged after a duplication event. - - - - - - - - - - - - - - - Paralogy that involves sets of syntenic blocks. - - - syntenic paralogous to - duplicon - paralogon - in syntenic paralogy relationship with - - - - - - Paralogy that involves sets of syntenic blocks. - - - DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y - - - - - - - - - - Syntenic homology that involves chromosomes of different species. - - - syntenic orthologous to - in syntenic orthology relationship with - - - - - - Syntenic homology that involves chromosomes of different species. - - - - - - - - - - - - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - - fractional homology - partial homologous to - segmental homology - mixed homology - modular homology - partial correspondence - percent homology - in partial homology relationship with - - - - - - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - ISBN:0123195837 - ISBN:978-0471984931 - - - - - - - - - - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - - MeSH:Structural_Homology,_Protein - protein structural homologous to - in protein structural homology relationship with - - - - - - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - - - - - - - - - - - - Structural homology that involves a pseudogenic feature and its functional ancestor. - - - pseudogene - SO:non_functional_homolog_of - non functional homologous to - in non functional homology relationship with - - - - - - Structural homology that involves a pseudogenic feature and its functional ancestor. - - SO:non_functional_homolog_of - - - - - - - - - - Historical homology that involves genes that diverged after a speciation event. - - - ECO:00000060 - SO:0000855 - SO:0000858 - SO:orthologous_to - orthologous to - The term is sometimes also used for anatomical structures. - in orthology relationship with - - - - - - Historical homology that involves genes that diverged after a speciation event. - - - - - - - - - - - - - - - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - - xenologous to - The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). - in xenology relationship with - - - - - - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - - - - - - - - - - - - Historical homology that involves two members sharing no other homologs in the lineages considered. - - - 1 to 1 homologous to - 1:1 homology - one-to-one homology - in 1 to 1 homology relationship with - - - - - - Historical homology that involves two members sharing no other homologs in the lineages considered. - - BGEE:curator - - - - - - - - - - - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - - 1 to 1 orthologous to - 1:1 orthology - one-to-one orthology - in 1 to 1 orthology relationship with - - - - - - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - - - - - - - - - - - - Paralogy that results from a whole genome duplication event. - - - ohnologous to - homoeology - in ohnology relationship with - - - - - - Paralogy that results from a whole genome duplication event. - - - - - - - - - - - - - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - - in-paralogous to - inparalogy - symparalogy - in in-paralogy relationship with - - - - - - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - - - - - - - - - - - Paralogy that results from a duplication preceding a given speciation event. - - - alloparalogy - out-paralogous to - outparalogy - in out-paralogy relationship with - - - - - - Paralogy that results from a duplication preceding a given speciation event. - - - - - - - - - - - - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - - pro-orthologous to - in pro-orthology relationship with - - - - - - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - - - - - - - - - - - - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - - semi-orthologous to - The converse of pro-orthologous. - in semi-orthology relationship with - - - - - - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - - - - - - - - - - - - Iterative homology that involves structures arranged along the main body axis. - - - serial homologous to - homonomy - in serial homology relationship with - - - - - - Iterative homology that involves structures arranged along the main body axis. - - - - - - - - - - - - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - - heterochronous homologous to - heterochrony - in heterochronous homology relationship with - - - - - - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - ISBN:978-0674639416 - - - - - - - - - - - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - - juvenification - pedomorphosis - in paedomorphorsis relationship with - - - - - - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - - ISBN:978-0674639416 - - - - - - - - - - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - in peramorphosis relationship with - - - - - - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - - - - - - - - - - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - in progenesis relationship with - - - - - - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - ISBN:978-0674639416 - - - - - - - - - - Paedomorphosis that is produced by a retardation of somatic development. - - - juvenilization - neotenous to - in neoteny relationship with - - - - - - Paedomorphosis that is produced by a retardation of somatic development. - - - ISBN:978-0674639416 - - - - - - - - - - Convergence that results from co-evolution usually involving an evolutionary arms race. - - - mimicrous to - in mimicry relationship with - - - - - - Convergence that results from co-evolution usually involving an evolutionary arms race. - - - - - - - - - - - - - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - - 1 to many orthologous to - 1:many orthology - one-to-many orthology - co-orthology - many to 1 orthology - in 1 to many orthology relationship with - - - - - - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - - - - - - - - - - - - Historical homology that involves two members of a larger set of homologs. - - - many to many homologous to - many-to-many homology - many:many homology - in many to many homology relationship with - - - - - - Historical homology that involves two members of a larger set of homologs. - - - - - - - - - - - - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - - 1 to many homologous to - one-to-many homology - 1:many homology - in 1 to many homology relationship with - - - - - - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - BGEE:curator - - - - - - - - - - - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - - apomorphous to - synapomorphy - in apomorphy relationship with - - - - - - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - ISBN:978-0252068140 - - - - - - - - - - Historical homology that is based on distant shared ancestry. - - - plesiomorphous to - symplesiomorphy - This term is usually contrasted to apomorphy. - in plesiomorphy relationship with - - - - - - Historical homology that is based on distant shared ancestry. - - ISBN:978-0252068140 - - - - - - - - - - - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - - deep genetic homology - deep homologous to - generative homology - homoiology - Used for structures in distantly related taxa. - in deep homology relationship with - - - - - - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - - - - - - - - - - - - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - - hemiplasous to - in hemiplasy relationship with - - - - - - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - - - - - - - - - - - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - - gametologous to - in gametology relationship with - - - - - - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - - - - - - - - - - - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - - MeSH:Chromosome_Pairing - chromosomal homologous to - in chromosomal homology relationship with - - - - - - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - ISBN:0195307615 - - - - - - - - - - - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - - many to many orthologous to - many-to-many orthology - many:many orthology - trans-orthology - co-orthology - trans-homology - in many to many orthology relationship with - - - - - - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - - - - - - - - - - - - - Paralogy that involves genes from the same species. - - - within-species paralogous to - in within-species paralogy relationship with - - - - - - Paralogy that involves genes from the same species. - - - - - - - - - - - - Paralogy that involves genes from different species. - - - between-species paralogous to - The genes have diverged before a speciation event. - in between-species paralogy relationship with - - - - - - Paralogy that involves genes from different species. - - - - - - - - - - - - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - - post-displacement - in postdisplacement relationship with - - - - - - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - - - - - - - - - - - Peramorphosis that is produced by a delay in the offset of development. - - - in hypermorphosis relationship with - - - - - - Peramorphosis that is produced by a delay in the offset of development. - - - ISBN:978-0674639416 - - - - - - - - - - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - - synologous to - in synology relationship with - - - - - - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - - - - - - - - - - - - - Orthology that involves functional equivalent genes with retention of the ancestral function. - - - ECO:0000080 - isoorthologous to - in isoorthology relationship with - - - - - - Orthology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - - tandem paralogous to - iterative paralogy - serial paralogy - in tandem paralogy relationship with - - - - - - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - - ISBN:978-0878932665 - - - - - - - - - - - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - - apomorphic tendency - cryptic homology - latent homologous to - underlying synapomorphy - homoiology - homoplastic tendency - re-awakening - Used for structures in closely related taxa. - in latent homology relationship with - - - - - - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - - - - ISBN:0199141118 - - - - - - - - - - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - - generative homology - syngenous to - Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. - in syngeny relationship with - - - - - - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - - DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R - - - - - - - - - - - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - - 1:1 paralogy - apparent 1:1 orthology - apparent orthologous to - pseudoorthology - The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. - in apparent orthology relationship with - - - - - - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - - - - - - - - - - - - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - - pseudoparalogous to - These genes may come out as paralogs in a single-genome analysis. - in pseudoparalogy relationship with - - - - - - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - - - - - - - - - - - - Historical homology that involves functional equivalent genes with retention of the ancestral function. - - - equivalogous to - This may include examples of orthology, paralogy and xenology. - in equivalogy relationship with - - - - - - Historical homology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - - interologous to - in interology relationship with - - - - - - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - - - - - - - - - - - - Similarity that is characterized by interchangeability in function. - - - functional similarity - in functional equivalence relationship with - - - - - - Similarity that is characterized by interchangeability in function. - - - - - - - - - - - - - Biological homology that involves parts of the same organism. - - - iterative homologous to - in iterative homology relationship with - - - - - - Biological homology that involves parts of the same organism. - - - - - - - - - - - - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - - duplicate xenology - multiple xenology - paraxenologous to - in paraxenology relationship with - - - - - - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - - - - - - - - - - - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - - plerologous to - This phenomenon is usually due to gene conversion process. - in plerology relationship with - - - - - - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - - - - - - - - - - - - Structural homology that involves structures with the same or similar relative positions. - - - homotopous to - Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. - in homotopy relationship with - - - - - - Structural homology that involves structures with the same or similar relative positions. - - - - ISBN:0123195837 - - - - - - - - - - Biological homology that involves an ectopic structure and the normally positioned structure. - - - heterotopy - in homeosis relationship with - - - - - - Biological homology that involves an ectopic structure and the normally positioned structure. - - - - - - - - - - - - - - Synology that results from allopolyploidy. - - - homoeologous to - On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. - in homoeology relationship with - - - - - - Synology that results from allopolyploidy. - - - - - - - - - - - - - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - - axis paramorphism - in paramorphism relationship with - - - - - - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - - - - - - - - - - - - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - - regulogous to - in regulogy relationship with - - - - - - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - - - - - - - - - - - - - - - - - - - 0 - - - 100 - - - - - Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - - 2018-05-22T16:43:28Z - This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. - has increased age-specific mortality rate - - - - - Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - PMID:24138933 - Wikipedia:Infant_mortality - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - continuant - - - - - - - - - - - - - - - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. - occurrent - - - - - - - - - - - - - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - independent continuant - - - - - - - - - spatial region - - - - - - - - - - - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - process - - - - - - - - - - disposition - - - - - - - - - - - - - - - - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - realizable entity - - - - - - - - - - - - - - - quality - - - - - - - - - - - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - specifically dependent continuant - - - - - - - - - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - role - - - - - - - - - - - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - generically dependent continuant - - - - - - - - - function - - - - - - - - - - - - - - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity - - - - - - - - - - - - - - - immaterial entity - - - - - - - - - - - - - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. - We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. - CALOHA:TS-2035 - FMA:68646 - GO:0005623 - KUPO:0000002 - MESH:D002477 - VHOG:0001533 - WBbt:0004017 - XAO:0003012 - The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). - cell - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CARO:mah - - - - - - - - - Any neuron having a sensory function; an afferent neuron conveying sensory impulses. - - BTO:0001037 - FMA:84649 - MESH:D011984 - WBbt:0005759 - sensory neuron - - - - - Any neuron having a sensory function; an afferent neuron conveying sensory impulses. - ISBN:0721662544 - - - - - - - - - - - true - - - - The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. - - BTO:0000938 - CALOHA:TS-0683 - FMA:54527 - VHOG:0001483 - WBbt:0003679 - nerve cell - These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. - neuron - - - - - The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. - MESH:D009474 - http://en.wikipedia.org/wiki/Neuron - - - - - - - - - - - - - - - A process during which an organism comes into contact with another entity. - exposure of organism - - - - - - - - - A system which has the disposition to environ one or more material entities. - 2013-09-23T16:04:08Z - EcoLexicon:environment - environment - In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. - environmental system - - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - - - - - - - - An environmental system which can sustain and allow the growth of an ecological population. - - - EcoLexicon:habitat - LTER:238 - SWEETRealm:Habitat - A habitat's specificity to an ecological population differentiates it from other environment classes. See Buttigieg et al. (2016; https://doi.org/10.1186/s13326-016-0097-6) for an explanation of ENVO's treatement of habitats. 3,849 of such habitat classes are available here: https://github.com/EnvironmentOntology/envo-habitats - habitat - - - - - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - This is the same as GO molecular function - molecular function - GO:0003674 - Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. - gene product or complex activity - molecular_function - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GOC:pdt - - - - - - - - - - - - true - - - Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. - E2 - E3 - KEGG_REACTION:R03876 - Reactome:R-HSA-1169394 - Reactome:R-HSA-1169395 - Reactome:R-HSA-1169397 - Reactome:R-HSA-1169398 - Reactome:R-HSA-1169402 - Reactome:R-HSA-1169405 - Reactome:R-HSA-1169406 - Reactome:R-HSA-1234163 - Reactome:R-HSA-1234172 - Reactome:R-HSA-1253282 - Reactome:R-HSA-1358789 - Reactome:R-HSA-1358790 - Reactome:R-HSA-1358792 - Reactome:R-HSA-1363331 - Reactome:R-HSA-168915 - Reactome:R-HSA-173542 - Reactome:R-HSA-173545 - Reactome:R-HSA-174057 - Reactome:R-HSA-174104 - Reactome:R-HSA-174144 - Reactome:R-HSA-174159 - Reactome:R-HSA-174195 - Reactome:R-HSA-174227 - Reactome:R-HSA-179417 - Reactome:R-HSA-180540 - Reactome:R-HSA-180597 - Reactome:R-HSA-182986 - Reactome:R-HSA-182993 - Reactome:R-HSA-183051 - Reactome:R-HSA-183084 - Reactome:R-HSA-183089 - Reactome:R-HSA-1852623 - Reactome:R-HSA-187575 - Reactome:R-HSA-1912357 - Reactome:R-HSA-1912386 - Reactome:R-HSA-1918092 - Reactome:R-HSA-1918095 - Reactome:R-HSA-1977296 - Reactome:R-HSA-1980074 - Reactome:R-HSA-1980118 - Reactome:R-HSA-201425 - Reactome:R-HSA-202453 - Reactome:R-HSA-202534 - Reactome:R-HSA-205118 - Reactome:R-HSA-209063 - Reactome:R-HSA-211734 - Reactome:R-HSA-2169050 - Reactome:R-HSA-2172172 - Reactome:R-HSA-2179276 - Reactome:R-HSA-2186747 - Reactome:R-HSA-2186785 - Reactome:R-HSA-2187368 - Reactome:R-HSA-2213017 - Reactome:R-HSA-264444 - Reactome:R-HSA-2682349 - Reactome:R-HSA-2730904 - Reactome:R-HSA-2737728 - Reactome:R-HSA-2769007 - Reactome:R-HSA-2900765 - Reactome:R-HSA-3000335 - Reactome:R-HSA-3134804 - Reactome:R-HSA-3134946 - Reactome:R-HSA-3249386 - Reactome:R-HSA-3780995 - Reactome:R-HSA-3781009 - Reactome:R-HSA-3788724 - Reactome:R-HSA-3797226 - Reactome:R-HSA-400267 - Reactome:R-HSA-4332236 - Reactome:R-HSA-446877 - Reactome:R-HSA-450358 - Reactome:R-HSA-451418 - Reactome:R-HSA-5357757 - Reactome:R-HSA-5362412 - Reactome:R-HSA-5483238 - Reactome:R-HSA-5607725 - Reactome:R-HSA-5607728 - Reactome:R-HSA-5607756 - Reactome:R-HSA-5607757 - Reactome:R-HSA-5610742 - Reactome:R-HSA-5610745 - Reactome:R-HSA-5610746 - Reactome:R-HSA-5652009 - Reactome:R-HSA-5655170 - Reactome:R-HSA-5660753 - Reactome:R-HSA-5667107 - Reactome:R-HSA-5667111 - Reactome:R-HSA-5668454 - Reactome:R-HSA-5668534 - Reactome:R-HSA-5675470 - Reactome:R-HSA-5684250 - Reactome:R-HSA-5691108 - Reactome:R-HSA-5693108 - Reactome:R-HSA-68712 - Reactome:R-HSA-69598 - Reactome:R-HSA-741386 - Reactome:R-HSA-75824 - Reactome:R-HSA-870449 - Reactome:R-HSA-8948709 - Reactome:R-HSA-8956106 - Reactome:R-HSA-9013069 - Reactome:R-HSA-9013974 - Reactome:R-HSA-9014342 - Reactome:R-HSA-918224 - Reactome:R-HSA-936412 - Reactome:R-HSA-936942 - Reactome:R-HSA-936986 - Reactome:R-HSA-9628444 - Reactome:R-HSA-9645394 - Reactome:R-HSA-9645414 - Reactome:R-HSA-9688831 - Reactome:R-HSA-9701000 - Reactome:R-HSA-9750946 - Reactome:R-HSA-975118 - Reactome:R-HSA-975147 - Reactome:R-HSA-9758604 - Reactome:R-HSA-9793444 - Reactome:R-HSA-9793485 - Reactome:R-HSA-9793679 - Reactome:R-HSA-9796346 - Reactome:R-HSA-9796387 - Reactome:R-HSA-9796626 - Reactome:R-HSA-9815507 - Reactome:R-HSA-9817362 - Reactome:R-HSA-983140 - Reactome:R-HSA-983153 - Reactome:R-HSA-983156 - Reactome:R-HSA-9833155 - Reactome:R-HSA-9833973 - Reactome:R-HSA-9834070 - Reactome:R-HSA-9861563 - Reactome:R-HSA-9861640 - ubiquitin conjugating enzyme activity - ubiquitin ligase activity - ubiquitin protein ligase activity - ubiquitin protein-ligase activity - ubiquitin-conjugating enzyme activity - GO:0004842 - ubiquitin-protein transferase activity - - - - - Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. - GOC:BioGRID - GOC:jh2 - PMID:9635407 - - - - - Reactome:R-HSA-1169394 - ISGylation of IRF3 - - - - - Reactome:R-HSA-1169395 - ISGylation of viral protein NS1 - - - - - Reactome:R-HSA-1169397 - Activation of ISG15 by UBA7 E1 ligase - - - - - Reactome:R-HSA-1169398 - ISGylation of host protein filamin B - - - - - Reactome:R-HSA-1169402 - ISGylation of E2 conjugating enzymes - - - - - Reactome:R-HSA-1169405 - ISGylation of protein phosphatase 1 beta (PP2CB) - - - - - Reactome:R-HSA-1169406 - ISGylation of host proteins - - - - - Reactome:R-HSA-1234163 - Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha - - - - - Reactome:R-HSA-1234172 - Nuclear VBC complex ubiquitinylates HIF-alpha - - - - - Reactome:R-HSA-1253282 - ERBB4 ubiquitination by WWP1/ITCH - - - - - Reactome:R-HSA-1358789 - Self-ubiquitination of RNF41 - - - - - Reactome:R-HSA-1358790 - RNF41 ubiquitinates ERBB3 - - - - - Reactome:R-HSA-1358792 - RNF41 ubiquitinates activated ERBB3 - - - - - Reactome:R-HSA-1363331 - Ubiquitination of p130 (RBL2) by SCF (Skp2) - - - - - Reactome:R-HSA-168915 - K63-linked ubiquitination of RIP1 bound to the activated TLR complex - - - - - Reactome:R-HSA-173542 - SMURF2 ubiquitinates SMAD2 - - - - - Reactome:R-HSA-173545 - Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling - - - - - Reactome:R-HSA-174057 - Multiubiquitination of APC/C-associated Cdh1 - - - - - Reactome:R-HSA-174104 - Ubiquitination of Cyclin A by APC/C:Cdc20 complex - - - - - Reactome:R-HSA-174144 - Ubiquitination of Securin by phospho-APC/C:Cdc20 complex - - - - - Reactome:R-HSA-174159 - Ubiquitination of Emi1 by SCF-beta-TrCP - - - - - Reactome:R-HSA-174195 - Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex - - - - - Reactome:R-HSA-174227 - Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex - - - - - Reactome:R-HSA-179417 - Multiubiquitination of Nek2A - - - - - Reactome:R-HSA-180540 - Multi-ubiquitination of APOBEC3G - - - - - Reactome:R-HSA-180597 - Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex - - - - - Reactome:R-HSA-182986 - CBL-mediated ubiquitination of CIN85 - - - - - Reactome:R-HSA-182993 - Ubiquitination of stimulated EGFR (CBL) - - - - - Reactome:R-HSA-183051 - CBL ubiquitinates Sprouty - - - - - Reactome:R-HSA-183084 - CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix - - - - - Reactome:R-HSA-183089 - CBL binds and ubiquitinates phosphorylated Sprouty - - - - - Reactome:R-HSA-1852623 - Ubiquitination of NICD1 by FBWX7 - - - - - Reactome:R-HSA-187575 - Ubiquitination of phospho-p27/p21 - - - - - Reactome:R-HSA-1912357 - ITCH ubiquitinates DTX - - - - - Reactome:R-HSA-1912386 - Ubiquitination of NOTCH1 by ITCH in the absence of ligand - - - - - Reactome:R-HSA-1918092 - CHIP (STUB1) mediates ubiquitination of ERBB2 - - - - - Reactome:R-HSA-1918095 - CUL5 mediates ubiquitination of ERBB2 - - - - - Reactome:R-HSA-1977296 - NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer - - - - - Reactome:R-HSA-1980074 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 - - - - - Reactome:R-HSA-1980118 - ARRB mediates NOTCH1 ubiquitination - - - - - Reactome:R-HSA-201425 - Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling - - - - - Reactome:R-HSA-202453 - Auto-ubiquitination of TRAF6 - - - - - Reactome:R-HSA-202534 - Ubiquitination of NEMO by TRAF6 - - - - - Reactome:R-HSA-205118 - TRAF6 polyubiquitinates NRIF - - - - - Reactome:R-HSA-209063 - Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex - - - - - Reactome:R-HSA-211734 - Ubiquitination of PAK-2p34 - - - - - Reactome:R-HSA-2169050 - SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7 - - - - - Reactome:R-HSA-2172172 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH2 - - - - - Reactome:R-HSA-2179276 - SMURF2 monoubiquitinates SMAD3 - - - - - Reactome:R-HSA-2186747 - Ubiquitination of SKI/SKIL by RNF111/SMURF2 - - - - - Reactome:R-HSA-2186785 - RNF111 ubiquitinates SMAD7 - - - - - Reactome:R-HSA-2187368 - STUB1 (CHIP) ubiquitinates SMAD3 - - - - - Reactome:R-HSA-2213017 - Auto-ubiquitination of TRAF3 - - - - - Reactome:R-HSA-264444 - Autoubiquitination of phospho-COP1(Ser-387 ) - - - - - Reactome:R-HSA-2682349 - RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels - - - - - Reactome:R-HSA-2730904 - Auto-ubiquitination of TRAF6 - - - - - Reactome:R-HSA-2737728 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants - - - - - Reactome:R-HSA-2769007 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants - - - - - Reactome:R-HSA-2900765 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants - - - - - Reactome:R-HSA-3000335 - SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA - - - - - Reactome:R-HSA-3134804 - STING ubiquitination by TRIM32 or TRIM56 - - - - - Reactome:R-HSA-3134946 - DDX41 ubiquitination by TRIM21 - - - - - Reactome:R-HSA-3249386 - DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1 - - - - - Reactome:R-HSA-3780995 - NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2 - - - - - Reactome:R-HSA-3781009 - NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1 - - - - - Reactome:R-HSA-3788724 - Cdh1:APC/C ubiquitinates EHMT1 and EHMT2 - - - - - Reactome:R-HSA-3797226 - Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease) - - - - - Reactome:R-HSA-400267 - BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins - - - - - Reactome:R-HSA-4332236 - CBL neddylates TGFBR2 - - - - - Reactome:R-HSA-446877 - TRAF6 is K63 poly-ubiquitinated - - - - - Reactome:R-HSA-450358 - Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation - - - - - Reactome:R-HSA-451418 - Pellino ubiquitinates IRAK1 - - - - - Reactome:R-HSA-5357757 - BIRC(cIAP1/2) ubiquitinates RIPK1 - - - - - Reactome:R-HSA-5362412 - SYVN1 ubiquitinates Hh C-terminal fragments - - - - - Reactome:R-HSA-5483238 - Hh processing variants are ubiquitinated - - - - - Reactome:R-HSA-5607725 - SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP - - - - - Reactome:R-HSA-5607728 - beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex - - - - - Reactome:R-HSA-5607756 - TRAF6 oligomer autoubiquitinates - - - - - Reactome:R-HSA-5607757 - K63polyUb-TRAF6 ubiquitinates TAK1 - - - - - Reactome:R-HSA-5610742 - SCF(beta-TrCP) ubiquitinates p-GLI1 - - - - - Reactome:R-HSA-5610745 - SCF(beta-TrCP) ubiquitinates p-GLI2 - - - - - Reactome:R-HSA-5610746 - SCF(beta-TrCP) ubiquitinates p-GLI3 - - - - - Reactome:R-HSA-5652009 - RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA - - - - - Reactome:R-HSA-5655170 - RCHY1 monoubiquitinates POLH - - - - - Reactome:R-HSA-5660753 - SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA - - - - - Reactome:R-HSA-5667107 - SIAH1, SIAH2 ubiquitinate SNCAIP - - - - - Reactome:R-HSA-5667111 - PARK2 K63-Ubiquitinates SNCAIP - - - - - Reactome:R-HSA-5668454 - K63polyUb-cIAP1,2 ubiquitinates TRAF3 - - - - - Reactome:R-HSA-5668534 - cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK - - - - - Reactome:R-HSA-5675470 - BIRC2/3 (cIAP1/2) is autoubiquitinated - - - - - Reactome:R-HSA-5684250 - SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2 - - - - - Reactome:R-HSA-5691108 - SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2 - - - - - Reactome:R-HSA-5693108 - TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains - - - - - Reactome:R-HSA-68712 - The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1 - - - - - Reactome:R-HSA-69598 - Ubiquitination of phosphorylated Cdc25A - - - - - Reactome:R-HSA-741386 - RIP2 induces K63-linked ubiquitination of NEMO - - - - - Reactome:R-HSA-75824 - Ubiquitination of Cyclin D1 - - - - - Reactome:R-HSA-870449 - TRIM33 monoubiquitinates SMAD4 - - - - - Reactome:R-HSA-8948709 - DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3 - - - - - Reactome:R-HSA-8956106 - VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha - - - - - Reactome:R-HSA-9013069 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH3 - - - - - Reactome:R-HSA-9013974 - Auto-ubiquitination of TRAF3 within activated TLR3 complex - - - - - Reactome:R-HSA-9014342 - K63-linked ubiquitination of RIP1 bound to the activated TLR complex - - - - - Reactome:R-HSA-918224 - DDX58 is K63 polyubiquitinated - - - - - Reactome:R-HSA-936412 - RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS - - - - - Reactome:R-HSA-936942 - Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 - - - - - Reactome:R-HSA-936986 - Activated TRAF6 synthesizes unanchored polyubiquitin chains - - - - - Reactome:R-HSA-9628444 - Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation - - - - - Reactome:R-HSA-9645394 - Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation - - - - - Reactome:R-HSA-9645414 - Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer - - - - - Reactome:R-HSA-9688831 - STUB1 ubiquitinates RIPK3 at K55, K363 - - - - - Reactome:R-HSA-9701000 - BRCA1:BARD1 heterodimer autoubiquitinates - - - - - Reactome:R-HSA-9750946 - TRAF2,6 ubiquitinates NLRC5 - - - - - Reactome:R-HSA-975118 - TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex - - - - - Reactome:R-HSA-975147 - Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane - - - - - Reactome:R-HSA-9758604 - Ubiquitination of IKBKG by TRAF6 - - - - - Reactome:R-HSA-9793444 - ITCH polyubiquitinates MLKL at K50 - - - - - Reactome:R-HSA-9793485 - PRKN polyubiquitinates RIPK3 - - - - - Reactome:R-HSA-9793679 - LUBAC ubiquitinates RIPK1 at K627 - - - - - Reactome:R-HSA-9796346 - MIB2 ubiquitinates RIPK1 at K377, K604, K634 - - - - - Reactome:R-HSA-9796387 - STUB1 ubiquitinates RIPK1 at K571, K604, K627 - - - - - Reactome:R-HSA-9796626 - MIB2 ubiquitinates CFLAR - - - - - Reactome:R-HSA-9815507 - MIB2 ubiquitinates CYLD at K338, K530 - - - - - Reactome:R-HSA-9817362 - SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex - - - - - Reactome:R-HSA-983140 - Transfer of Ub from E2 to substrate and release of E2 - - - - - Reactome:R-HSA-983153 - E1 mediated ubiquitin activation - - - - - Reactome:R-HSA-983156 - Polyubiquitination of substrate - - - - - Reactome:R-HSA-9833155 - Ubiquitination of STAT2 - - - - - Reactome:R-HSA-9833973 - ISGylation of PKR - - - - - Reactome:R-HSA-9834070 - PRKN ubiquitinates MOM substrates - - - - - Reactome:R-HSA-9861563 - CTLH E3 ligase ubiquitinates LDHA - - - - - Reactome:R-HSA-9861640 - CTLH E3 ligase ubiquitinates PKM-1 - - - - - - - - A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. - NIF_Subcellular:sao1702920020 - Wikipedia:Cell_nucleus - cell nucleus - horsetail nucleus - GO:0005634 - nucleus - - - - - A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. - GOC:go_curators - - - - - horsetail nucleus - GOC:al - GOC:mah - GOC:vw - PMID:15030757 - - - - - - - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - jl - 2012-09-19T15:05:24Z - Wikipedia:Biological_process - biological process - physiological process - single organism process - single-organism process - GO:0008150 - Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. - biological process - biological_process - - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - GOC:pdt - - - - - - - - - - - - true - - - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - Reactome:R-HSA-6788855 - Reactome:R-HSA-6788867 - phosphokinase activity - GO:0016301 - Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. - kinase activity - - - - - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - ISBN:0198506732 - - - - - Reactome:R-HSA-6788855 - FN3KRP phosphorylates PsiAm, RibAm - - - - - Reactome:R-HSA-6788867 - FN3K phosphorylates ketosamines - - - - - - - - - - - - true - - - Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. - Reactome:R-HSA-141367 - Reactome:R-HSA-162914 - GO:0019107 - myristoyltransferase activity - - - - - Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. - GOC:ai - - - - - Reactome:R-HSA-141367 - Myristoylation of tBID by NMT1 - - - - - Reactome:R-HSA-162914 - Myristoylation of Nef - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - planned process - Injecting mice with a vaccine in order to test its efficacy - - A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material - - - - - - - - - assay - Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. - - A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. - 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. - Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683. - PlanAndPlannedProcess Branch - measuring - scientific observation - OBI branch derived - assay - - - - - - - - - container - - A device that can be used to restrict the location of material entities over time - 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) - PERSON: Bjoern Peters - container - - - - - - - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device - - - - - - - - - organism - animal - fungus - plant - virus - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism - - - - - - - - - A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. - disease - - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000001 - quality - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATOC:GVG - - - - - - - - - A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - - ramified - ramiform - PATO:0000402 - branched - - - - - A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - WordNet:WordNet - - - - - - - - - A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. - PATO:0001199 - linear - - - - - A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. - ISBN:0881923214 - - - - - - - - - A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity. - proportion - proportionality - proportionality to - quotient - rate - PATO:0001470 - Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio. - ratio - - - - - A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity. - https://orcid.org/0000-0001-8314-2140 - - - - - Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio. - https://orcid.org/0000-0001-8314-2140 - - - - - - - - - A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. - - 2009-10-06T04:37:14Z - PATO:0002124 - laminar - - - - - A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. - PATOC:GVG - - - - - - - - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, - An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. - This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. - - - 2017-06-05T17:55:39Z - obsolete exposure event or process - https://github.com/oborel/obo-relations/pull/173 - true - - - - - - - - - - - - - - Any entity that is ordered in discrete units along a linear axis. - - sequentially ordered entity - - - - - - - - - Any individual unit of a collection of like units arranged in a linear order - - An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. - sequence atomic unit - - - - - - - - - Any entity that can be divided into parts such that each part is an atomical unit of a sequence - - Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. - sequence bearer - - - - - - - - - A material entity consisting of multiple components that are causally integrated. - May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 - - http://www.jbiomedsem.com/content/4/1/43 - system - - - - - - - - - Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. - - - AAO:0010825 - AEO:0000003 - BILA:0000003 - CARO:0000003 - EHDAA2:0003003 - EMAPA:0 - FMA:305751 - FMA:67135 - GAID:781 - HAO:0000003 - MA:0003000 - MESH:D000825 - SCTID:362889002 - TAO:0000037 - TGMA:0001823 - VHOG:0001759 - XAO:0003000 - ZFA:0000037 - http://dbpedia.org/ontology/AnatomicalStructure - biological structure - connected biological structure - UBERON:0000061 - - - - - anatomical structure - - - - - Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. - CARO:0000003 - - - - - connected biological structure - CARO:0000003 - - - - - - - - - A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. - CARO:0001001 - NLX:147821 - funiculus - nerve fiber bundle - neural fiber bundle - UBERON:0000122 - - - neuron projection bundle - - - - - A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. - CARO:0001001 - FBC:DOS - FBbt:00005099 - - - - - nerve fiber bundle - FBbt:00005099 - - - - - - - - - - - Anatomical entity that has mass. - - - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - UBERON:0000465 - - - - - material anatomical entity - - - - - Anatomical entity that has mass. - http://orcid.org/0000-0001-9114-8737 - - - - - - - - - - Anatomical entity that has no mass. - - - AAO:0010265 - AEO:0000007 - BILA:0000007 - CARO:0000007 - EHDAA2:0003007 - FMA:67112 - HAO:0000007 - TAO:0001835 - TGMA:0001827 - VHOG:0001727 - immaterial physical anatomical entity - UBERON:0000466 - - - - - immaterial anatomical entity - - - - - Anatomical entity that has no mass. - http://orcid.org/0000-0001-9114-8737 - - - - - immaterial physical anatomical entity - FMA:67112 - - - - - - - - - - - true - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - - AAO:0010841 - AEO:0000000 - BFO:0000004 - BILA:0000000 - BIRNLEX:6 - CARO:0000000 - EHDAA2:0002229 - FMA:62955 - HAO:0000000 - MA:0000001 - NCIT:C12219 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - WBbt:0000100 - XAO:0000000 - ZFA:0100000 - UBERON:0001062 - - - - - anatomical entity - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - FMA:62955 - http://orcid.org/0000-0001-9114-8737 - - - - - UMLS:C1515976 - ncithesaurus:Anatomic_Structure_System_or_Substance - - - - - - - - - A vessel through which blood circulates in the body. - consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - vascular element - AAO:0011004 - AEO:0000207 - BTO:0001102 - CALOHA:TS-0080 - EFO:0000817 - EHDAA2:0003252 - EHDAA:240 - EMAPA:32743 - EMAPA:35993 - FMA:50722 - FMA:63183 - GAID:169 - MA:0000060 - MAT:0000393 - MESH:D001808 - NCIT:C12679 - NLXANAT:090901 - SCTID:361097006 - TAO:0002137 - UMLS:C0005847 - VHOG:0001250 - Wikipedia:Blood_vessel - XAO:0001011 - ZFA:0005314 - region of vascular tree organ - vascular tree organ region - UBERON:0001981 - - - - - - - - blood vessel - - - - - A vessel through which blood circulates in the body. - BTO:0001102 - Wikipedia:Blood_vessel - - - - - vascular element - EMAPA:35993 - - - - - UMLS:C0005847 - ncithesaurus:Blood_Vessel - - - - - region of vascular tree organ - FMA:50722 - - - - - vascular tree organ region - FMA:50722 - - - - - - - - - Any of the smallest blood vessels connecting arterioles with venules. - not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element - AAO:0010252 - BTO:0002045 - CALOHA:TS-2006 - EFO:0001906 - EMAPA:35198 - EV:0100035 - FMA:63194 - MA:0000065 - MESH:D002196 - NCIT:C12685 - NLXANAT:090902 - TAO:0005250 - UMLS:C0935624 - VHOG:0001253 - Wikipedia:Capillary - XAO:0000116 - ZFA:0005250 - blood capillary - capillary vessel - UBERON:0001982 - - - - - - - - capillary - https://github.com/obophenotype/uberon/issues/2186 - - - - - Any of the smallest blood vessels connecting arterioles with venules. - ISBN:0073040584 - Wikipedia:Capillary - https://github.com/obophenotype/uberon/issues/137 - - - - - UMLS:C0935624 - ncithesaurus:Capillary - - - - - - - - - An anatomical structure that has more than one cell as a part. - - - CARO:0010000 - multicellular structure - UBERON:0010000 - - - - - multicellular anatomical structure - - - - - An anatomical structure that has more than one cell as a part. - CARO:0010000 - - - - - multicellular structure - FBbt:00100313 - - - - - - - - - phenotype - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - ready for release - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - ## Elucidation - -This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; - -## How to interpret (informal) - -First the &quot;atemporal&quot; FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. - -## Example - - Class: nucleus - SubClassOf: part_of some cell - - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) - -## Notes - -This interpretation is *not* the same as an at-all-times relation - axiom holds for all times - - - - - - - - ## Elucidation - -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. - -## Example: - - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm - - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - relation has no temporal argument - - - - - - - - Researcher ORCID=0000-0001-6677-8489 - Aleix Puig-Barbé - - - - - Researcher ORCID=0000-0001-6677-8489 - - - - - - Aleix Puig-Barbé - - - - - - - - - Researcher - Austin Meier - - - - - Researcher - - - - - - Austin Meier - - - - - - - - - researcher - Shawn Zheng Kai Tan - - - - - researcher - - - - - - Shawn Zheng Kai Tan - - - - - - - - - researcher - Raymund Stefancsik - - - - - researcher - - - - - - Raymund Stefancsik - - - - - - - - - researcher, metadata, diseases, University of Maryland - Lynn Schriml - - - - - researcher, metadata, diseases, University of Maryland - - - - - - Lynn Schriml - - - - - - - - - researcher - William D Duncan - - - - - researcher - - - - - - William D Duncan - - - - - - - - - researcher (ORCID 0000-0002-1373-1705) - Clare Pilgrim - - - - - researcher (ORCID 0000-0002-1373-1705) - - - - - - Clare Pilgrim - - - - - - - - - data scientist - Anne Thessen - - - - - data scientist - - - - - - Anne Thessen - - - - - - - - - researcher (ORCID 0000-0002-2999-0103) - Jie Zheng - - - - - researcher (ORCID 0000-0002-2999-0103) - - - - - - Jie Zheng - - - - - - - - - researcher - Pier Luigi Buttigieg - - - - - researcher - - - - - - Pier Luigi Buttigieg - - - - - - - - - researcher - Christian J Stoeckert - - - - - researcher - - - - - - Christian J Stoeckert - - - - - - - - - bioinformatics researcher - Christopher J. Mungall - - - - - bioinformatics researcher - - - - - - Christopher J. Mungall - - - - - - - - - researcher - David Osumi-Sutherland - - - - - researcher - - - - - - David Osumi-Sutherland - - - - - - - - - researcher - Lauren E. Chan - - - - - researcher - - - - - - Lauren E. Chan - - - - - - - - - researcher - Marie-Angélique Laporte - - - - - researcher - - - - - - Marie-Angélique Laporte - - - - - - - - - researcher - James P. Balhoff - - - - - researcher - - - - - - James P. Balhoff - - - - - - - - - researcher - Damion M Dooley - - - - - researcher - - - - - - Damion M Dooley - - - - - - - - - researcher - Lindsay G Cowell - - - - - researcher - - - - - - Lindsay G Cowell - - - - - - - - - Canadian biocurator - Pascale Gaudet - - - - - Canadian biocurator - - - - - - Pascale Gaudet - - - - - - - - - researcher - Mathias Brochhausen - - - - - researcher - - - - - - Mathias Brochhausen - - - - - - - - - Researcher ORCID=0000-0003-1909-9269 - S. Clint Dowland - - - - - Researcher ORCID=0000-0003-1909-9269 - - - - - - S. Clint Dowland - - - - - - - - - researcher - Anna Maria Masci - - - - - researcher - - - - - - Anna Maria Masci - - - - - - - - - Researcher ORCID=0000-0003-2620-0345 - Asiyah Yu Lin - - - - - Researcher ORCID=0000-0003-2620-0345 - - - - - - Asiyah Yu Lin - - - - - - - - - software/data engineer - Jorrit Poelen - - - - - software/data engineer - - - - - - Jorrit Poelen - - - - - - - - - American chemist - Charles Tapley Hoyt - - - - - American chemist - - - - - - Charles Tapley Hoyt - - - - - - - - - - - - data item - data item - - - information content entity - information content entity - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolete_core - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - placeholder removed - placeholder removed - - - terms merged - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - - - ontology term requester - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - denotator type - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - universal - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - is denotator type - Relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - - - defined class - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - named class expression - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - antisymmetric property - part_of antisymmetric property xsd:true - Use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - has ID digit count - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - has ID range allocated - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - has ID policy for - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - has ID prefix - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - has associated axiom(nl) - - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - has associated axiom(fol) - - - is allocated id range - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - Add as annotation triples in the granting ontology - is allocated id range - - - may be identical to - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - may be identical to - - - scheduled for obsoletion on or after - Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. - Chris Mungall, Jie Zheng - scheduled for obsoletion on or after - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label - - - ontology module - I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. - ontology file - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - ontology module - - - base ontology module - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - base ontology module - - - - editors ontology module - An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. - source ontology module - editors ontology module - - - main release ontology module - An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. - TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module - main release ontology module - - - bridge ontology module - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - bridge ontology module - - - - import ontology module - A subset ontology module that is intended to be imported from another ontology. - TODO: add axioms that indicate this is the output of a module extraction process. - import file - import ontology module - - - - subset ontology module - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - subset ontology module - - - - - curation subset ontology module - A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. - curation subset ontology module - - - analysis ontology module - An ontology module that is intended for usage in analysis or discovery applications. - analysis subset ontology module - - - single layer ontology module - A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. - ribbon subset - single layer subset ontology module - - - exclusion subset ontology module - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - exclusion subset ontology module - - - external import ontology module - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - external import ontology module - - - species subset ontology module - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - species subset ontology module - - - - reasoned ontology module - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - reasoned ontology module - - - - generated ontology module - An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. - TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process - generated ontology module - - - template generated ontology module - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - template generated ontology module - - - - - - taxonomic bridge ontology module - taxonomic bridge ontology module - - - ontology module subsetted by expressivity - ontology module subsetted by expressivity - - - obo basic subset ontology module - A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. - -Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). - -An ontology is OBO Basic if and only if it has the following characteristics: -DAG -Unidirectional -No Dangling Clauses -Fully Asserted -Fully Labeled -No equivalence axioms -Singly labeled edges -No qualifier lists -No disjointness axioms -No owl-axioms header -No imports - obo basic subset ontology module - - - - ontology module subsetted by OWL profile - ontology module subsetted by OWL profile - - - EL++ ontology module - EL++ ontology module - - - The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - - out of scope - - - This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. - OBO Operations call - - logical characteristic of object property - - - The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. - This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). - - domain entity does not exist - - - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) - A synonym type for describing abbreviations or initalisms - - abbreviation - - - A synonym type for describing ambiguous synonyms - - ambiguous synonym - - - A synonym type for describing dubious synonyms - - dubious synonym - - - EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) - A synonym type for describing layperson or colloquial synonyms - - layperson synonym - - - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) - A synonym type for describing pluralization synonyms - - plural form - - - CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) - A synonym type for describing UK spelling variants - - UK spelling synonym - - - A synonym type for common misspellings - - misspelling - - - A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway - - misnomer - - - MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. - A synonym type for names that have been used as primary labels in the past. - - previous name - - - The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College - A synonym type for the legal entity name - - legal name - - - CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label - The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. - - INN - International Nonproprietary Name - - - nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis - A synonym type for describing Latin term synonyms. - - latin term - - - NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. - A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. - - acronym - - - A serial number such as "12324X"; a stop sign; a written proper name such as "OBI - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - - has symbol - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/tmp/obi-download.owl b/src/ontology/tmp/obi-download.owl index e6bda0f..7054a46 100644 --- a/src/ontology/tmp/obi-download.owl +++ b/src/ontology/tmp/obi-download.owl @@ -7,15 +7,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester @@ -82,7 +79,7 @@ http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2025-05-01 + 2026-05-08 @@ -104,32 +101,10 @@ - - - - Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. - Really of interest to developers only - BFO OWL specification label - - - - - - - - - Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 - Person:Alan Ruttenberg - Really of interest to developers only - BFO CLIF specification label - - - - - + editor preferred label editor preferred label editor preferred term editor preferred term @@ -138,7 +113,7 @@ The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - + editor preferred label editor preferred label editor preferred term editor preferred term @@ -155,7 +130,6 @@ A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - example of usage @@ -192,8 +166,11 @@ definition textual definition + A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. + English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + The official definition. 2012-04-05: Barry Smith @@ -216,7 +193,6 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition definition textual definition @@ -232,7 +208,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note @@ -247,7 +222,6 @@ We also have the outstanding issue of how to aim different definitions to differ 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - term editor @@ -263,9 +237,7 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - alternative term @@ -279,7 +251,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source @@ -304,7 +275,6 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg - curator note @@ -314,13 +284,14 @@ We also have the outstanding issue of how to aim different definitions to differ term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + the URL for an ontology term tracker issue, such as https://github.com/monarch-initiative/mondo/issues/7588 - An IRI or similar locator for a request or discussion of an ontology term. + A URL for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item + @@ -360,7 +331,6 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - imported from @@ -509,7 +479,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - elucidation @@ -522,7 +491,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language - has associated axiom(nl) @@ -535,7 +503,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax - has associated axiom(fol) @@ -600,7 +567,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label @@ -720,11 +686,24 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + The property is intended to be used exclusively on synonym assertions, to express that the synonym in question is the preference of a specific community. For example, one community may prefer to say call a disease "A" and another one "B" (but they are the same thing). + A provenance property that denotes a synonym to be the preferred one for a specific community. + + + 2025-06-02 + preferred label for community + + + + CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) - A synonym type for describing abbreviations or initalisms + A synonym type for describing abbreviations or initialisms 2023-03-03 @@ -899,6 +878,19 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + The Developing Mouse Brain Atlas Ontology (DBMA) ontology uses part-of in its hierarchy, so this would correspond to the following turtle: `<https://purl.brain-bican.org/ontology/dmbao/dmbao.owl> a owl:Ontology; OMO:0003014 rdfs:subClassOf, BFO:0000050`. + Relates an ontology to predicates/properties that should be used by user interfaces to render the hierarchical structure of the ontology. Typically, this is rdfs:subClassOf, but in ontologies that are partonomies, this might also include BFO:0000050 (part of). Tools like OLS can use predicates annotated with this property for rendering the ontology class hierarchy. There can be more than one hierarchical property. In the absence of any, it should be assumed that it is rdfs:subClassOf. + + + 2025-09-17 + has ontology hierarchical property + + + + @@ -912,12 +904,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1051,12 +1037,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1185,6 +1165,12 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 + + + + + + @@ -1194,12 +1180,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - @@ -1295,17 +1275,14 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - label + label + A human readable name for this class. label + label @@ -1316,12 +1293,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + realized in @@ -1456,13 +1394,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes @@ -1471,15 +1403,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - preceded by - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + preceded by @@ -1488,50 +1415,43 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + precedes - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in + + + + executed by + + + + + + + + intended to realize + + + + + + + + has plan - + - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process + + intended plan process type @@ -1539,10 +1459,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has measurement unit label - + has measurement unit label @@ -1551,9 +1469,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is about + A (currently) primitive relation that relates an information artifact to an entity. - is about @@ -1563,9 +1480,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - denotes + + A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically - denotes @@ -1575,9 +1492,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is quality measurement of + m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q - is quality measurement of @@ -1586,9 +1502,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - denoted by + inverse of the relation 'denotes' - denoted by @@ -1597,10 +1512,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has coordinate unit label - has coordinate unit label @@ -1610,9 +1522,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is duration of + relates a process to a time-measurement-datum that represents the duration of the process - is duration of @@ -1654,11 +1565,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + has specified input see is_input_of example_of_usage - The inverse property of is specified input of + The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters @@ -1690,11 +1601,11 @@ A continuant cannot have an occurrent as part: use 'participates in'. - + is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay - A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified input of @@ -1743,10 +1654,10 @@ For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Qu - + has specified output - The inverse property of is specified output of + The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter @@ -1910,10 +1821,10 @@ instance level relation [GOC:cjm] - + is specified output of - A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified output of @@ -2011,7 +1922,7 @@ level of radioactivity is_proxy_for level of toxicity - + achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' @@ -2130,7 +2041,7 @@ level of radioactivity is_proxy_for level of toxicity - + objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. @@ -2255,15 +2166,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + - @@ -2377,15 +2288,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2394,16 +2297,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - has characteristic @@ -2412,15 +2306,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in participates in @@ -2429,16 +2315,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -2447,11 +2324,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as @@ -2461,10 +2333,6 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes @@ -2474,15 +2342,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this catalysis function is a function of this enzyme + function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + function of @@ -2491,14 +2353,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this red color is a quality of this apple + quality of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + quality of @@ -2507,14 +2364,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this investigator role is a role of this person + role of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + role of @@ -2523,13 +2375,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) + has function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function + has function @@ -2538,12 +2386,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - this apple has quality this red color + has quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality + has quality @@ -2552,13 +2397,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) + has role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role + has role @@ -2567,11 +2408,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - + has disposition a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence + has disposition @@ -2580,8 +2419,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. + disposition of + inverse of has disposition + disposition of @@ -2590,47 +2430,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - derives from - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - + derives from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from derives from - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - derives into - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - location of @@ -2640,97 +2451,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in + located in - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - - 2D boundary of - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - has boundary - has_2D_boundary - - has 2D boundary - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + immediately preceded by @@ -2739,11 +2472,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - David Osumi-Sutherland - ends_at_start_of - meets - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + immediately precedes @@ -2752,14 +2482,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + has component w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - + has component - @@ -2767,11 +2493,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + capable of A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - has function realized in - capable of + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + + capable of @@ -2779,9 +2506,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - surrounded by - x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y + surrounded by + x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x surrounded by @@ -2796,15 +2522,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + inverse of surrounded by + surrounds + + + + - - - move to BFO? - Allen - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporal relation + temporally related to + + temporally related to @@ -2812,61 +2544,50 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - + starts inverse of starts with - Chris Mungall - Allen + starts - + - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + has input - + - - - - has member is a mereological relation between a collection and an item. - SIO - - has member + + p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. + has output - + - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true + + inverse of enables + enabled by - + - - DEPRECATED bearer of - true + + + has member + has member is a mereological relation between a collection and an item. + + has member @@ -2888,17 +2609,47 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - - has measurement value - - has measurement value + + has quantity + + + + + Number of protons in an atomic nucleus + has atomic number + + + + + + + + + has number of atomic nuclei + + + + + + + + has inchi string + + + + + + + + + + @@ -2972,518 +2723,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - entity - Entity - Julius Caesar - Verdi’s Requiem - the Second World War - your body mass index - BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - entity - - - - - Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf - - per discussion with Barry Smith - - - - - - An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) - - - - - - - - - - - - - - - - - continuant - Continuant - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - continuant - - - - - Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants - - - - - - A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) - - - - - - if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) - - - - - - if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) - - - - - - if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] - - - - - - (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] - - - - - - (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] - - - - - - (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] - - - - - - - - - - - - - - - - occurrent - Occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. - BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region - BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - occurrent - - - - - Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. - - per discussion with Barry Smith - - - - - Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. - - - - - - An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) - - - - - - Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) - - - - - - b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) - - - - - - (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] - - - - - - (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] - - - - - - - - - - - - ic - IndependentContinuant - a chair - a heart - a leg - a molecule - a spatial region - an atom - an orchestra. - an organism - the bottom right portion of a human torso - the interior of your mouth - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - - independent continuant - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - - - - - - For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) - - - - - - For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) - - - - - - (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] - - - - - - (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - - - - - - - - - s-region - SpatialRegion - BFO 2 Reference: Spatial regions do not participate in processes. - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - spatial region - - - - - Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. - - per discussion with Barry Smith - - - - - A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) - - - - - - All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) - - - - - - (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] - - - - - - (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] - - - - - - - - - - t-region - TemporalRegion - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - temporal region - - - - - Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional - - per discussion with Barry Smith - - - - - A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) - - - - - - All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) - - - - - - Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) - - - - - - (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] - - - - - - (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] - - - - - - (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] - - - - - - - - - - 2d-s-region - TwoDimensionalSpatialRegion - an infinitely thin plane in space. - the surface of a sphere-shaped part of space - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - two-dimensional spatial region - - - - - A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) - - - - - - (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] - - - - - - - - - - st-region - SpatiotemporalRegion - the spatiotemporal region occupied by a human life - the spatiotemporal region occupied by a process of cellular meiosis. - the spatiotemporal region occupied by the development of a cancer tumor - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - Every spatiotemporal region occupies_spatiotemporal_region itself. - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - spatiotemporal region - - - - - A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) - - - - - - All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) - - - - - - Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) - - - - - - Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) - - - - - - Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) - - - - - - (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] - - - - - - (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] - - - - - - (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] - - - - - - (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] - - - - - - - process - Process - a process of cell-division, \ a beating of the heart - a process of meiosis - a process of sleeping - the course of a disease - the flight of a bird - the life of an organism - your process of aging. - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - + process - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - - - - - - (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] - - @@ -3491,226 +2736,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - disposition - Disposition - an atom of element X has the disposition to decay to an atom of element Y - certain people have a predisposition to colon cancer - children are innately disposed to categorize objects in certain ways. - the cell wall is disposed to filter chemicals in endocytosis and exocytosis - BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - disposition - - - - b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) - - - - - - If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) - - - - - - (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] - - - - - - (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] - - - - - realizable - RealizableEntity - the disposition of this piece of metal to conduct electricity. - the disposition of your blood to coagulate - the function of your reproductive organs - the role of being a doctor - the role of this boundary to delineate where Utah and Colorado meet - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - + realizable entity - - - - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) - - - - - - All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) - - - - - - (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] - - - - - - (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] - - - - - - - - - - 0d-s-region - ZeroDimensionalSpatialRegion - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - zero-dimensional spatial region - - - - - A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) - - - - - - (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] - - - - - - - - - - quality - Quality - the ambient temperature of this portion of air - the color of a tomato - the length of the circumference of your waist - the mass of this piece of gold. - the shape of your nose - the shape of your nostril - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - quality - - - - - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) - - - - - - If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) - - - - - - (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] - - - - - - (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] - - - - - - - - - - - sdc - SpecificallyDependentContinuant - Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key - of one-sided specifically dependent continuants: the mass of this tomato - of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. - the disposition of this fish to decay - the function of this heart: to pump blood - the mutual dependence of proton donors and acceptors in chemical reactions [79 - the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction - the pink color of a medium rare piece of grilled filet mignon at its center - the role of being a doctor - the shape of this hole. - the smell of this portion of mozzarella - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - - specifically dependent continuant - - - - - Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. - - per discussion with Barry Smith - - - - - (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] - - - - - - (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] - - - - - - b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - - @@ -3718,183 +2754,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - role - Role - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - the priest role - the role of a boundary to demarcate two neighboring administrative territories - the role of a building in serving as a military target - the role of a stone in marking a property boundary - the role of subject in a clinical trial - the student role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - role - - - - b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) - - - - - - (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] - - - - - - - - - - fiat-object - FiatObjectPart - or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 - the FMA:regional parts of an intact human body. - the Western hemisphere of the Earth - the division of the brain into regions - the division of the planet into hemispheres - the dorsal and ventral surfaces of the body - the upper and lower lobes of the left lung - BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - fiat object - - - - - b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) - - - - - - (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] - - - - - - - - - - 1d-s-region - OneDimensionalSpatialRegion - an edge of a cube-shaped portion of space. - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - one-dimensional spatial region - - - - - A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) - - - - - - (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] - - - - - - - - - - object-aggregate - ObjectAggregate - a collection of cells in a blood biobank. - a swarm of bees is an aggregate of members who are linked together through natural bonds - a symphony orchestra - an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) - defined by fiat: the aggregate of members of an organization - defined through physical attachment: the aggregate of atoms in a lump of granite - defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container - defined via attributive delimitations such as: the patients in this hospital - the aggregate of bearings in a constant velocity axle joint - the aggregate of blood cells in your body - the nitrogen atoms in the atmosphere - the restaurants in Palo Alto - your collection of Meissen ceramic plates. - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - object aggregate - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects - - - - - - ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. - - - - - - b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) - - - - - - (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] - - - - - - - - - - 3d-s-region - ThreeDimensionalSpatialRegion - a cube-shaped region of space - a sphere-shaped region of space, - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - three-dimensional spatial region - - - - - A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) - - - - - - (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] - - @@ -3902,105 +2763,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - site - Site - Manhattan Canyon) - a hole in the interior of a portion of cheese - a rabbit hole - an air traffic control region defined in the airspace above an airport - the Grand Canyon - the Piazza San Marco - the cockpit of an aircraft - the hold of a ship - the interior of a kangaroo pouch - the interior of the trunk of your car - the interior of your bedroom - the interior of your office - the interior of your refrigerator - the lumen of your gut - your left nostril (a fiat part – the opening – of your left nasal cavity) - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - site - - - - b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) - - - - - - (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] - - - - - - - - - - object - Object - atom - cell - cells and organisms - engineered artifacts - grain of sand - molecule - organelle - organism - planet - solid portions of matter - star - BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. - BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). - BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 - BFO 2 Reference: an object is a maximal causally unified material entity - BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - object - - - - - b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) - - - - - - - - - - gdc - GenericallyDependentContinuant - The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. - the pdf file on your laptop, the pdf file that is a copy thereof on my laptop - the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - - generically dependent continuant - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - - - - - - (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] - - @@ -4008,439 +2772,40 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - function - Function - the function of a hammer to drive in nails - the function of a heart pacemaker to regulate the beating of a heart through electricity - the function of amylase in saliva to break down starch into sugar - BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - function - - - - A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) - - - - - - (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] - - - - - - - - - - p-boundary - ProcessBoundary - the boundary between the 2nd and 3rd year of your life. - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - process boundary - - - - - p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) - - - - - - Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) - - - - - - (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] - - - - - - (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] - - - - - - - - - - - 1d-t-region - OneDimensionalTemporalRegion - the temporal region during which a process occurs. - BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - one-dimensional temporal region - - - - - A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) - - - - - - (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] - - - - - material - MaterialEntity + material entity - a flame - a forest fire - a human being - a hurricane - a photon - a puff of smoke - a sea wave - a tornado - an aggregate of human beings. - an energy wave - an epidemic - the undetached arm of a human being An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 - BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. - BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. + Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - material entity - - - - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) - - - - - - Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) - - - - - - every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) - - - - - - (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] - - - - - - (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] - - - - - - - - - - cf-boundary - ContinuantFiatBoundary - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. - BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - Every continuant fiat boundary is located at some spatial region at every time at which it exists - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - continuant fiat boundary - - - - - b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) - - - - - - Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. - - - - - - (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] - - - - immaterial - ImmaterialEntity - BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 - + immaterial entity - - - - - 1d-cf-boundary - OneDimensionalContinuantFiatBoundary - The Equator - all geopolitical boundaries - all lines of latitude and longitude - the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. - the median sulcus of your tongue - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - one-dimensional continuant fiat boundary - - - - - a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) - - - - - - (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] - - - - - - + - - - - process-profile - ProcessProfile - On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels - One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. - The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - process profile - - - - - b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) - - - - - - b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) - - - - - - (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] - - - - - - (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] - - - - - - - - - - r-quality - RelationalQuality - John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. - a marriage bond, an instance of love, an obligation between one person and another. - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - relational quality - - - - - b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) - - - - - - (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] - - - - - - - - - - 2d-cf-boundary - TwoDimensionalContinuantFiatBoundary - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - two-dimensional continuant fiat boundary - - - - - a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) - - - - - - (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] - - - - - - - - - - 0d-cf-boundary - ZeroDimensionalContinuantFiatBoundary - the geographic North Pole - the point of origin of some spatial coordinate system. - the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - zero-dimensional continuant fiat boundary - - - - - zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. - - requested by Melanie Courtot - - - - - - a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) - - - - - - (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] - - - - - - - - - - 0d-t-region - ZeroDimensionalTemporalRegion - a temporal region that is occupied by a process boundary - right now - the moment at which a child is born - the moment at which a finger is detached in an industrial accident - the moment of death. - temporal instant. - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - zero-dimensional temporal region - - - - - A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) - - - - - - (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] - - - - - - - - - - history - History - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - history + + + Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. + electron - - - - A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) - - @@ -4449,7 +2814,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ insulin - A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. + A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the β cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies. insulin @@ -4459,7 +2824,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + water An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms @@ -4471,7 +2836,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ATP An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways. @@ -4491,7 +2856,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ biotin - An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. + An organic heterobicyclic compound that consists of 2-oxohexahydro-1<em>H</em>-thieno[3,4-<em>d</em>]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins. biotin @@ -4501,9 +2866,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cholesterol - A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. + A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3β-hydroxy group. cholesterol @@ -4513,7 +2878,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ammonia An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. @@ -4525,7 +2890,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phospholipid A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. @@ -4537,7 +2902,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + nitrite The nitrogen oxoanion formed by loss of a proton from nitrous acid. @@ -4549,9 +2914,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + carbon dioxide - A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. + A one-carbon compound with formula CO<small><sub>2</sub></small> in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. carbon dioxide @@ -4563,7 +2928,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ peptide - Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. + Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from α-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. peptide @@ -4573,7 +2938,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + globulin type One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma. @@ -4585,7 +2950,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatinine A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. @@ -4597,9 +2962,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + mycophenolic acid - A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. + A member of the class of 2-benzofurans that is 2-benzofuran-1(3<em>H</em>)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2<i>E</i>)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by <em>Penicillium brevi-compactum, P. stoloniferum, P. echinulatum</em> and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases. mycophenolic acid @@ -4609,7 +2974,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + creatine A glycine derivative having methyl and amidino groups attached to the nitrogen. @@ -4621,7 +2986,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bilirubin IXalpha A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. @@ -4645,9 +3010,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + progesterone - A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. + A C<small><sub>21</sub></small>-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species. progesterone @@ -4657,7 +3022,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogensulfite hydrogensulfite @@ -4668,7 +3033,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + homocysteine A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain. @@ -4680,7 +3045,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + glucose An aldohexose used as a source of energy and metabolic intermediate. @@ -4692,9 +3057,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + testosterone - An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. + An androstanoid having 17β-hydroxy and 3-oxo groups, together with unsaturation at C-4‒C-5.. testosterone @@ -4704,9 +3069,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methemoglobin - A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin. + A hemoprotein that is the ferric (Fe<small><sup>3+</small></sup>) form of hemoglobin. methemoglobin @@ -4716,7 +3081,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydrogencarbonate The carbon oxoanion resulting from the removal of a proton from carbonic acid. @@ -4728,9 +3093,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + cortisol - A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. + A 17α-hydroxy-C<small><sub>21</sub></small>-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the "stress hormone" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses. cortisol @@ -4740,7 +3105,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5'-adenylyl sulfate An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups. @@ -4752,7 +3117,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + triglyceride Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. @@ -4764,7 +3129,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chloride A halide anion formed when chlorine picks up an electron to form an an anion. @@ -4776,7 +3141,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3-hydroxybutyric acid A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics. @@ -4788,7 +3153,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bile salt A sodium salt of the conjugate of any bile acid with either glycine or taurine. @@ -4797,23 +3162,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - - - - molecular entity - Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. - We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well - - molecular entity - - - - - + cytochalasin cytochalasin @@ -4824,7 +3176,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + estradiol A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. @@ -4836,21 +3188,35 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-ethyl-N-nitrosourea - A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. + A member of the class of <em>N</em>-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups. N-ethyl-N-nitrosourea + + + + + hormone + Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds. + + hormone + + + + - + + proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + Nuclear particle of charge number +1, spin ½ and rest mass of 1.007276470(12) u. proton @@ -4860,7 +3226,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + iron cation iron cation @@ -4871,7 +3237,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + luciferin A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase. @@ -4880,10 +3246,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + nitrogen atom + + nitrogen atom + + + + - + amikacin An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group. @@ -4895,7 +3272,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium chloride An inorganic chloride salt having sodium(1+) as the counterion. @@ -4907,7 +3284,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + uric acid An oxopurine that is the final oxidation product of purine metabolism. @@ -4919,7 +3296,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lead(0) lead(0) @@ -4930,9 +3307,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + vancomycin - A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile. + A complex glycopeptide from <em>Streptomyces orientalis</em>. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria <em>Staphylococcus aureus</em> and <em>Clostridium difficile</em>. vancomycin @@ -4944,7 +3321,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ rac-lactic acid - A racemate comprising equimolar amounts of (R)- and (S)-lactic acid. + A racemate comprising equimolar amounts of (<i>R</i>)- and (<i>S</i>)-lactic acid. rac-lactic acid @@ -4954,7 +3331,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + acrylamide A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia. @@ -4966,9 +3343,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dehydroepiandrosterone - An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. + An androstanoid that is androst-5-ene substituted by a β-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands. dehydroepiandrosterone @@ -4978,7 +3355,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 3,3',5'-triiodothyronine 3,3',5'-triiodothyronine @@ -4989,7 +3366,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tobramycin A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring. @@ -5001,7 +3378,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium(1+) A monoatomic monocation obtained from sodium. @@ -5013,7 +3390,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + potassium(1+) A monoatomic monocation obtained from potassium. @@ -5025,7 +3402,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hydroxyl hydroxyl @@ -5036,20 +3413,29 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + deuterium atom - The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second). + The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek δευτερον, second). deuterium atom + + + + + Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. + neutron + + + + - + thyroxine An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions. @@ -5061,7 +3447,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + ruthenium atom ruthenium atom @@ -5069,6 +3455,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + bile acid + Any member of a group of hydroxy-5β-cholanic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. In mammals bile acids almost invariably have 5β-configuration. + + bile acid + + + + @@ -5090,7 +3488,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadodiamide hydrate The hydrate of gadodiamide. @@ -5102,7 +3500,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadoteridol A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5114,9 +3512,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phenol red - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney. phenol red @@ -5126,7 +3524,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium citrate dihydrate The dihydrate of trisodium citrate. @@ -5138,7 +3536,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + methyl group An alkyl group that is the univalent group derived from methane by removal of a hydrogen atom. @@ -5147,14 +3545,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + - - - atom - A chemical entity constituting the smallest component of an element having the chemical properties of the element. - - atom + + + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 + atomic nucleus @@ -5162,7 +3566,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + elemental oxygen elemental oxygen @@ -5173,7 +3577,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rare earth metal atom rare earth metal atom @@ -5184,7 +3588,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + rhodium atom A cobalt group element atom of atomic number 45. @@ -5196,7 +3600,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium atom gadolinium atom @@ -5207,7 +3611,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + terbium atom terbium atom @@ -5220,7 +3624,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ nucleic acid - A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. + A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), <small>D</small>-ribose or 2-deoxy-<small>D</small>-ribose and phosphoric acid. nucleic acid @@ -5242,7 +3646,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + amino acid A carboxylic acid containing one or more amino groups. @@ -5254,7 +3658,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + macromolecule A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. polymer @@ -5267,7 +3671,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + hemoglobin hemoglobin @@ -5278,7 +3682,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + fatty acid Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. @@ -5290,7 +3694,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + gadolinium molecular entity gadolinium molecular entity @@ -5301,7 +3705,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + phosphate ion A phosphorus oxoanion that is the conjugate base of phosphoric acid. @@ -5310,10 +3714,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + A particle smaller than an atom. + subatomic particle + + + + - + gadodiamide A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI). @@ -5325,9 +3740,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + folic acids - A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units. + A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more <small>L</small>-glutamic acid units. folic acids @@ -5337,7 +3752,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + sodium phosphate sodium phosphate @@ -5348,7 +3763,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5367,7 +3782,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5376,7 +3791,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ phosphorus-33 atom - The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2. + The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin <small><sup>1</small></sup>/<small><sub>2</sub></small>. phosphorus-33 atom @@ -5417,6 +3832,17 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cytochrome P450 + + cytochrome P450 + + + + @@ -5456,7 +3882,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium cation calcium cation @@ -5467,7 +3893,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + calcium ion calcium ion @@ -5478,7 +3904,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + magnesium cation Any magnesium ion that is positively charged. @@ -5510,7 +3936,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ digoxigenin - A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis. + A hydroxy steroid that consists of 5β-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3β-, 12β- and 14β-positions. It has been isolated from the plant species of the genus <em>Digitalis</em>. digoxigenin @@ -5520,7 +3946,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA(4-) A tetracarboxylic acid anion formed by deprotonation of all four carboxy groups in ethylenediaminetetraacetic acid (EDTA). @@ -5532,7 +3958,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + deoxyribonucleotide A nucleotide in which the ribose moiety has one or more of its hydroxy groups substituted by hydrogen. @@ -5544,9 +3970,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + digoxin - A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. + A cardenolide glycoside that is digitoxin β-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, <em>Digitalis lanata</em>, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small. digoxin @@ -5567,7 +3993,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 5-bromo-2'-deoxyuridine A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase. @@ -5579,7 +4005,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + low-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL). @@ -5591,7 +4017,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + high-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). @@ -5603,15 +4029,37 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + chromium-51 - A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. + A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of γ rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival. chromium-51 + + + + + 2'-(4-ethoxyphenyl)-5-(4-methylpiperazin-1-yl)-2,5'-bibenzimidazole + + 2'-(4-ethoxyphenyl)-5-(4-methylpiperazin-1-yl)-2,5'-bibenzimidazole + + + + + + + + + resorufin + + resorufin + + + + @@ -5667,7 +4115,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tritiated thymidine Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis. @@ -5679,7 +4127,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + dimethyl sulfate The dimethyl ester of sulfuric acid. @@ -5691,7 +4139,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + diethyl pyrocarbonate The diethyl ester of dicarbonic acid. @@ -5703,7 +4151,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 1,1-dihydroxy-3-ethoxy-2-butanone A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position. @@ -5715,9 +4163,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide - A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents. + A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two <em>N</em>-substituents. N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide @@ -5727,9 +4175,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + N-methylisatoic anhydride - A 3,1-benzoxazin-1,4-dione having an N-methyl substituent. + A 3,1-benzoxazin-1,4-dione having an <em>N</em>-methyl substituent. N-methylisatoic anhydride @@ -5739,9 +4187,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + (S)-1-(4-bromoacetamidobenzyl)EDTA - A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration. + A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (<i>S</i>)-configuration. (S)-1-(4-bromoacetamidobenzyl)EDTA @@ -5751,7 +4199,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + EDTA methidiumpropylamide A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe. @@ -5763,19 +4211,31 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + bromophenol blue - 3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. + 3<em>H</em>-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye. bromophenol blue + + + + + 1-methyl-7-nitroisatoic anhydride + A 3,1-benzoxazin-1,4-dione having an <em>N</em>-methyl substituent and a nitro group at the 7-position. + + 1-methyl-7-nitroisatoic anhydride + + + + - + tacrolimus hydrate A hydrate that is the monohydrate form of tacrolimus. @@ -5787,7 +4247,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + oxygen radical An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species. @@ -5799,7 +4259,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + lipoprotein A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. @@ -5811,7 +4271,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + thyroid stimulating hormone thyroid stimulating hormone @@ -5822,7 +4282,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Luteinizing hormone Luteinizing hormone @@ -5833,7 +4293,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + Follicle stimulating hormone Follicle stimulating hormone @@ -5844,9 +4304,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + 25-hydroxyvitamin D2 - A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group. + A hydroxycalciol that is vitamin D<small><sub>2</sub></small> in which the hydrogen at position 25 has been replaced by a hydroxy group. 25-hydroxyvitamin D2 @@ -5856,9 +4316,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + tris - A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC. + A primary amino compound that is <em>tert</em>-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7—9; p<em>K</em><small><sub>a</sub></small> = 8.3 at 20 °C; p<em>K</em><small><sub>a</sub></small> = 7.82 at 37 °C. tris @@ -5960,7 +4420,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -5980,24 +4440,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - cell line cell + + + + + + A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture - + 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. cell line cell - - - - - - - - - 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. - @@ -6005,9 +4459,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mortal cell line cell A cell line cell that is capable of replicating a limited number of times in culture before undergoing senescence. - mortal cell line cell @@ -6017,9 +4469,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immortal cell line cell A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. - immortal cell line cell @@ -6028,7 +4478,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + @@ -6041,11 +4491,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cell line A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). - cell line @@ -6067,9 +4515,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immortal cell line A cell line that is expected to be capable of indefinite propagation in an vitro culture. - immortal cell line @@ -6098,9 +4544,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mortal cell line A cell line is able to support only a limited number of passages in vitro. - mortal cell line @@ -6109,11 +4553,11 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - cell + PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. cell @@ -6153,26 +4597,12 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - primary cultured cell A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged. - primary cultured cell - - - - - obsolete native cell - OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). - - obsolete native cell - - - - @@ -6196,9 +4626,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - cultured cell A cell in vitro that is or has been maintained or propagated as part of a cell culture. - cultured cell @@ -6208,9 +4636,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - sperm A mature male germ cell that develops from a spermatid. - sperm @@ -6220,9 +4646,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - fibroblast + + + + + + + + + + + + A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. - fibroblast @@ -6232,9 +4668,20 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - epithelial cell + + + + + + + + + + + + + A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. - epithelial cell @@ -6244,21 +4691,27 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mesothelial cell A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement. - mesothelial cell + + + + + A cell found predominately in the blood. + blood cell + + + + - T cell A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. - T cell @@ -6267,22 +4720,52 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - mast cell + + + + + + + + + + + + + A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. - mast cell + + + + + + + + + + + + + + + + + A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system. + oligodendrocyte + + + + - hepatocyte The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. - hepatocyte @@ -6291,10 +4774,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - erythrocyte + A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. - erythrocyte @@ -6303,10 +4784,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - platelet + A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation. - platelet @@ -6315,10 +4794,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - macrophage + A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. - macrophage @@ -6328,21 +4805,28 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - B cell A lymphocyte of B lineage that is capable of B cell mediated immunity. - B cell + + + + + A cell that initiates an electrical signal and passes that signal to another cell. + electrically signaling cell + + + + - - dendritic cell + + A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). - dendritic cell @@ -6351,10 +4835,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + - neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. - neuron @@ -6364,9 +4847,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - lymphocyte A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. - lymphocyte @@ -6376,9 +4857,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - megakaryocyte A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release. - megakaryocyte @@ -6388,9 +4867,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - reticulocyte + + + + + + + + + + + + An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. - reticulocyte @@ -6400,9 +4889,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - band form neutrophil A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative. - band form neutrophil @@ -6412,9 +4899,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - nucleate erythrocyte An erythrocyte having a nucleus. - nucleate erythrocyte @@ -6423,11 +4908,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - monocyte Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. - monocyte @@ -6437,16 +4919,13 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - + - experimentally modified cell in vitro A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. - experimentally modified cell in vitro @@ -6456,9 +4935,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - natural killer cell A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. - natural killer cell @@ -6468,9 +4945,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD4-positive, alpha-beta T cell + A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. - CD4-positive, alpha-beta T cell @@ -6480,21 +4956,39 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD8-positive, alpha-beta T cell A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. - CD8-positive, alpha-beta T cell + + + + + A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration. + radial glial cell + + + + - leukocyte + + + + + + + + + + + + An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. - leukocyte @@ -6503,10 +4997,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - basophil + + + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. - basophil @@ -6515,10 +5020,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + - eosinophil + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. - eosinophil @@ -6527,10 +5043,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + - neutrophil + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. - neutrophil @@ -6540,9 +5067,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - immature neutrophil Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking. - immature neutrophil @@ -6551,10 +5076,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - plasma cell + A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. - plasma cell @@ -6564,9 +5087,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - alpha-beta T cell A T cell that expresses an alpha-beta T cell receptor complex. - alpha-beta T cell @@ -6576,9 +5097,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - CD8-positive, alpha-beta cytotoxic T cell A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. - CD8-positive, alpha-beta cytotoxic T cell @@ -6588,9 +5107,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - mature NK T cell A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. - mature NK T cell @@ -6600,9 +5117,19 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - promyelocyte + + + + + + + + + + + + A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative. - promyelocyte @@ -6611,11 +5138,21 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - - mononuclear cell + + + + + + + + + + + + + A leukocyte with a single non-segmented nucleus in the mature form. - - mononuclear cell + mononuclear leukocyte @@ -6624,9 +5161,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - malignant cell A neoplastic cell that is capable of entering a surrounding tissue - malignant cell @@ -6636,9 +5171,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - metamyelocyte A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. - metamyelocyte @@ -6648,9 +5181,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - myelocyte A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses. - myelocyte @@ -6660,21 +5191,49 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - neural cell + + + + + + + + + + + + A cell that is part of the nervous system. - neural cell + + + + + An epithelial cell of the respiratory tract epithelium. These cells have an endodermal origin. + respiratory tract epithelial cell + + + + + + + + + A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + neural crest cell + + + + - segmented neutrophil of bone marrow A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface. - segmented neutrophil of bone marrow @@ -6684,22 +5243,303 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - peripheral blood mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. - peripheral blood mononuclear cell + + + + + obsolete elementary charge + true + + + + + + + + + + + + + + + + A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. + atom + + + + + + + + + + + + + + + A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. + This molecular entity is different than ChEBI's 'molecular entity'. + We would like to have cardinality restrictions on the logic, but there are some technical limitations. + molecule + + + + + + + + + obsolete macromolecular entity + true + + + + + + + + + + obsolete subcellular structure + true + + + + + + + + + A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. + gross anatomical part + + + + + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + obsolete geographical location + true + + + + + + + + + + + + + + + + + completely executed planned process + + + + + + + + + A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. + nucleic acid chain + + + + + + + + + + obsolete immaterial anatomical entity + true + + + + + + + + + obsolete gene product + true + + + + + + + + + + obsolete action specification + true + + + + - complex of molecules - A complex of two or more molecular entities that are not covalently bound. - - complex of molecules + + + + + + + A complex of two or more molecules that are not covalently bound. + complex of molecules + + + + + + + + + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + planned process + + + + + + + + + failed planned process + + + + + + + + + + + + + + + + + + + + + + + A completely executed planned process that intends to output material entities from input material entities + material processing + + + + + + + + + obsolete cellular membrane + true + + + + + + + + + obsolete physical information carrier + true + + + + + + + + + characteristic + + + + + + + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + + + + + + + + + + + + A processed material entity which is designed to be capable of a process. + device @@ -6740,6 +5580,83 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + A material part of an astronomical body. + geophysical entity + + + + + + + + + An environmental system which includes both living and non-living components. + ecosystem + + + + + + + + + A process in which includes the components of an environmental system as participants. + environmental system process + + + + + + + + + food material by consumer group + + food material by consumer group + + + + + + + + + food material + Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience + + food material + + + + + + + + + animal feed + Food material which can be used to meet nutritional requirements of animals, particularly livestock such as cattle, goats, sheep, horses, chickens and pigs. + + animal feed + + + + + + + + + food material for animals + Food product for animal covers foods intended for consumption by domesticated animals. + + food material for animals + + + + @@ -6806,6 +5723,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neural crest cell migration + The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo. + + neural crest cell migration + + + + + + + + + neuron migration + The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature. + + neuron migration + + + + @@ -6891,6 +5832,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hematopoietic progenitor cell differentiation + The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells. + + hematopoietic progenitor cell differentiation + + + + @@ -6984,6 +5937,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + renal system process + An organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila). + + renal system process + + + + + + + + + heart process + A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. + + heart process + + + + @@ -6999,7 +5976,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + glomerular filtration The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein. @@ -7014,7 +5991,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + This is the same as GO molecular function + gene product or complex activity molecular_function @@ -7096,10 +6075,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - L-alanine:2-oxoglutarate aminotransferase activity - Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate. + L-alanine:2-oxoglutarate transaminase activity + Catalysis of the reaction: L-alanine + 2-oxoglutarate = pyruvate + L-glutamate. - L-alanine:2-oxoglutarate aminotransferase activity + L-alanine:2-oxoglutarate transaminase activity @@ -7120,10 +6099,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - L-aspartate:2-oxoglutarate aminotransferase activity + L-aspartate:2-oxoglutarate transaminase activity Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate. - L-aspartate:2-oxoglutarate aminotransferase activity + L-aspartate:2-oxoglutarate transaminase activity @@ -7156,10 +6135,10 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - glutamate dehydrogenase [NAD(P)+] activity - Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+. + L-glutamate dehydrogenase [NAD(P)+] activity + Catalysis of the reaction: L-glutamate + NAD(P)+ + H2O = 2-oxoglutarate + NH4+ + NAD(P)H + H+. - glutamate dehydrogenase [NAD(P)+] activity + L-glutamate dehydrogenase [NAD(P)+] activity @@ -7169,7 +6148,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ glutathione transferase activity - Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group. + Catalysis of the reaction: RX + glutathione = an S-substituted glutathione + a halide anion + H+. glutathione transferase activity @@ -7205,7 +6184,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ RNA nuclease activity - Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA. + Catalysis of the cleavage of phosphodiester bonds in chains of RNA. RNA nuclease activity @@ -7227,6 +6206,15 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + + + + + cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). @@ -7296,6 +6284,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of DNA repair + Any process that modulates the frequency, rate or extent of DNA repair. + + regulation of DNA repair + + + + @@ -7320,6 +6320,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + apoptotic process + A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died. + + apoptotic process + + + + @@ -7344,6 +6356,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + plasma membrane organization + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + + plasma membrane organization + + + + @@ -7368,6 +6392,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + female pregnancy + The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. + + female pregnancy + + + + + + + + + embryo implantation + Attachment of the blastocyst to the uterine lining. + + embryo implantation + + + + @@ -7392,14 +6440,32 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + growth factor activity + The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation. + + growth factor activity + + + + - + + + + + + biological_process A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + biological process biological_process @@ -7453,6 +6519,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + glial cell migration + The orderly movement of a glial cell, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system. + + glial cell migration + + + + @@ -7465,6 +6543,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + response to toxic substance + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus. + + response to toxic substance + + + + @@ -7549,6 +6639,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cell migration + The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. + + cell migration + + + + + + + + + oxidoreductase activity + Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. + + oxidoreductase activity + + + + @@ -7585,6 +6699,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + cytolysis + The rupture of cell membranes and the loss of cytoplasm. + + cytolysis + + + + @@ -7669,6 +6795,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + neuron differentiation + The process in which a relatively unspecialized cell acquires specialized features of a neuron. + + neuron differentiation + + + + + + + + + neuron projection development + The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites). + + neuron projection development + + + + @@ -8190,7 +7340,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - + + @@ -8200,6 +7351,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ protein-containing complex A ribosome is a protein complex. A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + This is not covalently bonded, which conflicts with changes to the parent definition. protein complex protein-containing complex @@ -8339,6 +7491,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of growth + Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development. + + regulation of growth + + + + @@ -8375,6 +7539,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + hormone biosynthetic process + The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone biosynthetic process + + + + + + + + + hormone catabolic process + The chemical reactions and pathways resulting in the breakdown of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone. + + hormone catabolic process + + + + @@ -8439,6 +7627,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + drinking behavior + The specific behavior of an organism relating to the intake of liquids, especially water. + + drinking behavior + + + + + + + + + neuron projection + A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. + + neuron projection + + + + @@ -8475,6 +7687,16 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Any constituent part of a virion, a complete fully infectious extracellular virus particle. + virion component + + + + @@ -8511,6 +7733,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + DNA-templated DNA replication maintenance of fidelity + A DNA metabolic process that prevents or corrects errors to ensure that DNA is replicated accurately. Errors can be corrected either by intrinsic DNA polymerase proofreading activity or via mismatch repair. + + DNA-templated DNA replication maintenance of fidelity + + + + @@ -8523,6 +7757,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + synapse + The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. + + synapse + + + + + + + + + luciferin monooxygenase activity + Catalysis of the generalized reaction: luciferin + O2 = oxidized luciferin + CO2 + light. There may be additional substrates and reactants involved in the reaction. The reaction results in light emission as luciferin returns to the ground state after enzymatic oxidation. + + luciferin monooxygenase activity + + + + @@ -8535,6 +7793,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + oligodendrocyte differentiation + The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system. + + oligodendrocyte differentiation + + + + + + + + + anatomical structure development + The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome. + + anatomical structure development + + + + @@ -8607,6 +7889,55 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + embryonic process involved in female pregnancy + A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother. + + embryonic process involved in female pregnancy + + + + + + + + + estrous cycle phase + The progression of physiological phases, occurring in the endometrium during the estrous cycle that recur at regular intervals during the reproductive years. The estrous cycle is an ovulation cycle where the endometrium is resorbed if pregnancy does not occur. + + estrous cycle phase + + + + + + + + + regulation of feeding behavior + Any process that modulates the rate, frequency or extent of the behavior associated with the intake of food. + + regulation of feeding behavior + + + + + + + + + + establishment of endothelial barrier + The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition. + + establishment of endothelial barrier + + + + @@ -8835,6 +8166,18 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + regulation of synapse maturation + Any process that modulates the extent of synapse maturation, the process that organizes a synapse so that it attains its fully functional state. + + regulation of synapse maturation + + + + @@ -8967,6 +8310,49 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + synaptic signaling + Cell-cell signaling to, from or within a synapse. + + synaptic signaling + + + + + + + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. + Overlaps with some cellular components from GO + cellular anatomical entity + + + + + + + + + neuron projection arborization + The process in which the anatomical structures of a neuron projection are generated and organized into branches. A neuron projection is any process extending from a neural cell, such as axons or dendrites. + + neuron projection arborization + + + + @@ -8991,6 +8377,30 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + negative regulation of cell wall organization or biogenesis + Any process that stops, prevents or reduces the frequency, rate or extent of cell wall organization or biogenesis. + + negative regulation of cell wall organization or biogenesis + + + + + + + + + mitotic DNA replication maintenance of fidelity + Any maintenance of fidelity that is involved in mitotic cell cycle DNA replication. + + mitotic DNA replication maintenance of fidelity + + + + @@ -9015,13 +8425,23 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ + + + + + Severity + The intensity or degree of a manifestation. + + Severity + + + + - conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. - conditional specification @@ -9031,9 +8451,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - measurement unit label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. - measurement unit label @@ -9043,9 +8461,7 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - objective specification A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. - objective specification @@ -9055,21 +8471,27 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - narrative object A narrative object is an information content entity that is a set of propositions. - narrative object + + + + + A directive information entity that describes an action the bearer will take. + action specification + + + + - datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label - datum label @@ -9079,10 +8501,8 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. - software @@ -9092,10 +8512,12 @@ interpreted by or directly executed by a processing unit. + data entity data item An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - + An information content entity that is intended to be one or more truthful statement(s) about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + data entity data item @@ -9105,9 +8527,7 @@ interpreted by or directly executed by a processing unit. - symbol An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - symbol @@ -9116,10 +8536,10 @@ interpreted by or directly executed by a processing unit. - + information content entity A generically dependent continuant that is about some thing. - + Pier: 'data, information or knowledge'. OR 'representation' information content entity @@ -9136,9 +8556,7 @@ interpreted by or directly executed by a processing unit. - scalar measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. - scalar measurement datum @@ -9148,9 +8566,7 @@ interpreted by or directly executed by a processing unit. - directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. - directive information entity @@ -9160,9 +8576,7 @@ interpreted by or directly executed by a processing unit. - dot plot A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. - dot plot @@ -9172,9 +8586,7 @@ interpreted by or directly executed by a processing unit. - graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. - graph @@ -9184,9 +8596,7 @@ interpreted by or directly executed by a processing unit. - rule A rule is an executable which guides, defines, restricts actions. - rule @@ -9196,9 +8606,7 @@ interpreted by or directly executed by a processing unit. - algorithm A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - algorithm @@ -9230,7 +8638,6 @@ interpreted by or directly executed by a processing unit. PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 - curation status specification @@ -9240,9 +8647,7 @@ interpreted by or directly executed by a processing unit. - density plot A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. - density plot @@ -9252,9 +8657,7 @@ interpreted by or directly executed by a processing unit. - report A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). - report @@ -9264,10 +8667,8 @@ interpreted by or directly executed by a processing unit. - data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file - data format specification @@ -9277,10 +8678,8 @@ Example: The ISO document specifying what encompasses an XML document; The instr - data set A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. - - data set + homogenous data collection @@ -9289,9 +8688,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. - image @@ -9313,9 +8710,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - plan specification A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. - plan specification @@ -9331,9 +8726,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. - measurement datum @@ -9356,9 +8749,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - conclusion textual entity A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. - conclusion textual entity @@ -9368,9 +8759,7 @@ Example: The ISO document specifying what encompasses an XML document; The instr - material information bearer A material entity in which a concretization of an information content entity inheres. - material information bearer @@ -9380,10 +8769,8 @@ Example: The ISO document specifying what encompasses an XML document; The instr - histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. - histogram @@ -9393,11 +8780,9 @@ distribution in terms of occurrence frequencies of different event classes. - heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. - heatmap @@ -9407,11 +8792,9 @@ two-dimensional map. - dendrogram A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. - dendrogram @@ -9421,9 +8804,7 @@ clustering algorithm. - scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. - scatter plot @@ -9460,9 +8841,7 @@ clustering algorithm. - textual entity A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. - textual entity @@ -9472,9 +8851,7 @@ clustering algorithm. - table A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions - table @@ -9484,9 +8861,7 @@ clustering algorithm. - figure An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. - figure @@ -9496,9 +8871,7 @@ clustering algorithm. - document A collection of information content entities intended to be understood together as a whole - document @@ -9508,9 +8881,7 @@ clustering algorithm. - publication A document that is the output of a publishing process. - publication @@ -9520,9 +8891,13 @@ clustering algorithm. - publication about an investigation + + + + + + A publication that is about an investigation - publication about an investigation @@ -9532,9 +8907,7 @@ clustering algorithm. - one dimensional cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region - one dimensional cartesian spatial coordinate datum @@ -9544,9 +8917,13 @@ clustering algorithm. - length measurement datum + + + + + + A scalar measurement datum that is the result of measurement of length quality - length measurement datum @@ -9579,9 +8956,7 @@ clustering algorithm. - mass measurement datum A scalar measurement datum that is the result of measurement of mass quality - mass measurement datum @@ -9591,9 +8966,7 @@ clustering algorithm. - time measurement datum A scalar measurement datum that is the result of measuring a temporal interval - time measurement datum @@ -9603,9 +8976,7 @@ clustering algorithm. - postal address A textual entity that is used as directive to deliver something to a person, or organization - postal address @@ -9615,8 +8986,6 @@ clustering algorithm. - email address - email address @@ -9625,10 +8994,8 @@ clustering algorithm. - - documenting + A planned process in which a document is created or added to by including the specified input in it. - documenting @@ -9638,10 +9005,8 @@ clustering algorithm. - line graph A line graph is a type of graph created by connecting a series of data points together with a line. - line graph @@ -9650,10 +9015,8 @@ points together with a line. - - assigning a centrally registered identifier + A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity - assigning a centrally registered identifier @@ -9663,9 +9026,7 @@ points together with a line. - centrally registered identifier symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. - centrally registered identifier symbol @@ -9675,9 +9036,7 @@ points together with a line. - centrally registered identifier registry A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. - centrally registered identifier registry @@ -9687,9 +9046,7 @@ points together with a line. - software application A software application is software that can be directly executed by some processing unit. - software application @@ -10021,6 +9378,17 @@ No imports + + + + + A process in which at least one of the participants is a molecule. + This is meant to capture processes that are more fundamental than macromolecular activities + physico-chemical process + + + + @@ -10415,7 +9783,7 @@ No imports - + Viruses Viruses @@ -10560,10 +9928,19 @@ No imports + + + + + cellular organism + + + + - + Treponema pallidum Treponema pallidum @@ -10585,8 +9962,9 @@ No imports - + Bacteria + bacteria eubacteria Bacteria @@ -10597,7 +9975,7 @@ No imports - + Archaea Archaea @@ -10611,6 +9989,7 @@ No imports Riboviria RNA viruses + RNA viruses and retroviruses RNA viruses and viroids Riboviria @@ -10644,9 +10023,8 @@ No imports - + Eukaryota - eucaryotes eukaryotes Eukaryota @@ -10659,6 +10037,7 @@ No imports Orthoherpesviridae + Herpesviridae Orthoherpesviridae @@ -10734,6 +10113,7 @@ No imports Metazoa + animals metazoans multicellular animals @@ -10753,6 +10133,17 @@ No imports + + + + + Pseudomonadati + + Pseudomonadati + + + + @@ -10828,7 +10219,7 @@ No imports Ascomycota - ascomycetes + ascomycete fungi sac fungi Ascomycota @@ -10853,6 +10244,7 @@ No imports Saccharomyces cerevisiae + Saccharomyces boulardii Saccharomyces cerevisiae 'var. diastaticus' baker's yeast brewer's yeast @@ -10982,7 +10374,7 @@ No imports - + Orientia tsutsugamushi Orientia tsutsugamushi @@ -11051,6 +10443,7 @@ No imports Rodentia rodent + rodents Rodentia @@ -11060,7 +10453,7 @@ No imports - + biological attribute biological attribute @@ -11223,30 +10616,21 @@ No imports - - - - - - - - - - - - - planned process + + obsolete planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. + We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived + 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process + This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) + + obsolete planned process + true @@ -11529,7 +10913,7 @@ objectives is a planned process. - + drug role @@ -11549,7 +10933,7 @@ objectives is a planned process. - + @@ -11584,7 +10968,7 @@ objectives is a planned process. - + physical document a book is a physical document @@ -11615,24 +10999,16 @@ objectives is a planned process. - - - - - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples + + obsolete processed material + Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material + PERSON: Alan Ruttenberg + + + obsolete processed material + true @@ -11919,7 +11295,7 @@ objectives is a planned process. - + polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles. @@ -11934,7 +11310,7 @@ objectives is a planned process. - + @@ -12041,7 +11417,21 @@ objectives is a planned process. - + + + + + + + + + + + + + + + @@ -12127,7 +11517,7 @@ objectives is a planned process. - + @@ -12190,7 +11580,7 @@ objectives is a planned process. - + culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 @@ -12332,38 +11722,21 @@ In regard to the statement that reagents are 'distinct' from the speci - - - - - - - - - - - - - - - - - - - - - material processing + + obsolete material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material - PERSON: Bjoern Peters + PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra - material transformation - OBI branch derived - material processing + OBI branch derived + + + obsolete material processing + true @@ -12478,7 +11851,7 @@ editor = PRS - + @@ -12867,7 +12240,7 @@ specimen can later be subject. - + @@ -13602,7 +12975,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13690,7 +13063,7 @@ An individual or juridicial or other body authorized under applicable law to con - + @@ -13986,7 +13359,7 @@ for now. - + @@ -14028,10 +13401,16 @@ for now. + + + + + + plan The plan of researcher X to perform an experiment according to a protocol. - A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived @@ -14193,8 +13572,8 @@ for now. - - + + @@ -14273,7 +13652,7 @@ for now. - + @@ -14372,14 +13751,14 @@ for now. - + - + @@ -14442,7 +13821,7 @@ need to add mobile phase as role - + @@ -14515,7 +13894,6 @@ need to add mobile phase as role - @@ -14629,7 +14007,7 @@ Proposal is to obsolete. - + @@ -14791,7 +14169,7 @@ Proposal is to obsolete. - + @@ -15143,7 +14521,7 @@ Proposal is to obsolete. - + @@ -15207,7 +14585,7 @@ Proposal is to obsolete. - + @@ -15468,7 +14846,7 @@ Proposal is to obsolete. - + @@ -15687,7 +15065,7 @@ activity) - + @@ -15708,7 +15086,7 @@ activity) - + @@ -16081,7 +15459,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16243,7 +15621,6 @@ that has_part some material entity is a material entity. If we add as equivalent genotyping assay - High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923 An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions. Philippe Rocca-Serra @@ -16258,7 +15635,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16327,7 +15704,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16627,7 +16004,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16737,7 +16114,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16747,7 +16124,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + manufacturing @@ -16950,7 +16327,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -16963,7 +16340,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. @@ -17152,7 +16529,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR sample holder An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. @@ -17366,7 +16743,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR tube washing system An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. @@ -17382,7 +16759,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR console A component of an NMR instrument that controls the activities of the other components. @@ -17689,7 +17066,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + NMR magnet A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. @@ -17748,7 +17125,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -17759,7 +17136,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -17772,33 +17149,20 @@ that has_part some material entity is a material entity. If we add as equivalent - - - - - - - - - - - - - - - - + + + - - + + - - + + clinical chemistry assay Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. - An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism. + An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a specimen collected from an organism in order to determine a phenotype of that organism. Philippe Rocca-Serra chemical pathology detection of analyte in blood sample @@ -17841,7 +17205,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18201,7 +17565,7 @@ that has_part some material entity is a material entity. If we add as equivalent - + @@ -18433,7 +17797,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + autosampler An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. @@ -18802,13 +18166,13 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + scattered molecular aggregate @@ -19699,15 +19063,6 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - - - - - - - - - @@ -19775,26 +19130,55 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - + + + + hematology assay Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 - An assay that studies blood and blood producing organs using a variety of techniques and instruments + An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments Philippe Rocca-Serra blood analysis haematology @@ -20229,7 +19613,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20272,11 +19656,11 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + - + device setting @@ -20375,7 +19759,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20383,7 +19767,7 @@ Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 - + @@ -20850,7 +20234,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + whole organism preparation @@ -21278,7 +20662,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21288,13 +20672,13 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + animal feeding @@ -21454,7 +20838,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21469,7 +20853,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21741,14 +21125,14 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + - + @@ -21811,7 +21195,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21879,7 +21263,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -21905,7 +21289,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22057,7 +21441,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22081,7 +21465,7 @@ http://sourceforge.net/p/obi/obi-terms/716/ - + @@ -22211,7 +21595,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + paired-end library PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. @@ -22306,7 +21690,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + host role @@ -22526,7 +21910,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + recombinant vector A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. @@ -22580,7 +21964,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + @@ -22605,7 +21989,7 @@ the role 'adjuvant role' inheres in some 'material entity' a - + single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs @@ -22630,13 +22014,11 @@ the role 'adjuvant role' inheres in some 'material entity' a - - - + cloning vector @@ -22783,7 +22165,6 @@ the role 'adjuvant role' inheres in some 'material entity' a - nucleic acid restriction enzyme digest A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site @@ -23255,6 +22636,7 @@ the role 'adjuvant role' inheres in some 'material entity' a + @@ -23489,11 +22871,11 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23565,7 +22947,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23598,7 +22980,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23689,14 +23071,14 @@ http://en.wikipedia.org/wiki/Survival_rate - + - + @@ -23765,7 +23147,6 @@ http://en.wikipedia.org/wiki/Survival_rate - amplified DNA Amplied DNA created by PCR @@ -23780,7 +23161,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -23813,24 +23194,15 @@ http://en.wikipedia.org/wiki/Survival_rate - - - - - - - - - - - - - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule - a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. + a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues placeholder for SO BP et al - primary structure of DNA macromolecule + + obsolete primary structure of DNA macromolecule + true @@ -23884,7 +23256,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + Berichrom(r) Antithrombin III (A) Kit For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution @@ -23921,7 +23293,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + fucoidan Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). @@ -23935,7 +23307,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24193,7 +23565,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24214,7 +23586,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + pill A dose of medicine or placebo in the form of a small pellet. @@ -24273,7 +23645,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + @@ -24281,7 +23653,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + measurement device A ruler, a microarray scanner, a Geiger counter. @@ -24406,7 +23778,7 @@ http://en.wikipedia.org/wiki/Survival_rate - + material maintenance A planned process with the objective to maintain some or all of the characteristics of an input material over time. @@ -24418,6 +23790,7 @@ http://en.wikipedia.org/wiki/Survival_rate + @@ -24446,7 +23819,7 @@ placeholder - + @@ -24474,7 +23847,7 @@ placeholder - + @@ -24495,7 +23868,7 @@ placeholder - + @@ -24577,23 +23950,14 @@ placeholder - - - - - - - - - - - - - primary structure of RNA molecule + + obsolete primary structure of RNA molecule The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters - primary structure of RNA molecule + + obsolete primary structure of RNA molecule + true @@ -25144,7 +24508,7 @@ placeholder - + @@ -25467,7 +24831,7 @@ Person: Chris Stoeckert - + @@ -25478,7 +24842,7 @@ Person: Chris Stoeckert - + @@ -25884,7 +25248,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26031,7 +25395,7 @@ J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. - + @@ -26055,7 +25419,7 @@ Dev call Nov 22, 2010: To reflect this, the term's label has been updated t - + @@ -26773,8 +26137,8 @@ Updated both textual and logical definition. Both input and output material of f - + labeled specimen A specimen that has been modified in order to be able to detect it in future experiments @@ -26794,7 +26158,7 @@ Updated both textual and logical definition. Both input and output material of f - + infectious agent is a material entity bearing the disposition to infect an organism @@ -26903,7 +26267,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26955,7 +26319,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -26963,7 +26327,7 @@ Updated both textual and logical definition. Both input and output material of f - + material separation device flow cytometer @@ -27045,7 +26409,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27122,7 +26486,7 @@ Updated both textual and logical definition. Both input and output material of f - + training process e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility @@ -27225,7 +26589,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27238,7 +26602,7 @@ Updated both textual and logical definition. Both input and output material of f - + @@ -27351,7 +26715,7 @@ Biochimie. 2010 Feb 18. - + service provider role @@ -27521,14 +26885,14 @@ Biochimie. 2010 Feb 18. - + - + processed specimen @@ -27593,7 +26957,7 @@ Biochimie. 2010 Feb 18. - + @@ -27813,7 +27177,7 @@ Biochimie. 2010 Feb 18. - + @@ -27844,7 +27208,7 @@ Biochimie. 2010 Feb 18. - + @@ -27852,7 +27216,7 @@ Biochimie. 2010 Feb 18. - + container A device that can be used to restrict the location of material entities over time @@ -27866,50 +27230,21 @@ Biochimie. 2010 Feb 18. - - - - - - - - - - - - - - - - - - - - - - - - - device + + obsolete device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. + 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. + 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. - device + + + obsolete device + true @@ -27989,11 +27324,11 @@ In the examples above, a reagent is an operational component of a device, but th - + - + @@ -28004,7 +27339,7 @@ In the examples above, a reagent is an operational component of a device, but th sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. - A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. + A data item that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data @@ -28111,7 +27446,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28531,7 +27866,7 @@ In the examples above, a reagent is an operational component of a device, but th - + @@ -28853,7 +28188,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -28945,7 +28280,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. @@ -29332,7 +28667,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -29349,7 +28684,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30083,7 +29418,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30091,7 +29426,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) @@ -30109,7 +29444,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30117,7 +29452,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + perturbation device A homogenizer is a perturbation device. @@ -30137,7 +29472,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30153,7 +29488,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + environmental control device A growth chamber is an environmental control device. @@ -30446,7 +29781,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30532,7 +29867,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30629,7 +29964,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30731,7 +30066,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30751,7 +30086,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30797,7 +30132,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30823,7 +30158,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -30883,7 +30218,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31032,7 +30367,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31052,7 +30387,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31283,7 +30618,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31355,7 +30690,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31457,7 +30792,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31477,7 +30812,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31651,7 +30986,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31719,7 +31054,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31864,7 +31199,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31918,7 +31253,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -31978,7 +31313,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32046,7 +31381,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32066,7 +31401,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32126,7 +31461,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32365,7 +31700,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32418,7 +31753,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + individual organism identifier @@ -32577,7 +31912,7 @@ JZ: based on textual definition of edited document, it can be defined as N&S - + @@ -32676,7 +32011,7 @@ Has term 'cell co-culturing' and 'maintaining cell culture' - + genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. @@ -32819,7 +32154,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -32830,7 +32165,7 @@ Supported by Alan on Nov 15, 2010 dev call - + @@ -33150,7 +32485,7 @@ All subtype will be defined by textual definition now. - + @@ -33166,11 +32501,11 @@ All subtype will be defined by textual definition now. - + - + service @@ -33320,15 +32655,6 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - @@ -33468,13 +32794,13 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + - + @@ -33486,7 +32812,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms @@ -37726,7 +37052,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -38335,7 +37661,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - + @@ -40990,32 +40316,7 @@ http://en.wikipedia.org/wiki/Strain_%28biology%29 - - - - - - - - - - - - - - - - - - - - - - - - - - + genetic characteristics information @@ -43395,7 +42696,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -43424,7 +42725,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44305,7 +43606,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -44361,7 +43662,7 @@ http://svitsrv25.epfl.ch/R-doc/library/qvalue.html - + @@ -46020,10 +45321,10 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + - + @@ -46044,30 +45345,20 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - - + + + - - + + + + + - - - - - - - - - - - - - - - - + + @@ -46727,7 +46018,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + material processing service @@ -47182,7 +46473,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + DNA sequence data @@ -49290,7 +48581,7 @@ http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=N - + purified material A mixture of peptide molecules that has been run through an HPLC column to remove 65 @@ -57712,7 +57003,7 @@ is realized in a specimen collection process. - + @@ -58378,7 +57669,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59378,7 +58669,7 @@ Concluding that a gene is upregulated in a tissue sample based on the band inten - + @@ -59730,7 +59021,7 @@ PMID: 23587118. - + @@ -59816,11 +59107,11 @@ When harvesting blood from a human, isolating T cells, and then limited dilution - + - + reagent @@ -60824,7 +60115,7 @@ The following are NOT conclusions based on data: data themselves; results from p - + cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. @@ -61926,7 +61217,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + selection PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. @@ -62006,7 +61297,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + @@ -62142,7 +61433,7 @@ Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ - + molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay @@ -62298,7 +61589,7 @@ http://vivoweb.org/ontology/core#FundingOrganization - + @@ -62520,7 +61811,7 @@ PMID: 23587118. - + freezing A planned process with the objective to bring some material entity to a temperature below its freezing point. @@ -62683,7 +61974,7 @@ PMID: 23587118. - + @@ -62718,7 +62009,7 @@ PMID: 23587118. - + @@ -62966,7 +62257,7 @@ PMID: 23587118. - + @@ -63205,7 +62496,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63213,7 +62504,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63276,7 +62567,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -63287,7 +62578,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64575,6 +63866,30 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. + + + + + + + + + + + + + + + + + + + + + + + + @@ -64689,54 +64004,6 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - histone modification identification by ChIP-Seq assay - - An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. - Chris Stoeckert - Jie Zheng - histone modification ChIP-Seq - Penn group - histone modification identification by ChIP-Seq assay - - - - - - - - - @@ -64745,39 +64012,10 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -64785,20 +64023,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - - - + @@ -64815,7 +64040,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64825,43 +64050,32 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - - - - - - - - - - - - + - + - transcription factor binding site identification by ChIP-chip assay + histone modification identification by ChIP-Seq assay - A transcription factor binding site assay that utilizes ChIP-chip technology. + An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. Chris Stoeckert Jie Zheng - TF Binding ChIP-chip + histone modification ChIP-Seq Penn group - transcription factor binding site identification by ChIP-chip assay + histone modification identification by ChIP-Seq assay - + - + - + @@ -64873,7 +64087,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -64881,7 +64095,132 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transcription factor binding site identification by ChIP-chip assay + + A transcription factor binding site assay that utilizes ChIP-chip technology. + Chris Stoeckert + Jie Zheng + TF Binding ChIP-chip + Penn group + transcription factor binding site identification by ChIP-chip assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -65665,7 +65004,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -65695,7 +65034,7 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + @@ -67343,11 +66682,11 @@ Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. - + - + @@ -68066,14 +67405,14 @@ https://www.doi.org/ - high performance liquid chromotography assay + high performance liquid chromatography assay On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. ImmPort HPLC PMID:9491555 - high performance liquid chromotography assay + high performance liquid chromatography assay @@ -70590,7 +69929,7 @@ https://www.doi.org/ - + microtome blade A device that is the part of a microtome used to slice specimens to a desired thickness. @@ -70705,7 +70044,7 @@ https://www.doi.org/ - + determination if assay will provide reliable results A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. @@ -71707,7 +71046,7 @@ https://www.doi.org/ - + delivery form for hormonal replacement therapy A processed material used for delivery of hormones in hormone replacement therapy. @@ -72310,7 +71649,7 @@ https://www.doi.org/ - + @@ -72321,7 +71660,7 @@ https://www.doi.org/ - + @@ -72884,11 +72223,11 @@ https://www.doi.org/ - + - + @@ -72909,11 +72248,11 @@ https://www.doi.org/ - + - + @@ -73264,7 +72603,7 @@ https://www.doi.org/ - + pipette A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. @@ -74913,7 +74252,7 @@ https://www.doi.org/ - + esophagus muscularis mucosa specimen A specimen that is derived from esophagus muscularis mucosa. @@ -75151,7 +74490,7 @@ https://www.doi.org/ - + coronary artery specimen A specimen that is derived from coronary artery. @@ -75480,7 +74819,7 @@ https://www.doi.org/ - + minor salivary gland specimen A specimen that is derived from minor salivary gland. @@ -75621,7 +74960,7 @@ https://www.doi.org/ - + sigmoid colon specimen A specimen that is derived from sigmoid colon. @@ -76336,7 +75675,7 @@ https://www.doi.org/ - + @@ -76358,7 +75697,7 @@ https://www.doi.org/ - + machine learning A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. @@ -78586,19 +77925,14 @@ https://www.doi.org/ - - - - - - - 1 - - - - - + + + + 1 + + + individual organism specimen A specimen composed of an individual organism to be studied in an investigation. @@ -78660,7 +77994,7 @@ https://www.doi.org/ - + @@ -78668,7 +78002,7 @@ https://www.doi.org/ - + @@ -78691,7 +78025,7 @@ https://www.doi.org/ - + @@ -78713,7 +78047,7 @@ https://www.doi.org/ - + @@ -81919,7 +81253,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + @@ -81927,7 +81261,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + molecular label @@ -82001,7 +81335,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + passage process A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. @@ -82125,7 +81459,7 @@ JZ (3-30-20): discussed on the OBI call. Since the REO was never actually regist - + cDNA library cDNA library lacks the non-coding and regulatory elements found in genomic DNA @@ -82893,7 +82227,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + personal protective device Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. PPE is equipment worn by a worker to minimize exposure to specific hazards. @@ -83079,7 +82413,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + apron A garment which is worn over other clothing and covers mainly the front of the body. @@ -83185,7 +82519,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + transparent partition A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. @@ -83333,7 +82667,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + specimen collection device A device used to collect a specimen. @@ -83402,7 +82736,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + cotton swab A device which is a cotton pad mounted on one or both ends of a stick. @@ -83466,7 +82800,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. @@ -83838,7 +83172,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + arthropod trap A device designed to catch arthropods. @@ -83897,7 +83231,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -83957,7 +83291,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + dipper for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. @@ -85421,11 +84755,11 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -85591,7 +84925,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + device for collection of resting adult arthropods A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. @@ -85607,7 +84941,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + well net for arthropod immatures A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. @@ -86312,8 +85646,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - + @@ -86701,7 +86034,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -86709,7 +86042,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87016,7 +86349,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87037,7 +86370,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + hand-held sweep net A device that consists of a network of mesh and is designed to capture adult arthropods. @@ -87414,7 +86747,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + common name of organism @@ -87502,7 +86835,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -87513,7 +86846,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -88421,7 +87754,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -90922,7 +90255,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre leukapheresis - A blood harvesting process in which white blood cells are separated from a blood specimen. + A blood specimen collection in which white blood cells are separated from a blood specimen. Hector Guzman-Orozco https://en.wikipedia.org/wiki/Leukapheresis leukapheresis @@ -91529,7 +90862,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre blood assay datum - A data item that is the specified output of a blood assay. + A data entity that is the specified output of a blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91582,7 +90915,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre feces assay datum - A data item that is the specified output of a feces assay. + A data entity that is the specified output of a feces assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91635,7 +90968,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre urine assay datum - A data item that is the specified output of a urine assay. + A data entity that is the specified output of a urine assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91688,7 +91021,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre induced sputum assay datum - A data item that is the specified output of a induced sputum assay. + A data entity that is the specified output of a induced sputum assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91760,7 +91093,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre cerebrospinal fluid assay datum - A data item that is the specified output of a cerebrospinal fluid assay. + A data entity that is the specified output of a cerebrospinal fluid assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -91944,7 +91277,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre umbilical cord blood assay datum - A data item that is the specified output of an umbilical cord blood assay. + A data entity that is the specified output of an umbilical cord blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 @@ -92822,7 +92155,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + mosquito membrane feeding device A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. @@ -93723,7 +93056,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -93731,7 +93064,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -94577,7 +93910,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre milk assay datum - A data item that is the specified output of a milk assay. + A data entity that is the specified output of a milk assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1515 @@ -94652,7 +93985,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf @@ -95568,7 +94901,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre antigen specific antibodies assay datum - A data item that is the specified output of an antigen specific antibodies assay. + A data entity that is the specified output of an antigen specific antibodies assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 @@ -96267,7 +95600,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -97825,7 +97158,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -98314,7 +97647,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100728,7 +100061,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100736,7 +100069,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100759,7 +100092,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100850,7 +100183,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100858,7 +100191,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100881,7 +100214,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100972,7 +100305,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -100980,7 +100313,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -101003,7 +100336,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -102898,22 +102231,17 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - - - - + + + + + + + + + + albumin-free serum A blood serum specimen that contains no albumin. @@ -102928,14 +102256,14 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - + @@ -102948,7 +102276,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasting @@ -102988,7 +102316,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + fasted @@ -103266,15 +102594,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - @@ -103357,7 +102676,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - lavage fluid specimen The collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present. @@ -103791,7 +103109,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103833,7 +103151,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103874,7 +103192,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103942,7 +103260,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -103966,7 +103284,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104022,7 +103340,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104033,7 +103351,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104080,7 +103398,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104091,7 +103409,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104138,7 +103456,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104149,7 +103467,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104196,7 +103514,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104207,7 +103525,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104254,7 +103572,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104265,7 +103583,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104312,7 +103630,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104323,7 +103641,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104370,7 +103688,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104381,7 +103699,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104428,7 +103746,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104439,7 +103757,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104486,7 +103804,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104497,7 +103815,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104550,7 +103868,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104561,7 +103879,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104614,7 +103932,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104625,7 +103943,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104770,7 +104088,7611 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + + + + + + + + + + + + + + + + + + + + + + + + + cell based DNA damage assay + + A cytometry assay that measures DNA damage in cells. + Jennifer Fostel + cell based DNA damage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell count assay + + A cytometry assay to determine the number of natural killer cells in a specimen + Jennifer Fostel + natural killer cell count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + natural killer cell percentage assay + + A cytometry assay that measures the percentage of natural killer cells in a specimen. + Jennifer Fostel + natural killer cell percentage assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + sperm count assay + + A cytometry assay to count the number of mature sperm in a specimen. + Jennifer Fostel + sperm count assay + + + + + + + + + survey administration assay + + An assay that obtains data from one or more participants by using a survey or questionnaire + Jennifer Fostel + survey administration assay + + + + + + + + + maximum data transformation + + A data transformation that has as its output the greatest value in the input data set. + Sebastian Duesing + maximum data transformation + + + + + + + + + minimum data transformation + + A data transformation that has as its output the least value in the input data set. + Sebastian Duesing + minimum data transformation + + + + + + + + + + + + + + + + + + + + + + + + + clinical history collection assay + A clinician asking a patient about the patient's smoking status. + + A clinical assay that produces a data item indicating whether an organism has ever had a particular disease, lifestyle factor, immune exposure, or medical procedure. + Sebastian Duesing + HCC + clinical history collection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + disease severity assay + Measuring bone mineral density to determine the severity of osteoporosis. + + An assay that measures the severity of a disease in an organism. + Sebastian Duesing + HCC + disease severity assay + + + + + + + + + + + + + + + genetic characteristic assay + Determining a patient's HLA type. + + An assay that produces information about a genetic characteristic of an organism. + Sebastian Duesing + HCC + genetic characteristic assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + blood type assay + Identifying a person's ABO blood type. + + An assay that classifies an organism's blood within one or more blood group classification systems by identifying antigens present in the blood. + Sebastian Duesing + https://medlineplus.gov/ency/article/003345.htm + blood type assay + + + + + + + + + manual muscle testing 8 score + + A clinical data item that quantifies the muscle function of a person based on the person's ability to hold a series of eight body positions that target different muscle groups. + Sebastian Duesing + MMT-8 + https://www.niehs.nih.gov/sites/default/files/research/resources/assets/docs/mmt8_grading_and_testing_procedures_for_the_abbreviated_8_muscle_groups_508.pdf + manual muscle testing 8 score + + + + + + + + + childhood myositis assessment scale score + + A clinical data item that quantifies the degree of muscle function in a child with myositis based on performance of 14 tasks associated with muscular strength and endurance. + Sebastian Duesing + CMAS + https://pubmed.ncbi.nlm.nih.gov/10524696/ + childhood myositis assessment scale score + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + capillary electrophoresis mass spectrometry assay + + A mass spectrometry assay where a sample mixture is first separated by capillary electrophoresis before being analysed by mass spectrometry. + Sebastian Duesing + CE-MS + Thomas Payne + https://en.wikipedia.org/wiki/Capillary_electrophoresis–mass_spectrometry + https://github.com/obi-ontology/obi/issues/1904 + Thomas Payne + capillary electrophoresis mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite outgrowth assay + + A cell differentiation assay that detects neurite outgrowth and/or branching + The UBERON term for neurite is Neuron projection (GO:0043005; A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.). Multiplexed fluorescent imaging can be used to detect nuclei in neuronal cell bodies using Hoechst dye and neurites using anti-beta III-tubulin antibody staining. Commonly measured are neurite length, number and/or number of branch points (arborization). + Jennifer Fostel + neurite outgrowth assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuronal differentiation assay + + A cell differentiation assay that measures differentiation of neurons. + Jennifer Fostel + neuronal differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligodendrocyte differentiation assay + + A cell differentiation assay that measures differentiation of oligodendrocytes. + Jennifer Fostel + oligodendrocyte differentiation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + regulation of synapse maturation assay + + A cell differentiation assay that measures synapse formation and maturation using antibodies to protein found in synaptic puncta. + Synaptic puncta is this context is a small (0.5 to 2 um) distinct localized cluster of proteins involved in synaptic transmission. + Jennifer Fostel + regulation of synapse maturation assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Ames assay + + A cell based DNA damage assay that uses several constructed bacterial strains to detect mutations. + The bacterial strains were originally constructed by Bruce Ames. Each carries a mutation in a gene involved in histidine synthesis. The cell requires histidine for growth but cannot produce it. The assay measures the creation of mutations that result in a return of function so that the cells can grow on a histidine-free medium. + Jennifer Fostel + Ames assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + micronucleus assay + + A cell based DNA damage assay in eukaryotic cells that detects cytoplasmic micronuclei. + The GO term "micronucleus" (GO:0031040) applies to protozoa but does not pertain to this case. Here micronucleus is a chromosome or fragment of a chromosome bounded by nuclear membrane that did not segregate properly at mitosis. + Jennifer Fostel + micronucleus assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + PIG-a assay + + A cell based DNA damage assay in eukaryotic cells that detects loss of function through mutation of the X-linked (single-copy) Pig-a gene. + The Pig-A gene encodes a product involved in biosynthesis of cell surface anchor glycosylphosphatidylinositol (GPI). + Jennifer Fostel + PIG-a assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin + + A cell viability assay using the NAD(P)H-aided conversion of resazurin to resorufin by metabolically active cells. + Resazurin is the active ingredient in alamar blue; has a blue color and is non-fluorescent. Resorufin has pink color and is fluorescent. Detection of resorufin can be by absorbance or fluorescence. + Jennifer Fostel + Alamar Blue viability assay + cell viability assay based on detection of resorufin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay using caspase abundance to detect apoptosis + + A cell death assay that uses fluorescence imaging-based detection of caspases involved in apoptosis + Caspases 3 and 7 are frequently used as indicators of apoptosis. + Jennifer Fostel + cell death assay using caspase abundance to detect apoptosis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay + + A cell viability assay which measures the number or proportion of dead cells in a population. + Jennifer Fostel + cell death assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + A cell viability assay based on detection of resorufin that uses fluorescence to quantify resorufin + Resazurin (active ingredient in alamar blue and CellTiter blue reagents) has a blue color and is not fluorescent. Resorufin is pink and fluorescent. This assay uses the commercial reagent CellTiter Blue (Promega) containing resazurin and fluorescence to detect resorufin. + Jennifer Fostel + CellTiter Blue viability assay + cell viability assay based on detection of resorufin using fluorescence to qualtify the presence of resorufin. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release + + A cell death assay that measures the release of intracellular LDH. + Jennifer Fostel + cell death assay detecting lactate dehydrogenase (LDH) release + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + A cell death assay detecting lactate dehydrogenase (LDH) release by absorbance of substrate + In this assay reagents are added so that LDH produces reduced nicotinamide adenine dinucleotide (NADH) when it catalyzes the oxidation of lactate to pyruvate, and the NADH converts a tetrazolium salt to a colored formazan product in the presence of an electron acceptor. This formazan product is detected by absorbance quality. + Jennifer Fostel + Cytotox 96 assay + cell death assay detecting lactate dehydrogenase (LDH) release using absorbance detection. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ovulation assessment in rodent assay + + A histological assay that measures the number of corpora lutea (UBERON:0002512) in the ovary of an organism; corpora lutea develop from the postovulatory follicle. + Jennifer Fostel + Corpus luteum count + ovulation assessment in rodent assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + macroscopic examination of material anatomical entity assay + + An assay that performs a macroscopic assessment of a material anatomical entity using the sense of sight. + Jennifer Fostel + macroscopic examination of material anatomical entity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pathological macroscopic examination of specimen assay + + A macroscopic examination of material anatomical entity assay performed on a post-mortem anatomical specimen. + one objective of this assay is to provide information about the character and extent of changes present and to inform on the cause of death. + Jennifer Fostel + Gross pathology assessment + pathological macroscopic examination of specimen assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle assay based on tissue morphology + + A histological assay that evaluates cells in the vaginal endometrium to assess the estrous cycle phase the subject was in at the time of specimen collection. + Jennifer Fostel + estrous cycle assay based on tissue morphology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo + + An organism development assay performed with a late embryo stage subject. + one objective of this assay is to assess anatomical structures and identify developmental phenotype + Jennifer Fostel + fetal examination + organism development assay in late embryo + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pregnancy assessment based on tissue morphology assay + + A histological assay that measures the number of implantation sites in an organism. + An implantation site in this context is the site in the endometrium where the fertilized egg attaches and embeds itself to begin development + Jennifer Fostel + implantation site count + pregnancy assessment based on tissue morphology assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell death assay using vital dye + + A cell death assay that uses the Trypan blue vital dye to stain cells which have lost membrane integrity. + Living cells exclude Trypan blue + Jennifer Fostel + cell death assay using vital dye + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite length assay + + A cytometry assay that uses a distance measurement assay to determine the length of a neurite. + A neurite is a neuronal process greater than 10 um extending from a neuron. + Jennifer Fostel + neurite length assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite degree of arborization assay + + A cytometry assay that measures the degree of arborization, or branching, in neuronal processes + Jennifer Fostel + neurite branch point count + neurite degree of arborization assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neurite count assay + + A cytometry assay that measures the number of neurites in a cultured specimen. + A neurite is a neuronal process greater than 10 um extending from a neuron. + Jennifer Fostel + neurite count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron count assay + + A cytometry assay that measures the number of neurons in a sample + Jennifer Fostel + neuron count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell-body-associated presynaptic puncta count assay + + A regulation of synapse maturation assay that determines the number of synaptic puncta in the cell body compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. + Jennifer Fostel + cell-body-associated presynaptic puncta count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + dendrite-associated presynaptic puncta count assay + + A regulation of synapse maturation assay that determines the number of synaptic puncta in the dendritic compartment of a neuron. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. + Jennifer Fostel + dendrite-associated presynaptic puncta count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + synapse per neuron assay + + A regulation of synapse maturation assay that determines the number of synaptic puncta in a culture and normalizes it by the number of neurons in the culture. + Synaptic puncta refers to a microscopic cluster of synaptic proteins. + Jennifer Fostel + synapse per neuron assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + absorbance quality detection assay + + An assay that measures the absorbance quality of the evaluant + the unit of this assay is absorbance unit (UO:0000269) + Jennifer Fostel + absorbance quality detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + hormone assay + + The analyte assay that measures the abundance of a hormone in a specimen. + Jennifer Fostel + hormone assay + + + + + + + + + chemiluminescent assay + + An analyte assay that detects a substance by measuring the release of light triggered by a chemical reaction. + SD + CLIA + HCC + HCC + chemiluminescent assay + + + + + + + + + electrochemiluminescence assay + + A chemiluminescent assay that detects a substance by measuring the release of light triggered by an electrochemical reaction. + SD + ECL + Meso Scale Discovery ECL + HCC + HCC + electrochemiluminescence assay + + + + + + + + + + + + + + + + + + + + + + proteomics by mass spectrometry assay + + A mass spectrometry assay that identifies and measures proteins. + SD + HCC + HCC + proteomics by mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + metabolomics by mass spectrometry assay + + A mass spectrometry assay that identifies and measures metabolites. + SD + HCC + HCC + metabolomics by mass spectrometry assay + + + + + + + + + + + + + + + + + + + + + + cellular indexing of transcriptomes and epitopes by sequencing + + An assay performed on single cells that simultaneously measures transcript expression via single-cell RNA sequencing and profiles surface proteins via sequencing of DNA-barcodes attached to antibodies recognizing particular surface proteins from individual cells. + SD + CITE-Seq + HCC + HCC + cellular indexing of transcriptomes and epitopes by sequencing + + + + + + + + + immune receptor repertoire profiling assay + + An assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors or T cell receptors within an input sample. + SD + HCC + HCC + immune receptor repertoire profiling assay + + + + + + + + + + + + + + + + + + + + antibody-dependent complement deposition assay + + An assay measuring antibody-dependent complement-dependent cytotoxicity. + SD + ADCD + HCC + HCC + antibody-dependent complement deposition assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial flagellin detection in plasma assay + + An analyte assay measuring bacterial flagellin in a plasma sample. + SD + HCC + HCC + bacterial flagellin detection in plasma assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial flagellin detection in feces assay + + An analyte assay measuring bacterial flagellin in a feces sample. + SD + HCC + HCC + bacterial flagellin detection in feces assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial lipopolysaccharide detection in plasma assay + + An analyte assay measuring bacterial lipopolysaccharide in a plasma sample. + SD + LPS + HCC + HCC + bacterial lipopolysaccharide detection in plasma assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + bacterial lipopolysaccharide detection in feces assay + + An analyte assay measuring bacterial lipopolysaccharide in a feces sample. + SD + LPS + HCC + HCC + bacterial lipopolysaccharide detection in feces assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + adenosine deaminase activity assay + + An analyte assay measuring adenosine deaminase activity in a sample. + SD + ADA + HCC + HCC + adenosine deaminase activity assay + + + + + + + + + pathogen neutralization assay + + An assay that measures neutralization of a pathogen. + SD + HCC + pathogen neutralization assay + + + + + + + + + bacterial neutralization assay + + A pathogen neutralization assay measuring neutralization of bacteria. + SD + HCC + bacterial neutralization assay + + + + + + + + + viral plaque assay + + An analyte assay measuring the number of discrete viral plaques. + SD + PMID:Ê25407402 + HCC + viral plaque assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + analyte detection by flow based bead assay + + An analyte assay that uses beads to measure the concentration of an analyte with a flow cytometer. + SD + HCC + HCC + analyte detection by flow based bead assay + + + + + + + + + bacterial lipopolysaccharide + + A molecule that is a component of the outermost membrane of the cell envelope of gram-negative bacteria and which consists of three parts: an outer core polysaccharide termed the O-antigen, an inner core oligosaccharide, and Lipid A, all covalently linked. + RV + SD + https://en.wikipedia.org/wiki/Lipopolysaccharide + Temporary term created for HCC & intended to be replaced with a term from a different ontology once one can be NTRed. + bacterial lipopolysaccharide + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine clarity assay + + A histological assay with urine evaluant that measures opacity of the urine + Jennifer Fostel + urine opacity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine color assay + + A histological assay with urine evaluant that measures color. + Jennifer Fostel + urine color assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + urine histological assay + + A histological assay with urine sediment as evaluant. + Frequently this assay detects the presence of cells, casts, crystals, bacteria and parasites. + Jennifer Fostel + urine histological assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + color detection assay + + An assay that measures the color of the evaluant + generally detected by sight, as a color indicator. + Jennifer Fostel + color detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + opacity determination assay + + An assay that measures the opacity of the evaluant + Jennifer Fostel + opacity determination assay + + + + + + + + + electrocardiograph + + An instrument for recording the changes of electrical potential occurring during the heartbeat used especially in diagnosing abnormalities of heart action. + Jennifer Fostel + https://www.merriam-webster.com/dictionary/electrocardiograph + electrocardiograph + + + + + + + + + biotelemeter + + A measurement device that also transmits the measurement information from a biological material to a distant station. + Jennifer Fostel + biotelemeter + + + + + + + + + multi-electrode array plate + + A measurement device consisting of grid of tightly spaced microscopic electrodes that can detect the electrical signals of cells in close proximity. + Multielectrode arrays can be embedded in the bottom of a well and cells can be cultured over the electrodes for passive, noninvasive monitoring of electrical activity. + Jennifer Fostel + multi-electrode array plate + + + + + + + + + Transepithelial Electrical Resistance (TEER) device + + A measurement device that measures monolayer barrier integrity via measurement of membrane potential and electrical resistance across a cell monolayer in culture. + Jennifer Fostel + Transepithelial Electrical Resistance (TEER) device + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle count assay + + An estrous cycle assay based on tissue morphology that determines the number of estrous cycles observed in a defined time. + Jennifer Fostel + estrous cycle count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + estrous cycle duration assay + + An estrous cycle assay based on tissue morphology that determines the average length of a full estrous cycle observed in a defined time. + Jennifer Fostel + estrous cycle duration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo based on examination of surface structure + + An organism development assay in late embryo that evaluates only the external surface structure of the organism + Jennifer Fostel + external fetal exam + organism development assay in late embryo based on examination of surface structure + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo based on examination of skeletal system + + An organism development assay in late embryo that evaluates the skeletal system of the organism + Jennifer Fostel + skeletal fetal exam + organism development assay in late embryo based on examination of skeletal system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + organism development assay in late embryo based on examination of anatomical system + + An organism development assay in late embryo that evaluates the anatomical system of the organism + Jennifer Fostel + visceral fetal exam + organism development assay in late embryo based on examination of anatomical system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + distance measurement assay + + An assay that measures the space between two entities. + Distance is a measure of the amount of space between two points. + Jennifer Fostel + distance measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + length measurement assay + + An assay that measures the distance between two points. + Typically length is a property of an object, the distance from end to end often in the largest dimension. + Jennifer Fostel + length measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + crown rump length + + A length measurement assay that measures the length of a neonate or fetus from crown of head to base of torso (rump) + Jennifer Fostel + crown rump length + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + path length assay + the distance traveled by a rodent in a maze + + An assay that measures the distance traveled in a defined period of time. + The total distance traveled by an entity in a given time; the sum of all segments in the path traveled if it is not straight. + Jennifer Fostel + path length assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell migration assay + + A distance measurement assay in which the migration of cells in culture is monitored by measuring the distance between the start position and the cell's location when observed. + This is the distance between the start and end points of cultured cells + Jennifer Fostel + cell migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + oligodendrocyte migration assay + + A cell migration assay that measures migration of an oligodendrocyte + Jennifer Fostel + oligodendrocyte migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + radial glial migration assay + + A cell migration assay that measures migration of a radial glia cell + Jennifer Fostel + radial glial migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron migration assay + + A cell migration assay that measures migration of a neuron + Jennifer Fostel + neuron migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neural crest cell migration assay + + A cell migration assay that measures migration of a neural crest cell + Jennifer Fostel + neural crest cell migration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + acidity quality assay + + An assay that measures the acidity of a specimen on the pH scale. + The measurement of pH is the negative logarithm to base ten of the hydrogen ion activity in a solution, this measures the degree of acidity or alkalinity. + Jennifer Fostel + acidity quality assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + specific gravity assay + + An assay that measures the specific gravity of a sample. + Specific gravity is the ratio of the density of the specimen to the ratio of water or other standard. + Jennifer Fostel + specific gravity assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + speed measurement assay + + An assay to determine the speed of an evaluant. + Speed is a physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position (PATO). + Jennifer Fostel + speed measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + velocity measurement assay + + An assay to measure the velocity of an evaluant + Velocity is a physical quality inhering in a bearer by virtue of the bearer's rate of change of the position (PATO). + Jennifer Fostel + velocity measurement assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + luminescence detection assay + + An assay that measures the luminescence of the evaluant + the unit of this assay is relative luminescence unit (UO:0000313) + Jennifer Fostel + luminescence detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell viability assay using luciferase to detect ATP in the cell + + A cell viability assay that uses an ATP bioluminescence assay to detect ATP in the living cell + one reagent is CellTiter Glo (Promega) which contains luciferase and luciferin. Luciferase uses ATP in the living cell to convert luciferin to oxyluciferin and light. + Jennifer Fostel + cell viability assay using luciferase to detect ATP in the cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + population count assay + + An assay that measures the number of elements in a portion of a population + Not a synonym of organism detection assay (OBI:0002738); "A population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area + Jennifer Fostel + population count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + hemolysis assay + + A hematology assay that measures the fragility of red blood cells by observing spillage of hemoglobin from burst cells. + Jennifer Fostel + hemolysis assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mean firing rate + + An electrophysiology assay that measures action potential events in neurons during a time period. + Jennifer Fostel + neuron action potential rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron burst rate assay + + An electrophysiology assay that measures the number of action potential bursts in neurons during a time period. + A burst is temporal arrangement of action potentials that occur close together in time followed by a period of quiescence. + Jennifer Fostel + neuron burst rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron interburst interval assay + + An electrophysiology assay that measures the elapsed time between consecutive action potential bursts in neurons. + A burst is temporal arrangement of action potentials that occur close together in time followed by a period of quiescence, the interburst interval. + Jennifer Fostel + neuron interburst interval assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neuron burst duration assay + + An electrophysiology assay that measures the time elapsed between the first action potential in a neuron burst and the last in that burst. + Jennifer Fostel + neuron burst duration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + interspike interval within a burst + + An electrophysiology assay that measures the time elapsed between the peaks of consecutive action potential spikes in a neuron burst. + Jennifer Fostel + action potential interval assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + rate of action potentials in neuron burst assay + + An electrophysiology assay that measures the number of action potential spikes occurring within a neuron burst + singleton spikes in the same time period unrelated to a neuron burst are not included in the count. + Jennifer Fostel + rate of action potentials in neuron burst assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body mass assay + + A mass measurement assay with evaluant an individual organism. + Jennifer Fostel + body mass assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body mass change assay + + A body mass assay that measures the change in body mass for a subject over a period of time. + Jennifer Fostel + body mass change assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + terminal body weight assay + + A body weight assay with evaluant individual organism specimen with quality dead. + Jennifer Fostel + body weight assay at death + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tissue mass assay + + A mass measurement assay with evaluant tissue or bodily fluid specimen. + Jennifer Fostel + tissue mass assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + tissue mass percent of body mass assay + + A mass measurement assay with evaluant tissue expressed as a percentage of the body weight of the organism from which the specimen was derived. + Jennifer Fostel + tissue mass percent of body mass assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + developmental marker age of attainment assessment + the age of the rat at testis descent, the age of a human child at first menses. + + An age determination assay which determines the age of the subject at the time of the change from a state where it did not have a developmental stage marker to one in which it does. + Jennifer Fostel + developmental marker age of attainment assessment + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cytochrome P450 assay + + A protein assay that measures the abundance of cytochrome P450 in a specimen. + Jennifer Fostel + cytochrome P450 assay + + + + + + + + + + + + + + + + + + + + growth factor assay + + An analyte assay to measure the abundance of one or more growth factors in a volume of sample. + A growth factor is a signalling role of a chemical substance in which it stimulates a biological system to proliferate, divide, differentiate, migrate, and so forth. + Jennifer Fostel + growth factor assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Hoechst dye assay + + A fluorescence imaging-based cell morphology assay that uses Hoechst dye 33342 + Hoechst dye binds to DNA and can be used to visualize nuclei. Often used to quantify cells, identify position over time, identify the cell body and other assays. + Jennifer Fostel + Hoechst dye assay + + + + + + + + + + + + + + + + + + + + hypersensitivity assay + + An immune response assay to assess the hypersensitivity response in an organism or cell culture. + Jennifer Fostel + hypersensitivity assay + + + + + + + + + super-resolution microscopy assay + + A type of light microscopy assay where the images are taken with a resolution higher than the diffraction limit. + Lachlan Whitehead + Marek Cmero + super resolution microscopy assay + http://purl.obolibrary.org/obo/MI_2213 + super-resolution microscopy assay + + + + + + + + + + + + + + + multi-photon microscope + + A microscope that uses simultaneous absorption of multiple photons to excite fluorescent molecules. + PERSON: Lachlan Whitehead + PERSON: Marek Cmero + PERSON: Pradeep Rajasekhar + MPLSM + multiphoton laser scanning microscope + two-photon excitation microscope + doi:10.1364/AOP.7.000276 + multiphoton microscope + + + + + + + + + + + + + + + light sheet microscope + + A microscope that uses illumination and detection objectives to image a sample illuminated with a thin sheet of laser light. + PERSON: Lachlan Whitehead + PERSON: Marek Cmero + light-sheet microscope + lightsheet microscope + doi:10.1016/B978-0-12-420138-5.00011-2 + light sheet microscope + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1M7 RNA structure mapping assay + PMID: 29551268 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methyl-7-nitroisatoic anhydride as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 1M7 probe + 1M7 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + NAI RNA structure mapping assay + PMID: 37674078 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-methylnicotinic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using NAI probe + NAI RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + NAI-N3 RNA structure mapping assay + PMID: 29804836 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-(azidomethyl)nicotinic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using NAI-N3 probe + NAI-N3 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 2A3 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 2-aminopyridine-3-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 2A3 probe + 2A3 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + I5 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using indoline-5-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using I5 probe + I5 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 1M4 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methylimidazole-4-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 1M4 probe + 1M4 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 6A3 RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 6-aminopyridine-3-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 6A3 probe + 6A3 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + B5 RNA structure mapping assay + PMID:33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using benzotriazole-5-carboxylic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using B5 probe + B5 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + NIC RNA structure mapping assay + PMID: 33398343 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using nicotinic acid imidazolide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using NIC probe + NIC RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + BzCN RNA structure mapping assay + PMID: 33453165 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using benzoyl cyanide as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using BzCN probe + BzCN RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 1M6 RNA structure mapping assay + PMID: 30341219 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 1-methyl-6-nitroisatoic anhydride as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 1M6 probe + 1M6 RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + 5NIA RNA structure mapping assay + PMID: 36062555 + + A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using 5-nitroisatoic anhydride as reagent and chemical probe + Victoria Begley (RNAcentral) + SHAPE mapping assay + single nucleotide resolution mapping assay using 5NIA probe + 5NIA RNA structure mapping assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + cell count assay + + An assay that measures the number of cells in a portion of a cell culture or tissue or bodily fluid + OBI:2100330 count bodily fluid cell count assay / OBI:2100345 bodily fluid cell count assay + Jennifer Fostel + cell count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + differential leukocyte count assay + + A hematology assay that measures the percentage of classes of leukocytes in a sample. + Jennifer Fostel + differential leukocyte count assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + electrocardiogram assay + + An electrophysiology assay that measures heart activity using electrodes placed to detect electrical signals from the heart. + related to electrocardiography (MAXO:0010203): A procedure that displays the electrical activity of the heart. + Jennifer Fostel + electrocardiogram assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + telemeter sensor detection assay + + An assay which uses an implanted telemeter to measure physiological data in a living organism and transmit the measures via radio waves to a recording device. + different types of telemeters can measure blood pressure, gross activity, heart rate, ECG, glucose and other physiological parameters. + Jennifer Fostel + telemeter sensor detection assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MEA assay + + A multi-unit recording assay using a multi-electrode array (MEA) on the surface of a well on a cell culture plate. + When cells capable of electrical signaling are cultured in the well the MEA grid can detect electrical signaling by the cells. + Jennifer Fostel + multi-electrode array assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + transepithelial / transendothelial electrical resistance (TEER) assay + An example would be a TEER assay to measure the integrity of a cell monolayer with apical surface exposed to air and basal surface in culture medium; this mimics the airway epithelium. + + An extracellular electrophysiology recording assay to measure the integrity of a cell monolayer + the assay measures electrical resistance by manually placing two chopstick-style electrodes on each side of a confluent cell layer. A low frequency current is applied and the resistance of the barrier is measured. + Jennifer Fostel + transepithelial / transendothelial electrical resistance (TEER) assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + number of active electrodes + + A multi-electrode array assay that measures the number of electrodes in a well where the mean rate of action potentials is at least 5 spikes per minute. + Jennifer Fostel + count of multi-electrode plate electrodes detecting action potential assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + number of bursting electrodes + + A multi-electrode array assay that measures the number of electrodes in a well where the burst rate is at least 0.5 bursts per minute. + A burst is temporal arrangement of action potentials that occur close together in time followed by a period of quiescence. + Jennifer Fostel + count of multi-electrode plate electrodes detecting neuron burst assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neural network spike rate assay + + An multi-electrode assay that measures the number of events when multiple electrodes simultaneously detect an action potential during a time period. + In a microelectrode array assay, the number of instances during a 15-minute recording when 5 or more electrodes in a well participate in an action potential burst at the same time. + Jennifer Fostel + neural network spike rate assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + neural network spike duration assay + + A multi-electrode assay that measures the mean duration of events when multiple electrodes detect an action potential + In a microelectrode array (MEA) assay, the time interval before and after the network spike peak when half as many electrodes are spiking as at the peak of the network spike . + Jennifer Fostel + neural network spike duration assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + network spike peak + + A multi-electrode array assay that measures the average number of electrodes detecting a network spike, measured at the peak of a network spike. + a network spike is defined in this context as an event when multiple electrodes detect an action potential + Jennifer Fostel + count of multi-electrode plate electrodes detecting spike peak assay + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + mean interspike interval in network spike + + A multi-electrode assay that measures the average interval between network spikes, events where multiple electrodes simultaneously detect an action potential. + The time interval between the peaks of consecutive network spikes in a microelectrode array (MEA). A network spike is an event where multiple electrodes simultaneously detect an action potential. + Jennifer Fostel + mean interspike interval in network spike + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -104778,35 +111700,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - - - - - - - - - - - cell based DNA damage assay + bile acid concentration assay - A cytometry assay that measures DNA damage in cells. + An analyte assay that measures the abundance of bile acid in a volume of sample. + The major component of bile acids are cholic and chenodeoxycholic acid. Jennifer Fostel - cell based DNA damage assay + bile acid concentration assay - + - - + + @@ -104818,7 +111730,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104829,7 +111741,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104841,30 +111753,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - natural killer cell count assay - - A cytometry assay to determine the number of natural killer cells in a specimen - Jennifer Fostel - natural killer cell count assay - - - - - - - - @@ -104873,10 +111761,10 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - - + + @@ -104884,17 +111772,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - + @@ -104905,24 +111783,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + - natural killer cell percentage assay + urea nitrogen assay - A cytometry assay that measures the percentage of natural killer cells in a specimen. + An analyte assay that measures the abundance of urea nitrogen. + urea nitrogen is the nitrogen component of urea found in a biological specimen Jennifer Fostel - natural killer cell percentage assay + urea nitrogen assay - + - - + + @@ -104934,7 +111813,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104945,7 +111824,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + @@ -104957,35 +111836,80 @@ b) that the amount of analyte/measurand detected is over some predetermined thre + + + + + + + + + + + + + + + + + + + + + + + + - + - sperm count assay + urea nitrogen concentration assay - A cytometry assay to count the number of mature sperm in a specimen. + A urea nitrogen assay that measures the abundance of urea nitrogen in a specimen + urea nitrogen is the nitrogen component of urea found in a biological specimen Jennifer Fostel - sperm count assay + urea nitrogen concentration assay - + - - - survey administration assay - - An assay that obtains data from one or more participants by using a survey or questionnaire - Jennifer Fostel - survey administration assay + + + randomized clinical trial + + A clinical trial in which the participants are divided by chance into separate groups that compare different treatments or other interventions. Using chance to divide people into groups means that the groups will be similar and that the effects of the treatments they receive can be compared more fairly. At the time of the trial, it is not known which treatment is best. + Sebastian Duesing + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/randomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + randomized clinical trial + + + + + + + + + non-randomized clinical trial + + A clinical trial in which the participants are not assigned by chance to different treatment groups. Participants may choose which group they want to be in, or they may be assigned to the groups by the researchers. + Sebastian Duesing + nonrandomized clinical trial + https://www.cancer.gov/publications/dictionaries/cancer-terms/def/nonrandomized-clinical-trial + https://github.com/obi-ontology/obi/issues/1891 + Charles Tapley Hoyt + non-randomized clinical trial @@ -105032,7 +111956,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + Epstein Barr virus transformed B cell PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. @@ -105047,7 +111971,7 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - + chimera An organism which contains cells or tissues with a different genotype @@ -105081,7 +112005,6 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - @@ -105155,31 +112078,22 @@ b) that the amount of analyte/measurand detected is over some predetermined thre - - - - - - - - - - - - organism - animal - fungus - plant - virus + + obsolete organism + animal + fungus + plant + virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. + 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism + WEB: http://en.wikipedia.org/wiki/Organism + + + obsolete organism + true @@ -105340,7 +112254,7 @@ This issue is outside the scope of OBI. - + @@ -105350,7 +112264,7 @@ This issue is outside the scope of OBI. - + xenograft @@ -105369,7 +112283,7 @@ This issue is outside the scope of OBI. - + @@ -105484,7 +112398,7 @@ Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39- - + screening library PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library] @@ -105514,7 +112428,6 @@ change biomaterial to material in definition - synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme @@ -105533,7 +112446,7 @@ DS: Is this synthetic an oxymoron to the biomaterial? - + @@ -105653,7 +112566,21 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ - + + + + + + + + + + + + + + + @@ -105685,7 +112612,7 @@ Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ data transformation The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. - A planned process that produces output data from input data. + A completely executed planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone @@ -107840,7 +114767,7 @@ In this equation b0 is the regression coefficient for the intercept and the bi v - + @@ -109676,28 +116603,23 @@ determinations of compounds. - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + pool of specimens A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. @@ -109784,7 +116706,7 @@ determinations of compounds. - + @@ -109812,7 +116734,7 @@ determinations of compounds. - + @@ -109836,7 +116758,7 @@ determinations of compounds. - + @@ -109959,15 +116881,16 @@ determinations of compounds. - comet assay + DNA damage comet assay PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. - An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis + A cell based DNA damage assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis Philippe Rocca-Serra SCGE assay + comet assay single cell gel electrophoresis assay PMID:7686265 - comet assay + DNA damage comet assay @@ -110069,7 +116992,6 @@ determinations of compounds. - denatured polymer Is a polymer which has lost secondary or tertiary structure @@ -110094,7 +117016,7 @@ determinations of compounds. - + decapitated organism Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids. J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 @@ -110188,7 +117110,6 @@ J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172 - methylated polymer Binding and penetration of methylated DNA into primary and transformed human cells. Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 @@ -110207,7 +117128,7 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 - + @@ -110215,8 +117136,8 @@ Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922 + - genetically modified organism A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis. Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 @@ -110402,7 +117323,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110423,7 +117344,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110456,7 +117377,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110489,11 +117410,11 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + - + @@ -110538,7 +117459,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + @@ -110687,7 +117608,7 @@ Nat Protoc. 2008;3(10):1550-8. PMID: 18802436 - + intentional overdosing @@ -110753,7 +117674,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110774,7 +117695,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110806,14 +117727,14 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + - + @@ -110876,7 +117797,7 @@ J Neurooncol. 1994;22(3):209-20. PMID: 7760097 - + @@ -110904,7 +117825,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -110931,7 +117852,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + validation PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16. @@ -111017,7 +117938,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -111235,7 +118156,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112165,7 +119086,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112199,7 +119120,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + particle delivery vessel FC 500 particle delivery vessel @@ -112285,7 +119206,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112307,7 +119228,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112549,7 +119470,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112640,7 +119561,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112711,7 +119632,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -112830,7 +119751,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113199,7 +120120,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113374,7 +120295,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -113449,7 +120370,7 @@ Manual editing of automatically recorded data in an anesthesia information manag - + @@ -114107,7 +121028,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114136,14 +121057,14 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114159,7 +121080,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114213,7 +121134,7 @@ defines and states the requirements (positive or negative) for an entity to be c - + @@ -114230,13 +121151,13 @@ defines and states the requirements (positive or negative) for an entity to be c - + - + @@ -114316,7 +121237,7 @@ Relates to the creation of a class 'selection rule' - + exposure of material to environment Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber. @@ -114436,7 +121357,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114463,11 +121384,11 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + @@ -114479,7 +121400,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114675,7 +121596,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114698,7 +121619,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114892,7 +121813,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114914,7 +121835,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -114977,7 +121898,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115074,7 +121995,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115096,7 +122017,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115152,7 +122073,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115226,7 +122147,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115266,7 +122187,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115287,17 +122208,17 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + - + - + @@ -115383,7 +122304,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115779,7 +122700,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115874,7 +122795,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -115995,7 +122916,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116110,8 +123031,8 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ + - @@ -116139,7 +123060,7 @@ discussed on obi-dev call 9/28/2015, details see: https://sourceforge.net/p/obi/ - + @@ -116167,7 +123088,7 @@ Isolation of proliferation factor of immature T-cell clone in concanavalin A-sti - + @@ -116235,7 +123156,7 @@ addition of has_role restriction - + @@ -116266,7 +123187,7 @@ old defintion: A mixture (collection) of cell components created by rupturing of - + @@ -116320,7 +123241,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - @@ -116350,7 +123270,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + assay bead Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. @@ -116675,7 +123595,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + Immunization in vivo @@ -116767,7 +123687,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116883,7 +123803,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116928,7 +123848,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + @@ -116936,7 +123856,7 @@ Possible ecological risks of transgenic organism release when transgenes affect - + host of immune response A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses. @@ -117204,7 +124124,6 @@ Possible ecological risks of transgenic organism release when transgenes affect - lymph node cell specimen @@ -118000,19 +124919,20 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - + - blood harvesting + blood specimen collection - A material separation where blood is taken from an organism. + A specimen collection in which blood is collected from an organism. IEDB + blood harvesting IEDB - blood harvesting + blood specimen collection @@ -118200,7 +125120,6 @@ MHB 3-5-13: Need to review axiom on this class in light of clarification that it - splenocyte specimen @@ -122002,7 +128921,7 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - + calcium cation assay An analyte assay that measures the abundance of calcium cation @@ -147892,18 +154811,6 @@ The content of that report on the IEDB website is here: http://iedb.org/refId/10 - - - - - phenotype - A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. - - phenotype - - - - @@ -147960,7 +154867,7 @@ realizes some 'host of immune response role' - + treatment A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process @@ -148010,7 +154917,7 @@ realizes some 'host of immune response role' health care provider role - A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. + A health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. health care provider role @@ -148044,7 +154951,7 @@ realizes some 'host of immune response role' - + parasite organism An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class. @@ -148068,7 +154975,7 @@ realizes some 'host of immune response role' - + quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities @@ -148077,6 +154984,18 @@ realizes some 'host of immune response role' + + + + + speed + A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position. + + speed + + + + @@ -148089,6 +155008,19 @@ realizes some 'host of immune response role' + + + + + + color + A composite chromatic quality composed of hue, saturation and intensity parts. + + color + + + + @@ -148125,6 +155057,18 @@ realizes some 'host of immune response role' + + + + + distance + A quality that is the extent of space between two entities. + + distance + + + + @@ -148305,6 +155249,18 @@ realizes some 'host of immune response role' + + + + + opacity + An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. + + opacity + + + + @@ -148317,6 +155273,18 @@ realizes some 'host of immune response role' + + + + + mass density + A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. + + mass density + + + + @@ -148404,7 +155372,7 @@ realizes some 'host of immune response role' - + physical object quality A quality which inheres in a continuant. @@ -148413,6 +155381,30 @@ realizes some 'host of immune response role' + + + + + full-spectrum EM radiation quality + An EM radiation quality that is independent of the EM wavelength range. + + full-spectrum EM radiation quality + + + + + + + + + absorption quality + A scalar EM radiation quality which obtains by the capacity of the bearer to retain radiation. + + absorption quality + + + + @@ -148749,6 +155741,18 @@ realizes some 'host of immune response role' + + + + + conductivity + A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium. + + conductivity + + + + @@ -148810,6 +155814,18 @@ realizes some 'host of immune response role' + + + + + electrical conductivity + A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity. + + electrical conductivity + + + + @@ -148834,6 +155850,18 @@ realizes some 'host of immune response role' + + + + + acidity + A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions). + + acidity + + + + @@ -148918,6 +155946,16 @@ realizes some 'host of immune response role' + + + + + A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. + electric charge + + + + @@ -148978,6 +156016,18 @@ realizes some 'host of immune response role' + + + + + velocity + A physical quality inhering in a bearer by virtue of the bearer's rate of change of the position. + + velocity + + + + @@ -149026,12 +156076,40 @@ realizes some 'host of immune response role' + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + collection of organisms + + + + + + + + + An anatomical entity that is or was part of a plant. + plant anatomical entity + + + + + protein antithrombin III is a protein + An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. protein @@ -149087,6 +156165,18 @@ realizes some 'host of immune response role' + + + + + adenosine deaminase + A protein that is a translation product of the human ADA gene or a 1:1 ortholog thereof. + + adenosine deaminase + + + + @@ -149279,6 +156369,16 @@ realizes some 'host of immune response role' + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + amino acid chain + + + + @@ -149412,6 +156512,30 @@ realizes some 'host of immune response role' + + + + + luciferase-like monooxygenase + A protein that is a translation product of the Escherichia coli K-12 yhbW gene or a 1:1 ortholog thereof. + + luciferase-like monooxygenase + + + + + + + + + bacterial protein + A protein that is encoded in the genome of some Bacteria <prokaryote>. + + bacterial protein + + + + @@ -149484,6 +156608,18 @@ realizes some 'host of immune response role' + + + + + modified histone + A histone that contains one or more amino acid modifications. + + modified histone + + + + @@ -149519,7 +156655,7 @@ realizes some 'host of immune response role' - + region A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. primary structure of sequence macromolecule @@ -149654,10 +156790,26 @@ realizes some 'host of immune response role' - - uterine cervix + + + + + + + + + + + + + + + + + + + Lower, narrow portion of the uterus where it joins with the top end of the vagina. - uterine cervix @@ -149666,10 +156818,8 @@ realizes some 'host of immune response role' - - pituitary gland + The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. - pituitary gland @@ -149678,10 +156828,14 @@ realizes some 'host of immune response role' - - peripheral nervous system + + + + + + + A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. - peripheral nervous system @@ -149690,10 +156844,26 @@ realizes some 'host of immune response role' - - lymph node + + + + + + + + + + + + + + + + + + + Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. - lymph node @@ -149702,22 +156872,50 @@ realizes some 'host of immune response role' - - urethra + + + + + + + The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. - urethra + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + anatomical structure + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + organ + + + + - life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. - life cycle stage @@ -149726,10 +156924,26 @@ realizes some 'host of immune response role' - - cloaca + + + + + + + + + + + + + + + + + + + Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. - cloaca @@ -149738,10 +156952,20 @@ realizes some 'host of immune response role' - - mouth + + + + + + + + + + + + + The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - mouth @@ -149751,9 +156975,7 @@ realizes some 'host of immune response role' - amniotic fluid Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid. - amniotic fluid @@ -149763,9 +156985,13 @@ realizes some 'host of immune response role' - blood + + + + + + A fluid that is composed of blood plasma and erythrocytes. - blood @@ -149774,10 +157000,26 @@ realizes some 'host of immune response role' - - amnion + + + + + + + + + + + + + + + + + + + The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected. - amnion @@ -149786,10 +157028,14 @@ realizes some 'host of immune response role' - - breast + + + + + + + The upper ventral region of the torso of an organism. - breast @@ -149799,21 +157045,33 @@ realizes some 'host of immune response role' - cervical mucus A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus. - cervical mucus + + + + + An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. + late embryo + + + + - - throat + + + + + + + In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. - throat @@ -149823,9 +157081,7 @@ realizes some 'host of immune response role' - renal medulla The inner portion of the kidney consisting of the renal pyramids. - renal medulla @@ -149835,9 +157091,7 @@ realizes some 'host of immune response role' - organism substance Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. - organism substance @@ -149846,22 +157100,57 @@ realizes some 'host of immune response role' + + + + + + + + + + - material anatomical entity + Anatomical entity that has mass. - material anatomical entity + + + + + + Anatomical entity that has no mass. + immaterial anatomical entity + + + + + + + + + + + + + + + Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. + anatomical system + + + + - - testis + + A gonad of a male animal. A gonad produces and releases sperm. - testis @@ -149870,10 +157159,8 @@ realizes some 'host of immune response role' - - anatomical cluster + Anatomical group whose component anatomical structures lie in close proximity to each other. - anatomical cluster @@ -149882,10 +157169,8 @@ realizes some 'host of immune response role' - - tissue + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. - tissue @@ -149894,10 +157179,14 @@ realizes some 'host of immune response role' - - multi-tissue structure + + + + + + + Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. - multi-tissue structure @@ -149907,9 +157196,13 @@ realizes some 'host of immune response role' - epithelium + + + + + + Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - epithelium @@ -149918,10 +157211,20 @@ realizes some 'host of immune response role' - - stomach + + + + + + + + + + + + + An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. - stomach @@ -149930,10 +157233,14 @@ realizes some 'host of immune response role' - - aorta + + + + + + + The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation. - aorta @@ -149942,10 +157249,8 @@ realizes some 'host of immune response role' - - heart + A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. - heart @@ -149954,10 +157259,8 @@ realizes some 'host of immune response role' - - brain + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. - brain @@ -149966,10 +157269,14 @@ realizes some 'host of immune response role' - - cerebral cortex + + + + + + + The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. - cerebral cortex @@ -149978,10 +157285,8 @@ realizes some 'host of immune response role' - - eye + An organ that detects light. - eye @@ -149990,10 +157295,8 @@ realizes some 'host of immune response role' - - leg + The portion of the hindlimb that contains both the stylopod and zeugopod. - leg @@ -150002,10 +157305,8 @@ realizes some 'host of immune response role' - - ovary + The gonad of a female organism which contains germ cells. - ovary @@ -150014,10 +157315,20 @@ realizes some 'host of immune response role' - - uterus + + + + + + + + + + + + + The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth. - uterus @@ -150026,10 +157337,20 @@ realizes some 'host of immune response role' - - vagina + + + + + + + + + + + + + A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. - vagina @@ -150039,9 +157360,20 @@ realizes some 'host of immune response role' - skin epidermis + + + + + + + + + + + + + The outer epithelial layer of the skin that is superficial to the dermis. - skin epidermis @@ -150050,10 +157382,9 @@ realizes some 'host of immune response role' - - respiratory system + + Functional system which consists of structures involved in respiration. - respiratory system @@ -150062,10 +157393,8 @@ realizes some 'host of immune response role' - - adipose tissue + Portion of connective tissue composed of adipocytes enmeshed in areolar tissue. - adipose tissue @@ -150074,10 +157403,26 @@ realizes some 'host of immune response role' - - strand of hair + + + + + + + + + + + + + + + + + + + A filament, mostly protein, that grows from follicles found in the dermis[WP]. - strand of hair @@ -150086,22 +157431,54 @@ realizes some 'host of immune response role' - - rectum + + + + + + + + + + + + + + + + + + + The terminal portion of the intestinal tube, terminating with the anus. - rectum + + + + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + - pleural fluid Transudate contained in the pleural cavity. - pleural fluid @@ -150111,9 +157488,7 @@ realizes some 'host of immune response role' - urine Excretion that is the output of a kidney. - urine @@ -150123,9 +157498,7 @@ realizes some 'host of immune response role' - sweat Secretion produced by a sweat gland. - sweat @@ -150135,9 +157508,7 @@ realizes some 'host of immune response role' - synovial fluid Joint fluid is a transudate of plasma that is actively secreted by synovial cells. - synovial fluid @@ -150146,10 +157517,14 @@ realizes some 'host of immune response role' - - diaphragm + + + + + + + A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control. - diaphragm @@ -150158,10 +157533,8 @@ realizes some 'host of immune response role' - - skeletal muscle tissue + Muscle tissue that consists primarily of skeletal muscle fibers. - skeletal muscle tissue @@ -150170,10 +157543,20 @@ realizes some 'host of immune response role' - - colon + + + + + + + + + + + + + A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. - colon @@ -150182,10 +157565,26 @@ realizes some 'host of immune response role' - - sigmoid colon + + + + + + + + + + + + + + + + + + + The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. - sigmoid colon @@ -150194,10 +157593,14 @@ realizes some 'host of immune response role' - - cortex of kidney + + + + + + + Outer cortical portion of the kidney, between the renal capsule and the renal medulla. - cortex of kidney @@ -150206,10 +157609,14 @@ realizes some 'host of immune response role' - - urinary bladder + + + + + + + Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. - urinary bladder @@ -150218,10 +157625,14 @@ realizes some 'host of immune response role' - - pancreas + + + + + + + An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]. - pancreas @@ -150231,9 +157642,7 @@ realizes some 'host of immune response role' - peritoneal fluid Transudate contained in the peritoneal cavity. - peritoneal fluid @@ -150242,10 +157651,26 @@ realizes some 'host of immune response role' - - tibial nerve + + + + + + + + + + + + + + + + + + + The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]. - tibial nerve @@ -150255,21 +157680,39 @@ realizes some 'host of immune response role' - cerebrospinal fluid A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. - cerebrospinal fluid + + + + + + + + + + + + + + + + + Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. + skeletal system + + + + - - arm + The part of the forelimb extending from the shoulder to the autopod[cjm]. - arm @@ -150278,10 +157721,14 @@ realizes some 'host of immune response role' - - knee joint + + + + + + + The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]. - knee joint @@ -150290,10 +157737,14 @@ realizes some 'host of immune response role' - - ankle joint + + + + + + + A joint that connects the hindlimb autopod and zeugopod skeletons. - ankle joint @@ -150303,9 +157754,7 @@ realizes some 'host of immune response role' - common carotid artery plus branches A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. - common carotid artery plus branches @@ -150314,10 +157763,20 @@ realizes some 'host of immune response role' - - digestive tract + + + + + + + + + + + + + A tube extending from the mouth to the anus. - digestive tract @@ -150326,10 +157785,14 @@ realizes some 'host of immune response role' - - upper respiratory tract + + + + + + + The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. - upper respiratory tract @@ -150338,10 +157801,14 @@ realizes some 'host of immune response role' - - lower respiratory tract + + + + + + + The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]. - lower respiratory tract @@ -150350,10 +157817,14 @@ realizes some 'host of immune response role' - - cheek + + + + + + + A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. - cheek @@ -150362,10 +157833,8 @@ realizes some 'host of immune response role' - - facial muscle + A muscle innervated by a facial nerve. - facial muscle @@ -150375,9 +157844,13 @@ realizes some 'host of immune response role' - coronary artery + + + + + + An artery that supplies the myocardium. - coronary artery @@ -150386,10 +157859,14 @@ realizes some 'host of immune response role' - - artery + + + + + + + An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. - artery @@ -150398,10 +157875,14 @@ realizes some 'host of immune response role' - - vein + + + + + + + Any of the tubular branching vessels that carry blood from the capillaries toward the heart. - vein @@ -150410,10 +157891,14 @@ realizes some 'host of immune response role' - - tongue + + + + + + + A muscular organ in the floor of the mouth. - tongue @@ -150422,10 +157907,20 @@ realizes some 'host of immune response role' - - nasopharynx + + + + + + + + + + + + + The section of the pharynx that lies above the soft palate. - nasopharynx @@ -150434,10 +157929,20 @@ realizes some 'host of immune response role' - - oropharynx + + + + + + + + + + + + + The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis. - oropharynx @@ -150447,9 +157952,19 @@ realizes some 'host of immune response role' - vitreous humor + + + + + + + + + + + + A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina. - vitreous humor @@ -150458,10 +157973,14 @@ realizes some 'host of immune response role' - - conjunctiva + + + + + + + The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball. - conjunctiva @@ -150470,10 +157989,32 @@ realizes some 'host of immune response role' - - nasal cavity mucosa + + + + + + + + + + + + + + + + + + + + + + + + + The mucous membrane that lines the nasal cavity[MP]. - nasal cavity mucosa @@ -150482,10 +158023,20 @@ realizes some 'host of immune response role' - - minor salivary gland + + + + + + + + + + + + + One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]. - minor salivary gland @@ -150495,9 +158046,7 @@ realizes some 'host of immune response role' - saliva A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. - saliva @@ -150506,10 +158055,20 @@ realizes some 'host of immune response role' - - caudate nucleus + + + + + + + + + + + + + Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species. - caudate nucleus @@ -150518,10 +158077,20 @@ realizes some 'host of immune response role' - - putamen + + + + + + + + + + + + + Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion. - putamen @@ -150531,9 +158100,19 @@ realizes some 'host of immune response role' - telencephalon + + + + + + + + + + + + Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. - telencephalon @@ -150543,9 +158122,7 @@ realizes some 'host of immune response role' - milk An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. - milk @@ -150555,9 +158132,7 @@ realizes some 'host of immune response role' - semen Organism substance that is composed of sperm cells suspended in seminal fluid. - semen @@ -150567,21 +158142,45 @@ realizes some 'host of immune response role' - bile Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. - bile + + + + + + + + + + + + + + + + + A vessel through which blood circulates in the body. + blood vessel + + + + - - placenta + + + + + + + Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. - placenta @@ -150591,9 +158190,7 @@ realizes some 'host of immune response role' - feces Portion of semisolid bodily waste discharged through the anus[MW,modified]. - feces @@ -150602,10 +158199,14 @@ realizes some 'host of immune response role' - - areola + + + + + + + Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple. - areola @@ -150615,9 +158216,19 @@ realizes some 'host of immune response role' - cerebellum + + + + + + + + + + + + Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. - cerebellum @@ -150626,10 +158237,8 @@ realizes some 'host of immune response role' - - thyroid gland + A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. - thyroid gland @@ -150638,10 +158247,14 @@ realizes some 'host of immune response role' - - lung + + + + + + + Respiration organ that develops as an outpocketing of the esophagus. - lung @@ -150650,10 +158263,26 @@ realizes some 'host of immune response role' - - dermis + + + + + + + + + + + + + + + + + + + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. - dermis @@ -150662,10 +158291,26 @@ realizes some 'host of immune response role' - - hypodermis + + + + + + + + + + + + + + + + + + + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. - hypodermis @@ -150674,10 +158319,14 @@ realizes some 'host of immune response role' - - skin of body + + + + + + + The organ covering the body that consists of the dermis and epidermis. - skin of body @@ -150686,10 +158335,8 @@ realizes some 'host of immune response role' - - spleen + The organ that functions to filter blood and to store red corpuscles and platelets. - spleen @@ -150698,10 +158345,8 @@ realizes some 'host of immune response role' - - liver + An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. - liver @@ -150710,10 +158355,20 @@ realizes some 'host of immune response role' - - ileum + + + + + + + + + + + + + The portion of the small intestine that extends from the jejunum to the colon. - ileum @@ -150722,10 +158377,26 @@ realizes some 'host of immune response role' - - integument + + + + + + + + + + + + + + + + + + + The dermis, epidermis and hypodermis. - integument @@ -150735,9 +158406,19 @@ realizes some 'host of immune response role' - peritoneum + + + + + + + + + + + + A serous membrane that lines the peritoneal cavity[VHOG,modified]. - peritoneum @@ -150746,10 +158427,8 @@ realizes some 'host of immune response role' - - prostate gland + The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. - prostate gland @@ -150758,10 +158437,8 @@ realizes some 'host of immune response role' - - adrenal gland + Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. - adrenal gland @@ -150771,21 +158448,55 @@ realizes some 'host of immune response role' - bone marrow + + + + + + + + + + + + The soft tissue that fills the cavities of bones. - bone marrow + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. + connective tissue + + + + + + + + + Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. + muscle tissue + + + + - - forelimb zeugopod + + + + + + + The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants. - forelimb zeugopod @@ -150794,10 +158505,8 @@ realizes some 'host of immune response role' - - manual digit + A digit that is part of a manus (hand). - manual digit @@ -150807,9 +158516,13 @@ realizes some 'host of immune response role' - lymph + + + + + + Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. - lymph @@ -150819,9 +158532,7 @@ realizes some 'host of immune response role' - pericardial fluid Transudate contained in the pericardial cavity.[FMA]. - pericardial fluid @@ -150830,10 +158541,8 @@ realizes some 'host of immune response role' - - tail + An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail. - tail @@ -150842,10 +158551,14 @@ realizes some 'host of immune response role' - - lymphoid system + + + + + + + The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. - lymphoid system @@ -150854,22 +158567,68 @@ realizes some 'host of immune response role' - - esophagus mucosa + + + + + + + + + + + + + + + + + + + A mucosa that is part of a esophagus [Automatically generated definition]. - esophagus mucosa + + + + + + + + + + + A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID]. + corpus luteum + + + + + + + + + An organ that functions as a secretory or excretory organ. + gland + + + + - - left cerebral hemisphere + + + + + + + A cerebral hemisphere that is in the left side of a brain. - left cerebral hemisphere @@ -150878,22 +158637,40 @@ realizes some 'host of immune response role' - - right cerebral hemisphere + + + + + + + A cerebral hemisphere that is in the right side of a brain. - right cerebral hemisphere + + + + + Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. + surface structure + + + + - - trachea + + + + + + + The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. - trachea @@ -150902,10 +158679,20 @@ realizes some 'host of immune response role' - - cranium + + + + + + + + + + + + + Upper portion of the skull that excludes the mandible (when present in the organism). - cranium @@ -150914,10 +158701,14 @@ realizes some 'host of immune response role' - - omentum + + + + + + + A fold of peritoneum originating at the stomach and supporting the viscera. - omentum @@ -150926,10 +158717,20 @@ realizes some 'host of immune response role' - - esophagus muscularis mucosa + + + + + + + + + + + + + A muscularis mucosa that is part of a esophagus. - esophagus muscularis mucosa @@ -150938,10 +158739,38 @@ realizes some 'host of immune response role' - - mucosa of nasopharynx + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a nasopharynx [Automatically generated definition]. - mucosa of nasopharynx @@ -150950,10 +158779,44 @@ realizes some 'host of immune response role' - - mucosa of oropharynx + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a oropharynx [Automatically generated definition]. - mucosa of oropharynx @@ -150962,10 +158825,26 @@ realizes some 'host of immune response role' - - middle nasal concha + + + + + + + + + + + + + + + + + + + The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha. - middle nasal concha @@ -150975,9 +158854,7 @@ realizes some 'host of immune response role' - bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. - bodily fluid @@ -150987,9 +158864,7 @@ realizes some 'host of immune response role' - respiratory system fluid/secretion A portion of organism substance that secreted_by a respiratory system. - respiratory system fluid/secretion @@ -150999,9 +158874,7 @@ realizes some 'host of immune response role' - atrium auricular region A small conical pouch projections located on the upper anterior portion of each atrium of the heart. - atrium auricular region @@ -151011,8 +158884,6 @@ realizes some 'host of immune response role' - digestive system secreted substance - digestive system secreted substance @@ -151022,9 +158893,13 @@ realizes some 'host of immune response role' - chorionic villus + + + + + + One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta. - chorionic villus @@ -151034,9 +158909,13 @@ realizes some 'host of immune response role' - meconium + + + + + + A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth. - meconium @@ -151046,9 +158925,7 @@ realizes some 'host of immune response role' - sputum Matter ejected from the lungs, bronchi, and trachea, through the mouth. - sputum @@ -151058,9 +158935,7 @@ realizes some 'host of immune response role' - tibial artery The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot. - tibial artery @@ -151069,10 +158944,8 @@ realizes some 'host of immune response role' - - esophagogastric junction + The junction between the esophagus and the stomach epithelium. - esophagogastric junction @@ -151081,22 +158954,62 @@ realizes some 'host of immune response role' - - tendon of biceps brachii + + + + + + + + + + + + + A tendon that attaches_to a biceps brachii. - tendon of biceps brachii + + + + + A body of a multi-cellular organism that is no longer living. + carcass + + + + + + + + + An organism containing a developing embryo, fetus, or unborn offspring within the body. + gravid organism + + + + - omental fat pad + + + + + + + + + + + + Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon. - omental fat pad @@ -151105,10 +159018,14 @@ realizes some 'host of immune response role' - - brachioradialis + + + + + + + Brachioradialis is a muscle of the forearm that acts to flex the forearm at the elbow. It is also capable of both pronation and supination, depending on the position of the forearm. It is attached to the distal styloid process of the radius by way of the brachioradialis tendon, and to the lateral supracondylar ridge of the humerus. - brachioradialis @@ -151118,9 +159035,13 @@ realizes some 'host of immune response role' - umbilical cord blood + + + + + + Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]. - umbilical cord blood @@ -151130,9 +159051,7 @@ realizes some 'host of immune response role' - arterial blood A blood that is part of a artery. - arterial blood @@ -151142,9 +159061,7 @@ realizes some 'host of immune response role' - venous blood A blood that is part of a vein. - venous blood @@ -151154,9 +159071,7 @@ realizes some 'host of immune response role' - capillary blood A blood that is part of a capillary. - capillary blood @@ -151165,10 +159080,26 @@ realizes some 'host of immune response role' - - suprapubic skin + + + + + + + + + + + + + + + + + + + Area of skin in the hypoastric region of the abdomen. - suprapubic skin @@ -151177,10 +159108,14 @@ realizes some 'host of immune response role' - - anterior nasal wall + + + + + + + Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule. - anterior nasal wall @@ -151190,9 +159125,7 @@ realizes some 'host of immune response role' - placental blood Blood located in the placenta. - placental blood @@ -151264,6 +159197,17 @@ realizes some 'host of immune response role' + + + + + speed/velocity unit + + speed/velocity unit + + + + @@ -151319,13 +159263,35 @@ realizes some 'host of immune response role' + + + + + phenotype + A phenotypic effect related to http://www.w3.org/2002/07/owl#Thing. + + phenotype + + + + + + + + + increased number of material anatomical entity in the urine + The presence of an increased number of material anatomical entity in the urine. + + increased number of material anatomical entity in the urine + + + + - - vaccine + Material entity that is manufactured to realize the vaccine function. - vaccine @@ -151335,9 +159301,7 @@ realizes some 'host of immune response role' - vaccination - A process of administering a vaccine in vivo to a recipient (e.g., human) with the intent to invoke a protective or therapeutic adaptive immune response. - + Process of administering a vaccine in vivo to a recipient (e.g., a human), with the intent to invoke a protective or therapeutic adaptive immune response. vaccination @@ -151390,8 +159354,11 @@ realizes some 'host of immune response role' failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + The term was initially used in an attempt to structure part of the ontology, but in retrospect failed to do a good job. + Terms created as placeholders with the expectation of being permanent should instead be deprecated using the "placeholder removed" (obo:IAO_0000226) justification. Person:Alan Ruttenberg + + failed exploratory term @@ -151415,7 +159382,7 @@ realizes some 'host of immune response role' organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release + The term was created to ease viewing/sorting terms for development purposes, but will not be included in a release. PERSON:Alan Ruttenberg organizational term @@ -151488,6 +159455,10 @@ realizes some 'host of immune response role' placeholder removed + The term was created to temporarily stand in for a semantic purpose, but is no longer needed, typically due to another permanent term being defined. + This reason is appropriate for a temporary term even if no permanent term is defined; for example if the need for the term no longer exists. If a permanent (replacement) term is defined, the deprecated term should reference the replacement with IAO:0100001. If no replacement is defined, it may be appropriate to reference alternative terms with oboInOwl:consider. + + placeholder removed @@ -151498,7 +159469,10 @@ realizes some 'host of immune response role' terms merged - An editor note should explain what were the merged terms and the reason for the merge. + The term has been combined with one or more other terms to create a more encompassing (merged) term. + The deprecated term should reference the merged term with obo:IAO_0100001. The replacement term should reference the original terms as sources using obo:RO_0001000 (derives_from). An editor note should explain what were the merged terms and the reason for the merge. + + terms merged @@ -151509,7 +159483,10 @@ realizes some 'host of immune response role' term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + The term has been replaced by a term imported from another ontology. + This is to be used when the original term has been replaced by a term imported from an other ontology. The deprecated term should reference the imported term with obo:IAO_0100001. + + term imported @@ -151520,7 +159497,10 @@ realizes some 'host of immune response role' term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + The term has been split into two or more new terms. + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split. The deprecated term should reference the replacement terms with obo:IAO_0100001. + + term split @@ -154934,10 +162914,12 @@ realizes some 'host of immune response role' The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. + This obsolesence reason should be used conservatively. Typical valid examples in disease ontologies are: unnecessary class grouping; mistaked creation of a disease associated to a phenotype. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 + + out of scope @@ -155625,12 +163607,6 @@ realizes some 'host of immune response role' microgram per liter - - - - - - @@ -155642,25 +163618,6 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - Person:Alan Ruttenberg - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - - - - To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) - - - - - - To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) - - geographic location A reference to a place on the Earth, by its name or by its geographical location. @@ -155678,48 +163635,16 @@ realizes some 'host of immune response role' /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + @@ -155742,198 +163667,9 @@ realizes some 'host of immune response role' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff --git a/src/ontology/tmp/ogms-preprocess.owl b/src/ontology/tmp/ogms-preprocess.owl index 03e7985..44a561d 100644 --- a/src/ontology/tmp/ogms-preprocess.owl +++ b/src/ontology/tmp/ogms-preprocess.owl @@ -1,52 +1,1176 @@ Prefix(:=) -Prefix(dce:=) +Prefix(dc:=) +Prefix(obo:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) +Prefix(foaf:=) +Prefix(rdf1:=) Prefix(rdfs:=) -Prefix(dcterms:=) +Prefix(terms:=) +Prefix(protege:=) +Prefix(oboInOwl:=) Ontology( Import() +Import() Import() Import() Import() +Import() Import() -Annotation(dcterms:description "None") -Annotation(dcterms:license ) -Annotation(dcterms:title "The Ontology for General Medical Science") - -Declaration(Class()) -Declaration(AnnotationProperty(dcterms:description)) -Declaration(AnnotationProperty(dcterms:license)) -Declaration(AnnotationProperty(dcterms:title)) +Annotation(dc:contributor "Matthew Diller"@en) +Annotation(dc:creator "Alan Ruttenberg") +Annotation(dc:creator "Albert Goldfain") +Annotation(dc:creator "Anand Kumar") +Annotation(dc:creator "Barry Smith") +Annotation(dc:creator "Bill Hogan") +Annotation(dc:creator "Brian Aevermann") +Annotation(dc:creator "Cornelius Rosse") +Annotation(dc:creator "Daniel Merico") +Annotation(dc:creator "Jie Zheng") +Annotation(dc:creator "Lindsay Cowell") +Annotation(dc:creator "Richard Scheuermann") +Annotation(dc:creator "Sivaram Arabandi") +Annotation(dc:creator "Werner Ceusters") +Annotation(dc:date "2009-08-07") +Annotation(dc:description "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. + +OGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."@en) +Annotation(dc:title "Ontology for General Medical Science") +Annotation(terms:license "http://creativecommons.org/licenses/by/4.0/") +Annotation(rdfs:comment "The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. + +The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl + +The OGMS developer site is https://github.com/OGMS/ogms + +If you are interested in participating in the development of OGMS, please send email to matthew.diller@nih.gov"@en) + +Declaration(Class(obo:BFO_0000001)) +Declaration(Class(obo:BFO_0000015)) +Declaration(Class(obo:BFO_0000016)) +Declaration(Class(obo:BFO_0000019)) +Declaration(Class(obo:BFO_0000023)) +Declaration(Class(obo:BFO_0000031)) +Declaration(Class(obo:BFO_0000040)) +Declaration(Class(obo:IAO_0000027)) +Declaration(Class(obo:IAO_0000030)) +Declaration(Class(obo:OBI_0000278)) +Declaration(Class(obo:OGMS_0000014)) +Declaration(Class(obo:OGMS_0000015)) +Declaration(Class(obo:OGMS_0000016)) +Declaration(Class(obo:OGMS_0000017)) +Declaration(Class(obo:OGMS_0000018)) +Declaration(Class(obo:OGMS_0000019)) +Declaration(Class(obo:OGMS_0000020)) +Declaration(Class(obo:OGMS_0000022)) +Declaration(Class(obo:OGMS_0000023)) +Declaration(Class(obo:OGMS_0000024)) +Declaration(Class(obo:OGMS_0000025)) +Declaration(Class(obo:OGMS_0000026)) +Declaration(Class(obo:OGMS_0000027)) +Declaration(Class(obo:OGMS_0000028)) +Declaration(Class(obo:OGMS_0000029)) +Declaration(Class(obo:OGMS_0000030)) +Declaration(Class(obo:OGMS_0000031)) +Declaration(Class(obo:OGMS_0000032)) +Declaration(Class(obo:OGMS_0000033)) +Declaration(Class(obo:OGMS_0000034)) +Declaration(Class(obo:OGMS_0000035)) +Declaration(Class(obo:OGMS_0000037)) +Declaration(Class(obo:OGMS_0000038)) +Declaration(Class(obo:OGMS_0000039)) +Declaration(Class(obo:OGMS_0000040)) +Declaration(Class(obo:OGMS_0000045)) +Declaration(Class(obo:OGMS_0000046)) +Declaration(Class(obo:OGMS_0000047)) +Declaration(Class(obo:OGMS_0000050)) +Declaration(Class(obo:OGMS_0000051)) +Declaration(Class(obo:OGMS_0000055)) +Declaration(Class(obo:OGMS_0000056)) +Declaration(Class(obo:OGMS_0000057)) +Declaration(Class(obo:OGMS_0000059)) +Declaration(Class(obo:OGMS_0000060)) +Declaration(Class(obo:OGMS_0000061)) +Declaration(Class(obo:OGMS_0000063)) +Declaration(Class(obo:OGMS_0000064)) +Declaration(Class(obo:OGMS_0000065)) +Declaration(Class(obo:OGMS_0000066)) +Declaration(Class(obo:OGMS_0000067)) +Declaration(Class(obo:OGMS_0000069)) +Declaration(Class(obo:OGMS_0000070)) +Declaration(Class(obo:OGMS_0000071)) +Declaration(Class(obo:OGMS_0000073)) +Declaration(Class(obo:OGMS_0000074)) +Declaration(Class(obo:OGMS_0000077)) +Declaration(Class(obo:OGMS_0000078)) +Declaration(Class(obo:OGMS_0000079)) +Declaration(Class(obo:OGMS_0000080)) +Declaration(Class(obo:OGMS_0000081)) +Declaration(Class(obo:OGMS_0000082)) +Declaration(Class(obo:OGMS_0000083)) +Declaration(Class(obo:OGMS_0000084)) +Declaration(Class(obo:OGMS_0000085)) +Declaration(Class(obo:OGMS_0000086)) +Declaration(Class(obo:OGMS_0000087)) +Declaration(Class(obo:OGMS_0000088)) +Declaration(Class(obo:OGMS_0000089)) +Declaration(Class(obo:OGMS_0000090)) +Declaration(Class(obo:OGMS_0000091)) +Declaration(Class(obo:OGMS_0000092)) +Declaration(Class(obo:OGMS_0000093)) +Declaration(Class(obo:OGMS_0000094)) +Declaration(Class(obo:OGMS_0000095)) +Declaration(Class(obo:OGMS_0000096)) +Declaration(Class(obo:OGMS_0000097)) +Declaration(Class(obo:OGMS_0000098)) +Declaration(Class(obo:OGMS_0000099)) +Declaration(Class(obo:OGMS_0000100)) +Declaration(Class(obo:OGMS_0000101)) +Declaration(Class(obo:OGMS_0000102)) +Declaration(Class(obo:OGMS_0000103)) +Declaration(Class(obo:OGMS_0000104)) +Declaration(Class(obo:OGMS_0000105)) +Declaration(Class(obo:OGMS_0000106)) +Declaration(Class(obo:OGMS_0000107)) +Declaration(Class(obo:OGMS_0000108)) +Declaration(Class(obo:OGMS_0000109)) +Declaration(Class(obo:OGMS_0000110)) +Declaration(Class(obo:OGMS_0000111)) +Declaration(Class(obo:OGMS_0000112)) +Declaration(Class(obo:OGMS_0000113)) +Declaration(Class(obo:OGMS_0000114)) +Declaration(Class(obo:OGMS_0000115)) +Declaration(Class(obo:OGMS_0000116)) +Declaration(Class(obo:OGMS_0000117)) +Declaration(Class(obo:OGMS_0000118)) +Declaration(Class(obo:OGMS_0000119)) +Declaration(Class(obo:OGMS_0000120)) +Declaration(Class(obo:OGMS_0000121)) +Declaration(Class(obo:OGMS_0000122)) +Declaration(Class(obo:OGMS_0000123)) +Declaration(Class(obo:OGMS_0000124)) +Declaration(Class(obo:OGMS_0000125)) +Declaration(Class(obo:OGMS_0000126)) +Declaration(Class(obo:OGMS_0000127)) +Declaration(Class(obo:OGMS_0000128)) +Declaration(Class(obo:OGMS_0000129)) +Declaration(Class(obo:OGMS_0000130)) +Declaration(Class(obo:OGMS_0000131)) +Declaration(Class(obo:OGMS_0000132)) +Declaration(Class(obo:OGMS_0000133)) +Declaration(Class(obo:OGMS_0000134)) +Declaration(Class(obo:OGMS_0000135)) +Declaration(Class(obo:OGMS_0000136)) +Declaration(Class(obo:OGMS_0000137)) +Declaration(Class(obo:OGMS_0000138)) +Declaration(Class(obo:OGMS_0000139)) +Declaration(Class(obo:OGMS_0000140)) +Declaration(Class(obo:OGMS_0000141)) +Declaration(Class(obo:OGMS_0000142)) +Declaration(Class(obo:OGMS_0000143)) +Declaration(Class(obo:OGMS_0000144)) +Declaration(Class(obo:OGMS_0000145)) +Declaration(Class(obo:OGMS_0000146)) +Declaration(Class(obo:OGMS_0000147)) +Declaration(Class(obo:OGMS_0000148)) +Declaration(Class(obo:OGMS_0000149)) +Declaration(Class(obo:OGMS_0000150)) +Declaration(AnnotationProperty(obo:IAO_0000115)) +Declaration(AnnotationProperty(obo:IAO_0000116)) +Declaration(AnnotationProperty(obo:IAO_0000117)) +Declaration(AnnotationProperty(obo:IAO_0000118)) +Declaration(AnnotationProperty(obo:IAO_0000119)) +Declaration(AnnotationProperty(obo:IAO_0000232)) +Declaration(AnnotationProperty(dc:creator)) +Declaration(AnnotationProperty(dc:date)) +Declaration(AnnotationProperty(dc:description)) +Declaration(AnnotationProperty(dc:publisher)) +Declaration(AnnotationProperty(dc:title)) +Declaration(AnnotationProperty(terms:license)) + + ############################ -# Annotation Properties +# Classes ############################ -# Annotation Property: dcterms:description (description) +# Class: obo:OGMS_0000014 (clinical finding) -AnnotationAssertion(rdfs:label dcterms:description "description") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000014 "A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000014 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000014 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000014 "creation date: 2010-07-19T10:18:02Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000014 "clinical finding") +SubClassOf(obo:OGMS_0000014 obo:OGMS_0000123) -# Annotation Property: dcterms:license (license) +# Class: obo:OGMS_0000015 (clinical history) -AnnotationAssertion(rdfs:label dcterms:license "license") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000015 "A series of statements representing health-relevant qualities of a patient and of a patient's family."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000015 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000015 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000015 "creation date: 2010-07-19T10:18:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000015 "clinical history") +SubClassOf(obo:OGMS_0000015 obo:OGMS_0000123) -# Annotation Property: dcterms:title (title) +# Class: obo:OGMS_0000016 (clinical picture) -AnnotationAssertion(rdfs:label dcterms:title "title") +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000016 "A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000016 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000016 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000016 "creation date: 2010-07-19T10:20:20Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000016 "clinical picture") +SubClassOf(obo:OGMS_0000016 obo:OGMS_0000123) +# Class: obo:OGMS_0000017 (clinical finding from image) +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000017 "An interpretation of an image that is the output of a clinical evaluation and supports an inference to an assertion about some quality of a patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000017 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000017 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000017 "creation date: 2009-06-23T10:21:10Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000017 "clinical finding from image"@en) +SubClassOf(obo:OGMS_0000017 obo:OGMS_0000014) -############################ -# Classes -############################ +# Class: obo:OGMS_0000018 (laboratory finding) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000018 "A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000018 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000018 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000018 "creation date: 2009-06-23T10:21:58Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000018 "laboratory finding") +SubClassOf(obo:OGMS_0000018 obo:OGMS_0000014) + +# Class: obo:OGMS_0000019 (preclinical finding) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000019 "A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000019 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000019 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000019 "creation date: 2009-06-23T10:22:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000019 "preclinical finding") +SubClassOf(obo:OGMS_0000019 obo:IAO_0000027) + +# Class: obo:OGMS_0000020 (symptom) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000020 "A process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000020 "note: defined class") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000020 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000020 "creation date: 2010-11-18T11:02:10Z +Updated: 2020-07-06") +AnnotationAssertion(rdfs:label obo:OGMS_0000020 "symptom") +SubClassOf(obo:OGMS_0000020 obo:BFO_0000015) + +# Class: obo:OGMS_0000022 (manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000022 "A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000022 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000022 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000022 "creation date: 2009-06-23T11:12:33Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000022 "manifestation of a disease") +SubClassOf(obo:OGMS_0000022 obo:BFO_0000019) + +# Class: obo:OGMS_0000023 (phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000023 "A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000023 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000023 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000023 "creation date: 2010-07-19T11:13:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000023 "phenotype") +SubClassOf(obo:OGMS_0000023 obo:BFO_0000019) + +# Class: obo:OGMS_0000024 (obsolete_sign) + +AnnotationAssertion(rdfs:comment obo:OGMS_0000024 "The class sign has been replaced by three seperate classes which reflect the different types of signs possible.") +AnnotationAssertion(rdfs:label obo:OGMS_0000024 "obsolete_sign") +AnnotationAssertion(owl:deprecated obo:OGMS_0000024 "true"^^xsd:boolean) + +# Class: obo:OGMS_0000025 (clinical manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000025 "A manifestation of a disease that is detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000025 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000025 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000025 "creation date: 2009-06-23T11:15:43Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000025 "clinical manifestation of a disease") +SubClassOf(obo:OGMS_0000025 obo:OGMS_0000022) + +# Class: obo:OGMS_0000026 (preclinical manifestation of a disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000026 "A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000026 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000026 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000026 "creation date: 2009-06-23T11:16:50Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000026 "preclinical manifestation of a disease") +SubClassOf(obo:OGMS_0000026 obo:OGMS_0000022) + +# Class: obo:OGMS_0000027 (clinical phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000027 "A clinically abnormal phenotype."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000027 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000027 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000027 "creation date: 2009-06-23T11:18:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000027 "clinical phenotype") +SubClassOf(obo:OGMS_0000027 obo:OGMS_0000023) + +# Class: obo:OGMS_0000028 (disease phenotype) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000028 "A clinically abnormal phenotype that is characteristic of a single disease."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000028 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000028 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000028 "creation date: 2009-06-23T11:18:39Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000028 "disease phenotype") +SubClassOf(obo:OGMS_0000028 obo:OGMS_0000023) + +# Class: obo:OGMS_0000029 (vital sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000029 "A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000029 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000029 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000029 "creation date: 2009-06-23T11:19:17Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000029 "vital sign") +SubClassOf(obo:OGMS_0000029 obo:OGMS_0000129) + +# Class: obo:OGMS_0000030 (predisposition to disease of type X) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000030 "A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000030 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000030 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000030 "creation date: 2009-06-23T11:20:25Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000030 "predisposition to disease of type X") +SubClassOf(obo:OGMS_0000030 obo:BFO_0000016) + +# Class: obo:OGMS_0000031 (disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000031 "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000031 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000031 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000031 "creation date: 2009-06-23T11:21:20Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000031 "disease") +SubClassOf(obo:OGMS_0000031 obo:BFO_0000016) + +# Class: obo:OGMS_0000032 (homeostasis) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000032 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000032 "creation date: 2009-06-23T11:22:01Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000032 "homeostasis") +SubClassOf(obo:OGMS_0000032 obo:BFO_0000016) + +# Class: obo:OGMS_0000033 (genetic predisposition to disease of type X) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000033 "A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000033 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000033 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000033 "creation date: 2009-06-23T11:23:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000033 "genetic predisposition to disease of type X") +SubClassOf(obo:OGMS_0000033 obo:OGMS_0000030) + +# Class: obo:OGMS_0000034 (acquired genetic disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000034 "A disease whose physical basis is an acquired genetic disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000034 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000034 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000034 "creation date: 2009-06-23T11:24:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000034 "acquired genetic disease") +SubClassOf(obo:OGMS_0000034 obo:OGMS_0000031) + +# Class: obo:OGMS_0000035 (constitutional genetic disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000035 "A disease whose physical basis is a constitutional genetic disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000035 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000035 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000035 "creation date: 2009-06-23T11:24:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000035 "constitutional genetic disease") +SubClassOf(obo:OGMS_0000035 obo:OGMS_0000031) + +# Class: obo:OGMS_0000037 (altered homeostasis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000037 "Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000037 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000037 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000037 "creation date: 2009-06-23T11:26:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000037 "altered homeostasis") +SubClassOf(obo:OGMS_0000037 obo:OGMS_0000032) + +# Class: obo:OGMS_0000038 (normal homeostasis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000038 "Homeostasis of a type that is not clinically abnormal."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000038 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000038 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000038 "creation date: 2009-06-23T11:27:28Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000038 "normal homeostasis") +SubClassOf(obo:OGMS_0000038 obo:OGMS_0000032) + +# Class: obo:OGMS_0000039 (configuration) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000039 "A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000039 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000039 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000039 "creation date: 2009-06-23T11:36:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000039 "configuration") +SubClassOf(obo:OGMS_0000039 obo:BFO_0000019) + +# Class: obo:OGMS_0000040 (pathological physical configuration) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000040 "A configuration which deviates in some way from a canonical configuration for a particular organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000040 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000040 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000040 "creation date: 2009-06-23T11:36:58Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000040 "pathological physical configuration") +SubClassOf(obo:OGMS_0000040 obo:OGMS_0000039) + +# Class: obo:OGMS_0000045 (disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000045 "A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000045 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000045 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000045 "creation date: 2009-06-23T11:39:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000045 "disorder") +SubClassOf(obo:OGMS_0000045 obo:BFO_0000040) + +# Class: obo:OGMS_0000046 (epigenetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000046 "A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000046 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000046 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000046 "creation date: 2009-06-23T11:40:27Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000046 "epigenetic disorder") +SubClassOf(obo:OGMS_0000046 obo:OGMS_0000045) + +# Class: obo:OGMS_0000047 (genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000047 "A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000047 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000047 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000047 "creation date: 2009-06-23T11:41:14Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000047 "genetic disorder") +SubClassOf(obo:OGMS_0000047 obo:OGMS_0000045) + +# Class: obo:OGMS_0000050 (acquired genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000050 "A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000050 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000050 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000050 "creation date: 2009-06-23T11:43:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000050 "acquired genetic disorder") +SubClassOf(obo:OGMS_0000050 obo:OGMS_0000047) + +# Class: obo:OGMS_0000051 (constitutional genetic disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000051 "A genetic disorder inherited during conception that is part of all cells in the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000051 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000051 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000051 "creation date: 2009-06-23T11:43:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000051 "constitutional genetic disorder") +SubClassOf(obo:OGMS_0000051 obo:OGMS_0000047) + +# Class: obo:OGMS_0000055 (clinical history taking) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000055 "A health care process in which a clinician elicits a description of previous sign and symptoms of disease from a patient or from a third party who is reporting on behalf of the patient."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000055 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000055 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000055 "creation date: 2009-06-23T11:49:16Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000055 "clinical history taking") +SubClassOf(obo:OGMS_0000055 obo:OGMS_0000108) + +# Class: obo:OGMS_0000056 (clinical laboratory test) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000056 "A measurement assay that has as input a patient-derived specimen and as output a data item that is about a quality of the specimen."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000056 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000056 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000056 "creation date: 2009-06-23T11:49:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000056 "clinical laboratory test") +SubClassOf(obo:OGMS_0000056 obo:OGMS_0000108) + +# Class: obo:OGMS_0000057 (physical examination) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000057 "A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000057 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000057 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000057 "creation date: 2010-07-19T11:50:18Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000057 "physical examination") +SubClassOf(obo:OGMS_0000057 obo:OGMS_0000108) + +# Class: obo:OGMS_0000059 (etiological process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000059 "A process in an organism that leads to a subsequent disorder."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000059 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000059 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000059 "creation date: 2009-06-23T11:53:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000059 "etiological process") +SubClassOf(obo:OGMS_0000059 obo:BFO_0000015) + +# Class: obo:OGMS_0000060 (bodily process) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000060 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000060 "creation date: 2009-06-23T11:53:49Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000060 "bodily process") +SubClassOf(obo:OGMS_0000060 obo:BFO_0000015) + +# Class: obo:OGMS_0000061 (pathological bodily process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000061 "A bodily process that is clinically abnormal."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000061 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000061 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000061 "creation date: 2009-06-23T11:54:29Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000061 "pathological bodily process") +SubClassOf(obo:OGMS_0000061 obo:OGMS_0000060) + +# Class: obo:OGMS_0000063 (disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000063 "The totality of all processes through which a given disease instance is realized."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000063 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000063 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000063 "creation date: 2009-06-23T11:55:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000063 "disease course") +SubClassOf(obo:OGMS_0000063 obo:BFO_0000015) + +# Class: obo:OGMS_0000064 (chronic disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000064 "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000064 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000064 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000064 "creation date: 2009-06-23T11:56:26Z + +10212020 + +for definition use: +http://purl.obolibrary.org/obo/PATO_0001863") +AnnotationAssertion(rdfs:label obo:OGMS_0000064 "chronic disease course") +SubClassOf(obo:OGMS_0000064 obo:OGMS_0000063) + +# Class: obo:OGMS_0000065 (progressive disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000065 "A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000065 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000065 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000065 "creation date: 2009-06-23T11:57:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000065 "progressive disease course") +SubClassOf(obo:OGMS_0000065 obo:OGMS_0000063) + +# Class: obo:OGMS_0000066 (transient disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000066 "A disease course that terminates in a return to normal homeostasis."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000066 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000066 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000066 "creation date: 2009-06-23T11:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000066 "transient disease course") +SubClassOf(obo:OGMS_0000066 obo:OGMS_0000063) + +# Class: obo:OGMS_0000067 (_undefined primitive term) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000067 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000067 "creation date: 2009-06-23T11:58:22Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000067 "_undefined primitive term") +SubClassOf(obo:OGMS_0000067 obo:BFO_0000001) + +# Class: obo:OGMS_0000069 (clinically abnormal) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000069 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000069 "creation date: 2009-06-23T11:59:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000069 "clinically abnormal") +SubClassOf(obo:OGMS_0000069 obo:OGMS_0000067) + +# Class: obo:OGMS_0000070 (physical basis) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000070 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000070 "creation date: 2009-06-23T12:00:09Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000070 "physical basis") +SubClassOf(obo:OGMS_0000070 obo:OGMS_0000067) + +# Class: obo:OGMS_0000071 (realization) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000071 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000071 "creation date: 2009-06-23T12:00:39Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000071 "realization") +SubClassOf(obo:OGMS_0000071 obo:OGMS_0000067) + +# Class: obo:OGMS_0000073 (diagnosis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000073 "The representation of a conclusion of a diagnostic process."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000073 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000073 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000073 "creation date: 2009-06-23T12:42:23Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000073 "diagnosis") +SubClassOf(obo:OGMS_0000073 obo:OGMS_0000123) + +# Class: obo:OGMS_0000074 (normal value) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000074 "A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000074 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000074 "http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000074 "creation date: 2009-06-26T10:31:34Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000074 "normal value") +SubClassOf(obo:OGMS_0000074 obo:BFO_0000031) + +# Class: obo:OGMS_0000077 (pathological formation) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000077 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000077 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000077 "creation date: 2009-07-13T02:14:59Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000077 "pathological formation") +SubClassOf(obo:OGMS_0000077 obo:BFO_0000040) + +# Class: obo:OGMS_0000078 (pathological anatomical structure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000078 "An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000078 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000078 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000078 "creation date: 2009-07-13T02:14:05Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000078 "pathological anatomical structure") +SubClassOf(obo:OGMS_0000078 obo:BFO_0000040) + +# Class: obo:OGMS_0000079 (portion of pathological body substance) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000079 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000079 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000079 "creation date: 2009-07-13T02:15:17Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000079 "portion of pathological body substance") +SubClassOf(obo:OGMS_0000079 obo:BFO_0000040) + +# Class: obo:OGMS_0000080 (pathological transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000080 "A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000080 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000080 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000080 "creation date: 2009-07-13T02:17:07Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000080 "pathological transformation") +SubClassOf(obo:OGMS_0000080 obo:OGMS_0000061) + +# Class: obo:OGMS_0000081 (pathological derivation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000081 "A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000081 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000081 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000081 "creation date: 2009-07-13T02:17:24Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000081 "pathological derivation") +SubClassOf(obo:OGMS_0000081 obo:OGMS_0000061) + +# Class: obo:OGMS_0000082 (pathological invasion) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000082 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000082 "http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000082 "creation date: 2009-07-13T02:17:47Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000082 "pathological invasion") +SubClassOf(obo:OGMS_0000082 obo:OGMS_0000061) + +# Class: obo:OGMS_0000083 (physical examination finding) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000083 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000083 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000083 "physical examination finding") +SubClassOf(obo:OGMS_0000083 obo:OGMS_0000014) + +# Class: obo:OGMS_0000084 (organism population) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000084 "An aggregate of organisms of the same type."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000084 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000084 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000084 "organism population") +SubClassOf(obo:OGMS_0000084 obo:BFO_0000040) + +# Class: obo:OGMS_0000085 (pain) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000085 "A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000085 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000085 "https://philarchive.org/rec/SMITAO-12") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000085 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000085 "pain") +SubClassOf(obo:OGMS_0000085 obo:OGMS_0000020) + +# Class: obo:OGMS_0000086 (syndrome) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000086 "A pattern of signs and symptoms that typically co-occur."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000086 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000086 "creation date: 2009-11-24T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000086 "syndrome") +SubClassOf(obo:OGMS_0000086 obo:BFO_0000019) + +# Class: obo:OGMS_0000087 (extended organism) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000087 "An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000087 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000087 "creation date: 2010-01-25T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000087 "extended organism") +SubClassOf(obo:OGMS_0000087 obo:BFO_0000040) + +# Class: obo:OGMS_0000088 (patient symptom report) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000088 "A communication from a patient about something they perceive as being abnormal about their body or life."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000088 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000088 "creation date: 2010-01-25T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000088 "patient symptom report") +SubClassOf(obo:OGMS_0000088 obo:IAO_0000030) + +# Class: obo:OGMS_0000089 (congenital disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000089 "A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000089 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000089 "congenital malformation") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000089 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000089 "congenital disorder") +SubClassOf(obo:OGMS_0000089 obo:BFO_0000040) + +# Class: obo:OGMS_0000090 (treatment) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000090 "A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000090 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000090 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:OGMS_0000090 "medical intervention"@en) +AnnotationAssertion(rdfs:label obo:OGMS_0000090 "treatment") +SubClassOf(obo:OGMS_0000090 obo:OGMS_0000096) + +# Class: obo:OGMS_0000091 (convalescence) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000091 "A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000091 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000091 "creation date: 2010-03-31T04:51:11Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000091 "convalescence") +SubClassOf(obo:OGMS_0000091 obo:BFO_0000015) + +# Class: obo:OGMS_0000092 (life course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000092 "A process which has as parts all the processes in which a given organism is participant."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000092 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000092 "creation date: 2010-03-31T04:51:11Z + +EDIT: 10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000092 "life course") +SubClassOf(obo:OGMS_0000092 obo:BFO_0000015) + +# Class: obo:OGMS_0000093 (prognosis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000093 "A hypothesis about some future part of a disease course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000093 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000093 "creation date: 2010-03-31T12:42:23Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000093 "prognosis") +SubClassOf(obo:OGMS_0000093 obo:IAO_0000027) + +# Class: obo:OGMS_0000094 (acute disease course) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000094 "A disease course with an acute onset"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000094 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000094 "creation date: 2010-07-19T11:57:44Z + +10212020 + +for definition use + +http://purl.obolibrary.org/obo/PATO_0000389") +AnnotationAssertion(rdfs:label obo:OGMS_0000094 "acute disease course") +SubClassOf(obo:OGMS_0000094 obo:OGMS_0000063) + +# Class: obo:OGMS_0000095 (inflammatory process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000095 "A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000095 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000095 "creation date: 2010-07-19T11:57:44Z + +Updated: 10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000095 "inflammatory process") +SubClassOf(obo:OGMS_0000095 obo:OGMS_0000060) + +# Class: obo:OGMS_0000096 (health care process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000096 "A planned process with the objective to improve or maintain the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000096 "Albert Goldfain +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000096 "creation date: 2011-02-21T09:57:44Z +editor date: 2017-04-18") +AnnotationAssertion(rdfs:label obo:OGMS_0000096 "health care process") +SubClassOf(obo:OGMS_0000096 obo:COB_0000035) + +# Class: obo:OGMS_0000097 (health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000097 "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter"@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000097 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000097 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000097 "health care encounter") +SubClassOf(obo:OGMS_0000097 obo:OGMS_0000096) + +# Class: obo:OGMS_0000098 (hospitalization) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000098 "A health care process in which a person is admitted to a hospital for treatment, diagnosis, or monitoring."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000098 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000098 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000098 "hospitalization") +SubClassOf(obo:OGMS_0000098 obo:OGMS_0000096) + +# Class: obo:OGMS_0000099 (outpatient encounter) + +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000099 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000099 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000099 "outpatient encounter") +SubClassOf(obo:OGMS_0000099 obo:OGMS_0000097) + +# Class: obo:OGMS_0000100 (inpatient encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000100 "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000100 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000100 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000100 "inpatient encounter") +SubClassOf(obo:OGMS_0000100 obo:OGMS_0000097) + +# Class: obo:OGMS_0000101 (emergency department encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000101 "A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000101 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000101 "creation date: 2011-02-21T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000101 "emergency department encounter") +SubClassOf(obo:OGMS_0000101 obo:OGMS_0000097) + +# Class: obo:OGMS_0000102 (injury) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000102 "A disorder that involves some structural damage that is immediately caused by a catastrophic external force."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000102 "At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. + +Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.") +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000102 "Albert Goldfain +Sagar Jain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000102 "creation date: 2011-09-20T09:57:44Z +edited date: 30 SEPT 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000102 "injury") +SubClassOf(obo:OGMS_0000102 obo:OGMS_0000045) + +# Class: obo:OGMS_0000103 (disease prophylaxis) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000103 "A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder."@en) +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000103 "Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question.") +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000103 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000103 "creation date: 2011-09-20T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000103 "disease prophylaxis") +SubClassOf(obo:OGMS_0000103 obo:COB_0000035) + +# Class: obo:OGMS_0000104 (diagnostic process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000104 "A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output)."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000104 "Albert Goldfain") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000104 "creation date: 2011-09-20T09:57:44Z") +AnnotationAssertion(rdfs:label obo:OGMS_0000104 "diagnostic process") +SubClassOf(obo:OGMS_0000104 obo:OGMS_0000096) + +# Class: obo:OGMS_0000105 (relapse) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000105 "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease.") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000105 "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000105 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000105 "recurrent") +AnnotationAssertion(dc:date obo:OGMS_0000105 "10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000105 "relapse"@en) +SubClassOf(obo:OGMS_0000105 obo:OBI_0000278) + +# Class: obo:OGMS_0000106 (remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000106 "A disease stage which is characterized by the lack of a manifestation of a disease") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000106 "A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000106 "Albert Goldfain +Richard Scheuermann +Sagar Jain") +AnnotationAssertion(dc:date obo:OGMS_0000106 "10 NOV 2015") +AnnotationAssertion(rdfs:label obo:OGMS_0000106 "remission"@en) +SubClassOf(obo:OGMS_0000106 obo:OBI_0000278) + +# Class: obo:OGMS_0000107 (ancillary health care process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000107 "A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient.") +AnnotationAssertion(dc:date obo:OGMS_0000107 "2017-04-18") +AnnotationAssertion(dc:publisher obo:OGMS_0000107 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000107 "ancillary health care process") +SubClassOf(obo:OGMS_0000107 obo:COB_0000035) + +# Class: obo:OGMS_0000108 (health care process assay) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000108 "A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.") +AnnotationAssertion(dc:date obo:OGMS_0000108 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000108 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000108 "health care process assay") +SubClassOf(obo:OGMS_0000108 obo:OGMS_0000096) + +# Class: obo:OGMS_0000109 (health care process biomaterial transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000109 "A health care process which results in physical changes in a specified input material") +AnnotationAssertion(dc:date obo:OGMS_0000109 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000109 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000109 "health care process biomaterial transformation") +SubClassOf(obo:OGMS_0000109 obo:OGMS_0000096) + +# Class: obo:OGMS_0000110 (health care process data transformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000110 "A health care process that produces output from input data") +AnnotationAssertion(dc:date obo:OGMS_0000110 "creation: 16MAY2017") +AnnotationAssertion(dc:publisher obo:OGMS_0000110 "Sagar Jain") +AnnotationAssertion(rdfs:label obo:OGMS_0000110 "health care process data transformation") +SubClassOf(obo:OGMS_0000110 obo:OGMS_0000096) + +# Class: obo:OGMS_0000111 (prophylactic treatment) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000111 "A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000111 "Creation date: 2018-11-27") +AnnotationAssertion(oboInOwl:hasExactSynonym obo:OGMS_0000111 "preventive intervention"@en) +AnnotationAssertion(rdfs:label obo:OGMS_0000111 "prophylactic treatment"@en) +SubClassOf(obo:OGMS_0000111 obo:OGMS_0000090) + +# Class: obo:OGMS_0000112 (therapeutic procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000112 "A treatment whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder or pathological process.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000112 "Creation data: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000112 "therapeutic procedure"@en) +SubClassOf(obo:OGMS_0000112 obo:OGMS_0000090) + +# Class: obo:OGMS_0000113 (chemotherapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000113 "A therapeutic procedure that uses synthetic or naturally-occurring chemicals") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000113 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000113 "chemotherapy procedure"@en) +SubClassOf(obo:OGMS_0000113 obo:OGMS_0000112) + +# Class: obo:OGMS_0000114 (immunotherapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000114 "A therapeutic procedure that uses immune system derived entities.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000114 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000114 "immunotherapy procedure"@en) +SubClassOf(obo:OGMS_0000114 obo:OGMS_0000112) + +# Class: obo:OGMS_0000115 (physical therapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000115 "A therapeutic procedure that uses physical conditioning") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000115 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000115 "physical therapy procedure"@en) +SubClassOf(obo:OGMS_0000115 obo:OGMS_0000112) + +# Class: obo:OGMS_0000116 (radiation therapy procedure) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000116 "A therapeutic procedure that uses radiation.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000116 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000116 "radiation therapy procedure"@en) +SubClassOf(obo:OGMS_0000116 obo:OGMS_0000112) + +# Class: obo:OGMS_0000117 (asymptomatic) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000117 "A disease stage characterized by the lack of symptoms associated with a given disease") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000117 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000117 "asymptomatic"@en) +SubClassOf(obo:OGMS_0000117 obo:OBI_0000278) + +# Class: obo:OGMS_0000118 (onset) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000118 "A disease stage that marks the beginning of a disease") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000118 "creation date 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000118 "onset"@en) +SubClassOf(obo:OGMS_0000118 obo:OBI_0000278) + +# Class: obo:OGMS_0000119 (acute onset) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000119 "A disease stage with a rapid unfolding of signs and symptoms") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000119 "creation date 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000119 "acute onset"@en) +SubClassOf(obo:OGMS_0000119 obo:OGMS_0000118) + +# Class: obo:OGMS_0000120 (complete remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000120 "A remission which is characterized by a prolonged lack of all manifestations of a disease") +AnnotationAssertion(rdfs:label obo:OGMS_0000120 "complete remission"@en) +SubClassOf(obo:OGMS_0000120 obo:OGMS_0000106) + +# Class: obo:OGMS_0000121 (partial remission) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000121 "A remission which is characterized by a prolonged lack of some manifestations of a disease") +AnnotationAssertion(rdfs:label obo:OGMS_0000121 "partial remission"@en) +SubClassOf(obo:OGMS_0000121 obo:OGMS_0000106) + +# Class: obo:OGMS_0000122 (recovered from disease) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000122 "A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000122 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000122 "recovered from disease"@en) +SubClassOf(obo:OGMS_0000122 obo:BFO_0000019) + +# Class: obo:OGMS_0000123 (clinical data item) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000123 "A data item that is about a patient and is the specified output of a health care process assay or diagnostic process") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000123 "creation date: 2018-11-27") +AnnotationAssertion(rdfs:label obo:OGMS_0000123 "clinical data item"@en) +SubClassOf(obo:OGMS_0000123 obo:IAO_0000027) + +# Class: obo:OGMS_0000124 (routine health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000124 "A health care encounter that is regularly scheduled for the purpose of health monitoring.") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000124 "routine clinical visit") +AnnotationAssertion(rdfs:label obo:OGMS_0000124 "routine health care encounter") +SubClassOf(obo:OGMS_0000124 obo:OGMS_0000099) + +# Class: obo:OGMS_0000125 (follow-up health care encounter) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000125 "A health care encounter that is scheduled for the purpose of assessing a known set of specific issues") +AnnotationAssertion(obo:IAO_0000118 obo:OGMS_0000125 "follow-up clinical visit") +AnnotationAssertion(rdfs:label obo:OGMS_0000125 "follow-up health care encounter") +SubClassOf(obo:OGMS_0000125 obo:OGMS_0000099) + +# Class: obo:OGMS_0000126 (congenital infection) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000126 "A congenital disorder arising as a result of an infectious process") +AnnotationAssertion(rdfs:label obo:OGMS_0000126 "congenital infection") +SubClassOf(obo:OGMS_0000126 obo:OGMS_0000089) + +# Class: obo:OGMS_0000127 (drug induced congenital malformation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000127 "A congenital disorder arising as a result of a drug exposure causing an anatomical abnormality") +AnnotationAssertion(rdfs:label obo:OGMS_0000127 "drug induced congenital malformation") +SubClassOf(obo:OGMS_0000127 obo:OGMS_0000089) + +# Class: obo:OGMS_0000128 (congenital process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000128 "A pathological bodily process that occurs in the fetus during fetal development") +AnnotationAssertion(rdfs:label obo:OGMS_0000128 "congenital process") +SubClassOf(obo:OGMS_0000128 obo:OGMS_0000061) + +# Class: obo:OGMS_0000129 (physical sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000129 "An abnormal material entity that is part of a patient and hypothesized to be clinically relevant.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000129 "Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension") +AnnotationAssertion(rdfs:label obo:OGMS_0000129 "physical sign") +SubClassOf(obo:OGMS_0000129 obo:BFO_0000040) + +# Class: obo:OGMS_0000130 (allergic disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000130 "The process in which an allergic disease unfolds.") +AnnotationAssertion(rdfs:label obo:OGMS_0000130 "allergic disease process") +SubClassOf(obo:OGMS_0000130 obo:OGMS_0000061) + +# Class: obo:OGMS_0000131 (cancer process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000131 "The process in which cancer unfolds") +AnnotationAssertion(rdfs:label obo:OGMS_0000131 "cancer process") +SubClassOf(obo:OGMS_0000131 obo:OGMS_0000061) + +# Class: obo:OGMS_0000132 (autoimmune disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000132 "The process in which an autoimmune disease unfolds.") +AnnotationAssertion(rdfs:label obo:OGMS_0000132 "autoimmune disease process") +SubClassOf(obo:OGMS_0000132 obo:OGMS_0000061) + +# Class: obo:OGMS_0000133 (progression stage) + +AnnotationAssertion(rdfs:label obo:OGMS_0000133 "progression stage") +SubClassOf(obo:OGMS_0000133 obo:OBI_0000278) + +# Class: obo:OGMS_0000134 (cancer progression stage) + +AnnotationAssertion(rdfs:label obo:OGMS_0000134 "cancer progression stage") +SubClassOf(obo:OGMS_0000134 obo:OGMS_0000133) + +# Class: obo:OGMS_0000135 (cancer progression stage 0) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000135 "A cancer progression stage characterized by abnormal cellular growth contained within normal tissue boundaries (e.g. carcinoma in situ).") +AnnotationAssertion(rdfs:label obo:OGMS_0000135 "cancer progression stage 0") +SubClassOf(obo:OGMS_0000135 obo:OGMS_0000134) + +# Class: obo:OGMS_0000136 (cancer progression stage I) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000136 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass.") +AnnotationAssertion(rdfs:label obo:OGMS_0000136 "cancer progression stage I") +SubClassOf(obo:OGMS_0000136 obo:OGMS_0000134) + +# Class: obo:OGMS_0000137 (cancer progression stage II) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000137 "A cancer progression stage characterized by abnormal cellular growth that extends well beyond normal local tissue boundaries as a contiguous mass.") +AnnotationAssertion(rdfs:label obo:OGMS_0000137 "cancer progression stage II") +SubClassOf(obo:OGMS_0000137 obo:OGMS_0000134) + +# Class: obo:OGMS_0000138 (cancer progression stage III) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000138 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to one or more regional draining lymph nodes.") +AnnotationAssertion(rdfs:label obo:OGMS_0000138 "cancer progression stage III") +SubClassOf(obo:OGMS_0000138 obo:OGMS_0000134) + +# Class: obo:OGMS_0000139 (cancer progression stage IV) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000139 "A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to other distant tissues besides lymph nodes.") +AnnotationAssertion(rdfs:label obo:OGMS_0000139 "cancer progression stage IV") +SubClassOf(obo:OGMS_0000139 obo:OGMS_0000134) + +# Class: obo:OGMS_0000140 (infectious disease process) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000140 "The process in which an infectious disease unfolds") +AnnotationAssertion(rdfs:label obo:OGMS_0000140 "infectious disease process") +SubClassOf(obo:OGMS_0000140 obo:OGMS_0000061) + +# Class: obo:OGMS_0000141 (processual sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000141 "An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant.") +AnnotationAssertion(rdfs:label obo:OGMS_0000141 "processual sign") +SubClassOf(obo:OGMS_0000141 obo:BFO_0000015) + +# Class: obo:OGMS_0000142 (qualitative sign) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000142 "An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant.") +AnnotationAssertion(obo:IAO_0000232 obo:OGMS_0000142 "Example: the color of a rash; the shape of a melanoma") +AnnotationAssertion(rdfs:label obo:OGMS_0000142 "qualitative sign") +SubClassOf(obo:OGMS_0000142 obo:BFO_0000019) + +# Class: obo:OGMS_0000143 (transplantation) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000143 "A therapeutic procedure in which a body part is transferred into a organism") +AnnotationAssertion(rdfs:label obo:OGMS_0000143 "transplantation") +SubClassOf(obo:OGMS_0000143 obo:OGMS_0000112) + +# Class: obo:OGMS_0000144 (solid organ transplant) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000144 "A transplantation in which the body part is a non-fluid tissue") +AnnotationAssertion(rdfs:label obo:OGMS_0000144 "solid organ transplant") +SubClassOf(obo:OGMS_0000144 obo:OGMS_0000143) + +# Class: obo:OGMS_0000145 (transfusion) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000145 "A transplantation in which the body part is a bodily fluid") +AnnotationAssertion(rdfs:label obo:OGMS_0000145 "transfusion") +SubClassOf(obo:OGMS_0000145 obo:OGMS_0000143) + +# Class: obo:OGMS_0000146 (tissue disorder) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000146 "A disorder of some macroscopic part of a tissue") +AnnotationAssertion(rdfs:label obo:OGMS_0000146 "tissue disorder") +SubClassOf(obo:OGMS_0000146 obo:OGMS_0000045) + +# Class: obo:OGMS_0000147 (neoplasm) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000147 "A tissue disorder that has resulted from a dysregulation of cell proliferation leading to a net increase in mass") +AnnotationAssertion(rdfs:label obo:OGMS_0000147 "neoplasm") +SubClassOf(obo:OGMS_0000147 obo:OGMS_0000146) + +# Class: obo:OGMS_0000148 (medication role) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000148 "A role borne by some material entity which can be delivered/administrated into some organism and the role is realized during a clinical treatment process aiming to treat symptoms, signs or diagnosed disease.") +AnnotationAssertion(obo:IAO_0000116 obo:OGMS_0000148 "Originally OBIB_0000026") +AnnotationAssertion(rdfs:label obo:OGMS_0000148 "medication role") +SubClassOf(obo:OGMS_0000148 obo:BFO_0000023) + +# Class: obo:OGMS_0000149 (patient-reported outcome) + +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000149 "A data item that is about a patient’s health that comes directly from the patient. A patient reported outcome can include subjective feelings regarding symptoms, functions in daily life, physical, mental, emotional, spiritual, and social well-being, and satisfaction with healthcare that has been received."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000149 "https://orcid.org/0000-0001-6378-1703") +AnnotationAssertion(obo:IAO_0000119 obo:OGMS_0000149 "https://www.cancer.gov/publications/dictionaries/cancer-terms/def/patient-reported-outcome") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0000-0001-9625-1899") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0000-0001-9990-8331") +AnnotationAssertion(dc:contributor obo:OGMS_0000149 "https://orcid.org/0009-0003-7246-1252") +AnnotationAssertion(oboInOwl:hasBroadSynonym obo:OGMS_0000149 "PRO"@en) +AnnotationAssertion(rdfs:comment obo:OGMS_0000149 "The outcome does not necessarily need to be related to a healthcare intervention. For example, it can be about a patient's overall quality of life related to a disease."@en) +AnnotationAssertion(rdfs:label obo:OGMS_0000149 "patient-reported outcome"@en) +SubClassOf(obo:OGMS_0000149 obo:IAO_0000027) -# Class: (root node) +# Class: obo:OGMS_0000150 (healthcare outcome report) -AnnotationAssertion(rdfs:label "root node"@en) +AnnotationAssertion(obo:IAO_0000115 obo:OGMS_0000150 "A data item about a persont's health status or condition resulting from healthcare interventions, treatments, or services."@en) +AnnotationAssertion(obo:IAO_0000117 obo:OGMS_0000150 "https://orcid.org/0000-0001-6378-1703") +AnnotationAssertion(dc:contributor obo:OGMS_0000150 "https://orcid.org/0000-0001-9990-8331") +AnnotationAssertion(dc:contributor obo:OGMS_0000150 "https://orcid.org/0009-0003-7246-1252") +AnnotationAssertion(rdfs:label obo:OGMS_0000150 "healthcare outcome report"@en) +SubClassOf(obo:OGMS_0000150 obo:IAO_0000027) ) \ No newline at end of file diff --git a/src/ontology/tmp/pre_seed.txt b/src/ontology/tmp/pre_seed.txt index f9d7dac..cd0d7c2 100644 --- a/src/ontology/tmp/pre_seed.txt +++ b/src/ontology/tmp/pre_seed.txt @@ -1,7 +1,148 @@ term -https://creativecommons.org/licenses/unspecified -http://purl.obolibrary.org/obo/OGMS_0000000 -http://purl.org/dc/terms/license -http://purl.org/dc/terms/description -http://purl.org/dc/terms/title +http://purl.obolibrary.org/obo/BFO_0000001 +http://purl.obolibrary.org/obo/OGMS_0000106 +http://purl.obolibrary.org/obo/BFO_0000019 +http://purl.obolibrary.org/obo/OBI_0000278 +http://purl.obolibrary.org/obo/BFO_0000015 +http://purl.obolibrary.org/obo/OGMS_0000045 +http://purl.obolibrary.org/obo/OGMS_0000060 +http://purl.obolibrary.org/obo/OGMS_0000030 +http://purl.obolibrary.org/obo/BFO_0000031 +http://purl.obolibrary.org/obo/OGMS_0000014 +http://purl.obolibrary.org/obo/BFO_0000040 +http://purl.obolibrary.org/obo/OGMS_0000061 +http://purl.obolibrary.org/obo/OGMS_0000090 +http://purl.obolibrary.org/obo/OGMS_0000099 +http://purl.obolibrary.org/obo/OGMS_0000039 +http://purl.obolibrary.org/obo/OGMS_0000134 +http://purl.obolibrary.org/obo/OGMS_0000022 +http://purl.obolibrary.org/obo/OGMS_0000063 +http://purl.obolibrary.org/obo/OGMS_0000032 +http://purl.obolibrary.org/obo/OGMS_0000096 +http://purl.obolibrary.org/obo/OGMS_0000143 +http://purl.obolibrary.org/obo/BFO_0000016 +http://purl.obolibrary.org/obo/OGMS_0000123 +http://purl.obolibrary.org/obo/OGMS_0000097 +http://purl.obolibrary.org/obo/IAO_0000027 +http://purl.obolibrary.org/obo/COB_0000035 +http://purl.obolibrary.org/obo/OGMS_0000112 +http://purl.obolibrary.org/obo/OGMS_0000020 +http://purl.obolibrary.org/obo/OGMS_0000108 +http://purl.obolibrary.org/obo/OGMS_0000129 +http://purl.obolibrary.org/obo/OGMS_0000047 +http://purl.obolibrary.org/obo/OGMS_0000067 +http://purl.obolibrary.org/obo/OGMS_0000023 +http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/OGMS_0000031 +http://purl.obolibrary.org/obo/OGMS_0000089 +http://purl.obolibrary.org/obo/OGMS_0000133 +http://purl.obolibrary.org/obo/OGMS_0000146 +http://purl.obolibrary.org/obo/OGMS_0000118 +http://purl.obolibrary.org/obo/IAO_0000030 +http://purl.obolibrary.org/obo/OGMS_0000120 +http://purl.obolibrary.org/obo/IAO_0000117 +http://purl.obolibrary.org/obo/OGMS_0000105 http://purl.obolibrary.org/obo/ogms.owl +http://purl.obolibrary.org/obo/OGMS_0000033 +http://purl.obolibrary.org/obo/OGMS_0000074 +http://purl.obolibrary.org/obo/OGMS_0000046 +http://purl.obolibrary.org/obo/OGMS_0000018 +http://purl.obolibrary.org/obo/OGMS_0000087 +http://purl.obolibrary.org/obo/OGMS_0000140 +http://purl.obolibrary.org/obo/OGMS_0000059 +http://purl.obolibrary.org/obo/OGMS_0000125 +http://purl.org/dc/terms/license +http://purl.obolibrary.org/obo/OGMS_0000040 +http://purl.obolibrary.org/obo/OGMS_0000138 +http://purl.obolibrary.org/obo/OGMS_0000081 +http://purl.obolibrary.org/obo/OGMS_0000025 +http://purl.obolibrary.org/obo/OGMS_0000094 +http://purl.obolibrary.org/obo/OGMS_0000066 +http://purl.obolibrary.org/obo/OGMS_0000038 +http://purl.obolibrary.org/obo/OGMS_0000079 +http://purl.obolibrary.org/obo/IAO_0000116 +http://purl.obolibrary.org/obo/OGMS_0000132 +http://purl.obolibrary.org/obo/OGMS_0000104 +http://purl.obolibrary.org/obo/OGMS_0000145 +http://purl.obolibrary.org/obo/OGMS_0000117 +http://purl.obolibrary.org/obo/OGMS_0000073 +http://purl.obolibrary.org/obo/OGMS_0000017 +http://purl.obolibrary.org/obo/OGMS_0000086 +http://purl.obolibrary.org/obo/OGMS_0000111 +http://purl.obolibrary.org/obo/OGMS_0000124 +http://purl.obolibrary.org/obo/OGMS_0000137 +http://purl.obolibrary.org/obo/OGMS_0000080 +http://purl.obolibrary.org/obo/OGMS_0000109 +http://purl.obolibrary.org/obo/OGMS_0000024 +http://purl.org/dc/elements/1.1/description +http://purl.obolibrary.org/obo/OGMS_0000093 +http://purl.obolibrary.org/obo/OGMS_0000065 +http://purl.org/dc/elements/1.1/publisher +http://purl.obolibrary.org/obo/OGMS_0000037 +http://purl.obolibrary.org/obo/OGMS_0000131 +http://purl.obolibrary.org/obo/OGMS_0000078 +http://purl.obolibrary.org/obo/IAO_0000115 +http://purl.org/dc/elements/1.1/creator +http://purl.obolibrary.org/obo/OGMS_0000103 +http://purl.obolibrary.org/obo/OGMS_0000144 +http://purl.obolibrary.org/obo/OGMS_0000116 +http://purl.obolibrary.org/obo/OGMS_0000016 +http://purl.obolibrary.org/obo/OGMS_0000085 +http://purl.obolibrary.org/obo/OGMS_0000057 +http://purl.obolibrary.org/obo/OGMS_0000110 +http://purl.obolibrary.org/obo/OGMS_0000029 +http://purl.obolibrary.org/obo/OGMS_0000098 +http://www.geneontology.org/formats/oboInOwl#hasExactSynonym +http://purl.obolibrary.org/obo/OGMS_0000136 +http://purl.obolibrary.org/obo/OGMS_0000051 +http://purl.obolibrary.org/obo/OGMS_0000149 +http://purl.obolibrary.org/obo/OGMS_0000092 +http://purl.obolibrary.org/obo/OGMS_0000064 +http://purl.obolibrary.org/obo/OGMS_0000077 +http://purl.obolibrary.org/obo/OGMS_0000130 +http://purl.obolibrary.org/obo/OGMS_0000102 +http://purl.obolibrary.org/obo/OGMS_0000115 +http://purl.obolibrary.org/obo/OGMS_0000128 +http://purl.obolibrary.org/obo/OGMS_0000071 +http://purl.obolibrary.org/obo/OGMS_0000015 +http://purl.obolibrary.org/obo/OGMS_0000084 +http://purl.obolibrary.org/obo/OGMS_0000056 +http://purl.obolibrary.org/obo/OGMS_0000028 +http://purl.obolibrary.org/obo/OGMS_0000150 +http://purl.obolibrary.org/obo/OGMS_0000069 +http://purl.obolibrary.org/obo/OGMS_0000122 +http://purl.obolibrary.org/obo/IAO_0000119 +http://purl.obolibrary.org/obo/OGMS_0000135 +http://purl.obolibrary.org/obo/OGMS_0000107 +http://purl.obolibrary.org/obo/OGMS_0000050 +http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym +http://purl.obolibrary.org/obo/OGMS_0000148 +http://purl.obolibrary.org/obo/OGMS_0000091 +http://purl.obolibrary.org/obo/OGMS_0000035 +http://purl.org/dc/elements/1.1/date +http://purl.obolibrary.org/obo/OGMS_0000101 +http://purl.obolibrary.org/obo/OGMS_0000142 +http://purl.obolibrary.org/obo/OGMS_0000114 +http://purl.obolibrary.org/obo/OGMS_0000127 +http://purl.obolibrary.org/obo/OGMS_0000070 +http://purl.obolibrary.org/obo/OGMS_0000083 +http://purl.obolibrary.org/obo/OGMS_0000055 +http://purl.obolibrary.org/obo/OGMS_0000027 +http://purl.obolibrary.org/obo/OGMS_0000121 +http://purl.obolibrary.org/obo/IAO_0000118 +http://purl.org/dc/elements/1.1/contributor +http://purl.obolibrary.org/obo/OGMS_0000147 +http://purl.obolibrary.org/obo/OGMS_0000119 +http://purl.obolibrary.org/obo/OGMS_0000034 +http://purl.obolibrary.org/obo/OGMS_0000100 +http://purl.obolibrary.org/obo/OGMS_0000019 +http://purl.obolibrary.org/obo/OGMS_0000088 +http://purl.obolibrary.org/obo/OGMS_0000141 +http://purl.obolibrary.org/obo/OGMS_0000113 +http://purl.obolibrary.org/obo/OGMS_0000126 +http://purl.org/dc/elements/1.1/title +http://purl.obolibrary.org/obo/IAO_0000232 +http://purl.obolibrary.org/obo/OGMS_0000139 +http://purl.obolibrary.org/obo/OGMS_0000082 +http://purl.obolibrary.org/obo/OGMS_0000026 +http://purl.obolibrary.org/obo/OGMS_0000095 diff --git a/src/ontology/tmp/ro-download.owl b/src/ontology/tmp/ro-download.owl deleted file mode 100644 index a3d3910..0000000 --- a/src/ontology/tmp/ro-download.owl +++ /dev/null @@ -1,17884 +0,0 @@ - - - - - The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. - - OBO Relations Ontology - 2025-03-05 - https://github.com/oborel/obo-relations/ - - - - - - - - - - - - - - - - - - - editor preferred term - - The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - editor preferred term - - - - - - - - example of usage - - A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - example of usage - example of usage - - - - - - - - has curation status - PERSON:Alan Ruttenberg - PERSON:Bill Bug - PERSON:Melanie Courtot - has curation status - - - - - - - - definition - - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. - 2012-04-05: -Barry Smith - -The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. - -Can you fix to something like: - -A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. - -Alan Ruttenberg - -Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. - -On the specifics of the proposed definition: - -We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. - -Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. - -We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition - definition - - - - - - - - editor note - - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - editor note - - - - - - - - term editor - - Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people - 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - term editor - - - - - - - - alternative label - - A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. - OBO Operations committee - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). - alternative label - - - - - - - - definition source - - Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 - PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - definition source - - - - - - - - curator note - - An administrative note of use for a curator but of no use for a user - PERSON:Alan Ruttenberg - curator note - - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'tracker item' can associate a tracker with a specific ontology term. - term tracker item - - - - - - - - imported from - - For external terms/classes, the ontology from which the term was imported - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - imported from - - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall - expand expression to - - - - - - - - expand assertion to - ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - - A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. - Chris Mungall - expand assertion to - - - - - - - - first order logic expression - An assertion that holds between an OWL Object Property and a string or literal, where the value of the string or literal is a Common Logic sentence of collection of sentences that define the Object Property. - PERSON:Alan Ruttenberg - first order logic expression - - - - - - - - - OBO foundry unique label - - An alternative name for a class or property which is unique across the OBO Foundry. - The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . - PERSON:Alan Ruttenberg - PERSON:Bjoern Peters - PERSON:Chris Mungall - PERSON:Melanie Courtot - GROUP:OBO Foundry <http://obofoundry.org/> - OBO foundry unique label - - - - - - - - elucidation - person:Alan Ruttenberg - Person:Barry Smith - Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms - elucidation - - - - - - - - has ontology root term - Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu - has ontology root term - - - - - - - - term replaced by - - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg - Add as annotation triples in the granting ontology - term replaced by - - - - - - - - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } - Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. - - - - defined by construct - - - - - - - - An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. - temporal interpretation - - - - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: ?X DisjointWith: RO_0002162 some ?Y - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> -PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> -CONSTRUCT { - in_taxon: a owl:ObjectProperty . - ?x owl:disjointWith [ - a owl:Restriction ; - owl:onProperty in_taxon: ; - owl:someValuesFrom ?taxon - ] . - ?x rdfs:subClassOf [ - a owl:Restriction ; - owl:onProperty in_taxon: ; - owl:someValuesFrom [ - a owl:Class ; - owl:complementOf ?taxon - ] - ] . -} -WHERE { - ?x never_in_taxon: ?taxon . -} - never in taxon - - - - - - - - - - A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B. - non-overlapping with - shares no parts with - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) - PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> -PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> -CONSTRUCT { - part_of: a owl:ObjectProperty . - [ - a owl:Restriction ; - owl:onProperty part_of: ; - owl:someValuesFrom ?x ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty part_of: ; - owl:someValuesFrom ?y - ] - ] -} -WHERE { - ?x mutually_spatially_disjoint_with: ?y . -} - mutually spatially disjoint with - - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - - - - - - - - An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. - taxonomic class assertion - - - - - - - - - - S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. [PHENOSCPAE:asilomar_mtg] - ambiguous for taxon - - - - - - - - - - S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. - - - This relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take ongoing coordinated effort to resolve. Example: metencephalon in teleost - dubious for taxon - - - - - - - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> -PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> -CONSTRUCT { - in_taxon: a owl:ObjectProperty . - ?witness rdfs:label ?label . - ?witness rdfs:subClassOf ?x . - ?witness rdfs:subClassOf [ - a owl:Restriction ; - owl:onProperty in_taxon: ; - owl:someValuesFrom ?taxon - ] . -} -WHERE { - ?x present_in_taxon: ?taxon . - BIND(IRI(CONCAT( - "http://purl.obolibrary.org/obo/RO_0002175#", - MD5(STR(?x)), - "-", - MD5(STR(?taxon)) - )) as ?witness) - BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) -} - The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. - present in taxon - - - - - - - - - - defined by inverse - - - - - - - - - An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. - logical macro assertion - http://purl.obolibrary.org/obo/ro/docs/shortcut-relations/ - - - - - - - - An assertion that holds between an OWL Annotation Property P and a non-negative integer N, with the interpretation: for any P(i j) it must be the case that | { k : P(i k) } | = N. - annotation property cardinality - - - - - - - - - - A logical macro assertion whose domain is an IRI for a class - The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL - logical macro assertion on a class - - - - - - - - - A logical macro assertion whose domain is an IRI for a property - logical macro assertion on a property - - - - - - - - - Used to annotate object properties to describe a logical meta-property or characteristic of the object property. - logical macro assertion on an object property - - - - - - - - - logical macro assertion on an annotation property - - - - - - - - - An assertion that holds between an OWL Object Property and a dispositional interpretation that elucidates how OWL Class Axioms or OWL Individuals that use this property are to be interpreted in a dispositional context. For example, A binds B may be interpreted as A have a mutual disposition that is realized by binding to the other one. - dispositional interpretation - - - - - - - - - 'pectoral appendage skeleton' has no connections with 'pelvic appendage skeleton' - A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. - shares no connection with - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) - has no connections with - - - - - - - - - inherited annotation property - - - - - - - - Connects an ontology entity (class, property, etc) to a URL from which curator guidance can be obtained. This assertion is inherited in the same manner as functional annotations (e.g. for GO, over SubClassOf and part_of) - curator guidance link - - - - - - - - - brain always_present_in_taxon 'Vertebrata' - forelimb always_present_in_taxon Euarchontoglires - S always_present_in_taxon T if every fully formed member of taxon T has part some S, or is an instance of S - This is a very strong relation. Often we will not have enough evidence to know for sure that there are no species within a lineage that lack the structure - loss is common in evolution. However, there are some statements we can make with confidence - no vertebrate lineage could persist without a brain or a heart. All primates are limbed. - never lost in - always present in taxon - - - - - - - - - This property was originally created for the annotation of developmental or life cycle stages, such as for example Carnegie Stage 20 in humans. - temporal logical macro assertion on a class - - - - - - - - - measurement property has unit - - - - - - - - - has start time value - http://purl.obolibrary.org/obo/ro/docs/temporal-durations/ - - - - - - - - - has end time value - - - - - - - - - - Count of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property. - start, days post fertilization - - - - - - - - - - Count of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property. - end, days post fertilization - - - - - - - - - - Count of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1. - start, years post birth - - - - - - - - - - Count of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2 - end, years post birth - - - - - - - - - - Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1. - start, months post birth - - - - - - - - - - Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2 - end, months post birth - - - - - - - - - - Defines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in. - month of gestation - - - - - - - - - - A relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological process - has developmental stage marker - - - - - - - - - - Count of number of days intervening between the start of the stage and the time of coitum. - For mouse staging: assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum) - start, days post coitum - - - - - - - - - - Count of number of days intervening between the end of the stage and the time of coitum. - end, days post coitum - - - - - - - - - - start, weeks post birth - - - - - - - - - - end, weeks post birth - - - - - - - - - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x subject-partner-in p, y object-partner-in p - is asymmetric relational form of process class - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - If Rel is the relational form of a process Pr, then it follow that: Rel(x,y) <-> exists p : Pr(p), x partner-in p, y partner-in p - is symmetric relational form of process class - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - R is the relational form of a process if and only if either (1) R is the symmetric relational form of a process or (2) R is the asymmetric relational form of a process - is relational form of process class - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y - The general property hierarchy is: - - "directly P" SubPropertyOf "P" - Transitive(P) - -Where we have an annotation assertion - - "directly P" "is direct form of" "P" - If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' - - is direct form of - - - - - - - - - - relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y - - is indirect form of - - - - - - - - - - logical macro assertion on an axiom - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - An annotation property that connects an object property to a class, where the object property is derived from or a shortcut property for the class. The exact semantics of this annotation may vary on a case by case basis. - is relational form of a class - - - - - - - - - A shortcut relationship that holds between two entities based on their identity criteria - logical macro assertion involving identity - - - - - - - - - A shortcut relationship between two entities x and y1, such that the intent is that the relationship is functional and inverse function, but there is no guarantee that this property holds. - in approximate one to one relationship with - - - - - - - - - x is approximately equivalent to y if it is the case that x is equivalent, identical or near-equivalent to y - The precise meaning of this property is dependent upon some contexts. It is intended to group multiple possible formalisms. Possibilities include a probabilistic interpretation, for example, Pr(x=y) > 0.95. Other possibilities include reified statements of belief, for example, "Database D states that x=y" - is approximately equivalent to - - - - - - - - - 'anterior end of organism' is-opposite-of 'posterior end of organism' - 'increase in temperature' is-opposite-of 'decrease in temperature' - x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - is opposite of - - - - - - - - - x is indistinguishable from y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). - is indistinguishable from - - - - - - - - - evidential logical macro assertion on an axiom - - - - - - - - - A relationship between a sentence and an instance of a piece of evidence in which the evidence supports the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. - axiom has evidence - - - - - - - - - A relationship between a sentence and an instance of a piece of evidence in which the evidence contradicts the axiom - This annotation property is intended to be used in an OWL Axiom Annotation to connect an OWL Axiom to an instance of an ECO (evidence type ontology class). Because in OWL, all axiom annotations must use an Annotation Property, the value of the annotation cannot be an OWL individual, the convention is to use an IRI of the individual. - axiom contradicted by evidence - - - - - - - - - In the context of a particular project, the IRI with CURIE NCBIGene:64327 (which in this example denotes a class) is considered to be representative. This means that if we have equivalent classes with IRIs OMIM:605522, ENSEMBL:ENSG00000105983, HGNC:13243 forming an equivalence set, the NCBIGene is considered the representative member IRI. Depending on the policies of the project, the classes may be merged, or the NCBIGene IRI may be chosen as the default in a user interface context. - this property relates an IRI to the xsd boolean value "True" if the IRI is intended to be the representative IRI for a collection of classes that are mutually equivalent. - If it is necessary to make the context explicit, an axiom annotation can be added to the annotation assertion - is representative IRI for equivalence set - OWLAPI Reasoner documentation for representativeElement, which follows a similar idea, but selects an arbitrary member - - - - - - - - - true if the two properties are disjoint, according to OWL semantics. This should only be used if using a logical axiom introduces a non-simple property violation. - - nominally disjoint with - - - - - - - - - Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0" - - 2018-03-13T23:59:29Z - is directional form of - - - - - - - - - - 2018-03-14T00:03:16Z - is positive form of - - - - - - - - - - 2018-03-14T00:03:24Z - is negative form of - - - - - - - - - part-of is homeomorphic for independent continuants. - R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C. - - 2018-10-21T19:46:34Z - R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C. - is homeomorphic for - - - - - - - - - - - 2020-09-22T11:05:29Z - valid_for_go_annotation_extension - - - - - - - - - - - 2020-09-22T11:05:18Z - valid_for_go_gp2term - - - - - - - - - - - 2020-09-22T11:04:12Z - valid_for_go_ontology - - - - - - - - - - - 2020-09-22T11:05:45Z - valid_for_gocam - - - - - - - - - - eco subset - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - subset_property - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - has broad synonym - has_broad_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 - - - - - - - - - disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41009"^^xsd:string - An annotation property that links an ontology entity or a statement to a prefixed identifier or URI. - - - 2024-03-18 - database_cross_reference - has cross-reference - - - - - - - - An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - has exact synonym - has_exact_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 - - - - - - - - - An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 - has narrow synonym - has_narrow_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 - - - - - - - - - has_obo_format_version - - - - - - - - An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 - has related synonym - has_related_synonym - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 - - - - - - - - - - - - - - - in_subset - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is defined by - - - - - is defined by - This is an experimental annotation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - - - - - - part of - - - http://www.obofoundry.org/ro/#OBO_REL:part_of - https://wiki.geneontology.org/Part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - - - - has part - - - - - - - - - - - realized in - this disease is realized in this disease course - this fragility is realized in this shattering - this investigator role is realized in this investigation - is realized by - realized_in - [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realized in - - - - - - - - - - realizes - this disease course realizes this disease - this investigation realizes this investigator role - this shattering realizes this fragility - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) - Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process - - realizes - - - - - - - - - accidentally included in BFO 1.2 proposal - - should have been BFO_0000062 - obsolete preceded by - true - - - - - - - - - - - - - - - - - - - - - - - - - preceded by - x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by - - preceded by - - - - - - - - - - - - - - - - - - - - precedes - x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - precedes - - - - - - - - - - - - - - - - - - - occurs in - b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in - - - - Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - - occurs in - https://wiki.geneontology.org/Occurs_in - - - - - - - - site of - [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process - - - - - - - - A relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist through the separation or transformation of a part of the old entity, and the new entity inherits a significant portion of the matter belonging to that part of the old entity. - derives from part of - - - - - - - - - A has part relationship between a whole and a part, where the number of parts present in the whole is higher than in comparable entities. - This relation is present in ENVO to support compositional classes such as "X-enriched soil". These will later be formalized, and a different relation from RO may be chosen. - has increased levels of - - - - - - - - - - - - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple - a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. - characteristic of - - - - - - - - - - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility - Inverse of characteristic_of - A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - - has characteristic - - - - - - - - - - - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation - a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in - participates in - - - - - - - - - - - - - - - - - - - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) - a relation between a process and a continuant, in which the continuant is somehow involved in the process - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant - has participant - - - - - - - - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes. - is concretized as - - - - - - - - - - - - - - - - - A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). - An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). - A relationship between a specifically dependent continuant or process and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant. - concretizes - - - - - - - - - - - this catalysis function is a function of this enzyme - a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence - A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - function of - - - - - - - - - - this red color is a quality of this apple - a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence - A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - quality of - - - - - - - - - - this investigator role is a role of this person - a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence - A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - role of - - - - - - - - - - - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) - a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence - A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function - has function - - - - - - - - - - this apple has quality this red color - a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence - A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - has quality - - - - - - - - - - - this person has role this investigator role (more colloquially: this person has this role of investigator) - a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence - A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role - has role - - - - - - - - - - - - a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence - has disposition - - - - - - - - - inverse of has disposition - - This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. - disposition of - - - - - - - - - OBSOLETE A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. - - - - Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). - obsolete in neural circuit with - true - - - - - - - - - OBSOLETE A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next, in which the direction is from the last to the first. - - - - Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). - obsolete upstream in neural circuit with - true - - - - - - - - - OBSOLETE A relation that holds between a neuron that is synapsed_by another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_by the next, in which the direction is from the last to the first. - - - - Obsoleted as no longer a useful relationship (all neurons in an organism are in a neural circuit with each other). - obsolete downstream in neural circuit with - true - - - - - - - - - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. - - derives from - - - - - - - - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity - This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into - - derives into - - - - - - - - - - is location of - my head is the location of my brain - this cage is the location of this rat - a relation between two independent continuants, the location and the target, in which the target is entirely within the location - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - location of - - - - - - - - contained in - Containment is location not involving parthood, and arises only where some immaterial continuant is involved. - Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - contained_in - obsolete contained in - - true - - - - - - - - contains - obsolete contains - - true - - - - - - - - - - - penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520) - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - is allergic trigger for - - - - - - - - - - - A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - is autoimmune trigger for - - - - - - - - - - penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334) - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - has allergic trigger - - - - - - - - - - A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity. - has autoimmune trigger - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - located in - my brain is located in my head - this rat is located in this cage - a relation between two independent continuants, the target and the location, in which the target is entirely within the location - Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus - Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - - located in - https://wiki.geneontology.org/Located_in - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - - - - - - - - - - the surface of my skin is a 2D boundary of my body - a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - - 2D boundary of - - - - - - - - - - May be obsoleted, see https://github.com/oborel/obo-relations/issues/260 - - - aligned with - - - - - - - - - - - my body has 2D boundary the surface of my skin - a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity - A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. - Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - has 2D boundary - - - - - - - - - A relation that holds between two neurons that are electrically coupled via gap junctions. - - - electrically_synapsed_to - - - - - - - - - - - The relationship that holds between a trachea or tracheole and an antomical structure that is contained in (and so provides an oxygen supply to). - - tracheates - - - - - - - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - innervated_by - - - - - - - - - - - - has synaptic terminal of - - - - - - - - - - - - - - - - - - - - - X outer_layer_of Y iff: -. X :continuant that bearer_of some PATO:laminar -. X part_of Y -. exists Z :surface -. X has_boundary Z -. Z boundary_of Y - -has_boundary: http://purl.obolibrary.org/obo/RO_0002002 -boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. - bounding layer of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. - Note from NCEAS meeting: consider changing primary label - - - Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. - coincident with - - - - - - - - - - A relation that applies between a cell(c) and a gene(g) , where the process of 'transcription, DNA templated (GO_0006351)' is occuring in in cell c and that process has input gene g. - - x 'cell expresses' y iff: -cell(x) -AND gene(y) -AND exists some 'transcription, DNA templated (GO_0006351)'(t) -AND t occurs_in x -AND t has_input y - cell expresses - - - - - - - - - - - x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - - regulates in other organism - - regulates in another organism - - - - - - - - - - - - A relationship that holds between a process that regulates a transport process and the entity transported by that process. - - - regulates transport of - - - - - - - - - - - - A part of relation that applies only between occurrents. - occurrent part of - - - - - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - - 2017-05-24T09:30:46Z - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - has positive regulatory component activity - - - - - - - - - - - 2017-05-24T09:36:08Z - A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity. - has necessary component activity - - - - - - - - - - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - - 2017-05-24T09:49:21Z - has component process - - - - - - - - - A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. - - 2017-07-19T17:30:36Z - has ligand - - - - - - - - - Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another. - - 2017-07-20T17:11:08Z - transports - - - - - - - - - A relationship between a process and a barrier, where the process occurs in a region spanning the barrier. For cellular processes the barrier is typically a membrane. Examples include transport across a membrane and membrane depolarization. - - 2017-07-20T17:19:37Z - occurs across - - - - - - - - - - - 2017-09-17T13:52:24Z - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - directly regulated by - - - - - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - - - - - - - - - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - - 2017-09-17T13:52:38Z - directly negatively regulated by - - - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - - - - - - - - - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - - 2017-09-17T13:52:47Z - directly positively regulated by - - - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - - - - - - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - - - - - - - - - - - - A relationship that holds between two images, A and B, where: -A depicts X; -B depicts Y; -X and Y are both of type T' -C is a 2 layer image consiting of layers A and B; -A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. -Note: A and B may be 2D or 3D. -Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - - 2017-12-07T12:58:06Z - in register with - - - - - A relationship that holds between two images, A and B, where: -A depicts X; -B depicts Y; -X and Y are both of type T' -C is a 2 layer image consiting of layers A and B; -A and B are aligned in C according to a shared co-ordinate framework so that common features of X and Y are co-incident with each other. -Note: A and B may be 2D or 3D. -Examples include: the relationship between two channels collected simultaneously from a confocal microscope; the relationship between an image dpeicting X and a painted annotation layer that delineates regions of X; the relationship between the tracing of a neuron on an EM stack and the co-ordinate space of the stack; the relationship between two separately collected images that have been brought into register via some image registration software. - - - - - - - - - - David Osumi-Sutherland - <= - - Primitive instance level timing relation between events - before or simultaneous with - - - - - - - - - - - x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - - t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with - - - - - - - - - - David Osumi-Sutherland - - t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2) - before - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002122 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which ends - - - - - - - - - - - - di - Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - encompasses - - - - - - - - - - - - - - David Osumi-Sutherland - - X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) - ends after - - - - - - - - - - - - - - David Osumi-Sutherland - starts_at_end_of - X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) - immediately preceded by - - - - - - - - - - David Osumi-Sutherland - - Previously had ID http://purl.obolibrary.org/obo/RO_0002123 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. - during which starts - - - - - - - - - - - - - - David Osumi-Sutherland - - starts before - - - - - - - - - - - - - - David Osumi-Sutherland - ends_at_start_of - meets - - - X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) - immediately precedes - - - - - - - - - - - David Osumi-Sutherland - io - - X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) - starts during - - - - - - - - - - - David Osumi-Sutherland - d - during - - - - - X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) - happens during - https://wiki.geneontology.org/Happens_during - - - - - - - - - David Osumi-Sutherland - o - overlaps - - X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). - ends during - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and a material anatomical entity that its soma is part of. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - - has soma location - - - - - - - - - - - - - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - fasciculates with - - - - - - - - - - - - - - - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( - <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - - axon synapses in - - - - - - - - - - - - - - - - - - - - - - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - synapsed by - - - - - - - - - - - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - - has plasma membrane part - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type Ib bouton. - - - BFO_0000051 some (GO_0061176 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type Ib terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_Ib_bouton_to - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type Is bouton. - - - BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type Is terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_Is_bouton_to - - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type II bouton. - - - BFO_0000051 some (GO_0061175 that BFO_0000051 some (that BFO_0000051 some (GO_0045202 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - Expands to: has_part some ('type II terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_II_bouton_to - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type II bouton. - - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061174 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type II terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_II_bouton - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type Ib bouton. - - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061176 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Ib terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_Ib_bouton - - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in - http://purl.obolibrary.org/obo/BFO_0000051 some ( - http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( - http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - - has postsynaptic terminal in - - - - - - - - - - - has neurotransmitter - releases neurotransmitter - - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type Is bouton. - - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0061177 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type Is terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_Is_bouton - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - - has presynaptic terminal in - - - - - - - - - - A relation between a motor neuron and a muscle that it synapses to via a type III bouton. - BFO_0000051 some (GO_0061177 that BFO_0000051 some (that BFO_0000051 some (GO_0097467 that BFO_0000051 some ( that BFO_0000050 some ?Y)))) - - - Expands to: has_part some ('type III terminal button' that has_part some ('pre-synaptic membrane' that part_of some ('synapse' that has_part some ('post-synaptic membrane' that part_of some ?Y)))) - synapsed_via_type_III_bouton_to - - - - - - - - - Relation between a muscle and a motor neuron that synapses to it via a type III bouton. - - BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0097467 that BFO_0000051 some GO_0045211 that BFO_0000050 some ?Y))) - - - Expands to: has_part some ('presynaptic membrane' that part_of some ('synapse' that has_part some ('type III terminal button' that has_part some 'postsynaptic membrane' that part_of some ?Y))))) - synapsed_by_via_type_III_bouton - - - - - - - - - - - - - - - - - - - - - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - N1 synapsed_to some N2 -Expands to: -N1 SubclassOf ( - has_part some ( - ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( - ‘synapse ; GO:0045202’ that has_part some ( - ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) - synapsed to - - - - - - - - - - - - - - - Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. - - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( - <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( - http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( - <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - - dendrite synapsed in - - - - - - - - - - - - - - - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in - <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - - has synaptic terminal in - - - - - - - - - - - - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y - http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - - - - - overlaps - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - - has fasciculating neuron projection - - - - - - - - - - - - - - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. -T innervates some R -Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - innervates - - - - - - - - - - - - - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - continuous with - FMA:85972 - - - - - - - - - - x partially overlaps y iff there exists some z such that z is part of x and z is part of y, and it is also the case that neither x is part of y or y is part of x - We would like to include disjointness axioms with part_of and has_part, however this is not possible in OWL2 as these are non-simple properties and hence cannot appear in a disjointness axiom - proper overlaps - (forall (?x ?y) - (iff - (proper_overlaps ?x ?y) - (and - (overlaps ?x ?y) - (not (part_of ?x ?y)) - (not (part_of ?y ?x))))) - - - partially overlaps - - - - - - - - - - - - d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a. - ancestral_stucture_of - evolutionarily_descended_from - derived by descent from - - - - - - - - - - - inverse of derived by descent from - - has derived by descendant - - - - - - - - - - - - - - - - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - VBO calls this homologous_to - shares ancestor with - - - - - - - - - - - - serially homologous to - - - - - - - - - lactation SubClassOf 'only in taxon' some 'Mammalia' - - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. - The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. - - 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - only in taxon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - life cycle stage of - - Connects a biological entity to its taxon of origin. - in taxon - - - - - - - - - - - A is spatially_disjoint_from B if and only if they have no parts in common - There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy - BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - - - spatially disjoint from - https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern - - - - - - - - - - - - - - - - - - - - - - - - - - - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - connected to - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - - - - - - - - - - - - - - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). - c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - connects - https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern - https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern - - - - - - - - - - - - - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - attached to part of - - - - - - - - - true - - - - - - - - - Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - supplies - - - - - - - - - Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. - Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - drains - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - has component - - - - - - - - - - - - - - - - - - - - - - A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). - - - has phenotype - - - - - - - - - - inverse of has phenotype - - - - phenotype of - - - - - - - - - - - - - - - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - This is the transitive form of the develops from relation - develops from - - - - - - - - - - - - - inverse of develops from - - - - - develops into - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - definition "x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x" - We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g. - - gene product of - - - - - - - - - - - - - - - every HOTAIR lncRNA is the gene product of some HOXC gene - every sonic hedgehog protein (PR:000014841) is the gene product of some sonic hedgehog gene - - x has gene product y if and only if x is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from y - - has gene product - - - - - - - - - - - - - - - - - - - - - - - - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - - expressed in - - - - - - - - - - - - - - - - - - - - - - - - - - - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - has developmental precursor - TODO - add child relations from DOS - directly develops from - - - - - - - - - - A parasite that kills or sterilizes its host - parasitoid of - - - - - - - - - inverse of parasitoid of - - has parasitoid - - - - - - - - - - inverse of directly develops from - developmental precursor of - - directly develops into - - - - - - - - - - - - - - - - - - - - - - - - - p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false - - - - regulates - - - - - - - - - - - - - - - p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) - - - - - negatively regulates - - - - - - - - - - - - - - - - - - - - p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - - - - - positively regulates - - - - - - - - - - - - - - - - 'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair')) - heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation') - - x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation. - Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from) - TODO: add homeomorphy axiom - This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants. - - has prototype - - - - - - - - - - - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' - A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - - capable of - - - - - - - - - - - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in - capable of part of - - - - - - - - - - true - - - - - - - - OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role - - agent in - - Obsoleted as the inverse property was obsoleted. - obsolete actively participates in - true - - - - - - - - OBSOLETE x has participant y if and only if x realizes some active role that inheres in y - - has agent - - obsolete has active participant - true - - - - - - - - - - - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - surrounded by - - - - - - - - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - - x adjacent to y if and only if x and y share a boundary. - This relation acts as a join point with BSPO - - - - - - adjacent to - - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - - - - - - - - - - inverse of surrounded by - - - - surrounds - - - - - - - - - - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 - - A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. - temporally related to - - - - - - - - - - - - inverse of starts with - - Chris Mungall - Allen - - starts - - - - - - - - - - - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by - - starts with - - - - - - - - - - - - - - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - develops from part of - - - - - - - - - - - - - - - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - develops in - - - - - - - - - A sub-relation of parasite-of in which the parasite that cannot complete its life cycle without a host. - obligate parasite of - - - - - - - - - A sub-relations of parasite-of in which the parasite that can complete its life cycle independent of a host. - facultative parasite of - - - - - - - - - - - - inverse of ends with - - Chris Mungall - - ends - - - - - - - - - - - - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by - - ends with - - - - - - - - - - - - - - - - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in - - has start location - - - - - - - - - - - - - - - - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in - - has end location - - - - - - - - - - - - - - - - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes - - - - - has input - https://wiki.geneontology.org/Has_input - - - - - - - - - - - - - - - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces - - - - - has output - https://wiki.geneontology.org/Has_output - - - - - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host stem (PO:0009047) - stem parasite of - - - - - - - - - A parasite-of relationship in which the host is a plant and the parasite that attaches to the host root (PO:0009005) - root parasite of - - - - - - - - - A sub-relation of parasite-of in which the parasite is a plant, and the parasite is parasitic under natural conditions and is also photosynthetic to some degree. Hemiparasites may just obtain water and mineral nutrients from the host plant. Many obtain at least part of their organic nutrients from the host as well. - hemiparasite of - - - - - - - - - X 'has component participant' Y means X 'has participant' Y and there is a cardinality constraint that specifies the numbers of Ys. - This object property is needed for axioms using has_participant with a cardinality contrainsts; e.g., has_particpant min 2 object. However, OWL does not permit cardinality constrains with object properties that have property chains (like has_particant) or are transitive (like has_part). - -If you need an axiom that says 'has_participant min 2 object', you should instead say 'has_component_participant min 2 object'. - - has component participant - - - - - - - - - A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event. - ExO:0000001 - has exposure receptor - - - - - - - - - A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event. - ExO:0000000 - has exposure stressor - - - - - - - - - A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor - ExO:0000055 - has exposure route - - - - - - - - - A broad relationship between an exposure event or process and the course takes from the source to the target. - http://purl.obolibrary.org/obo/ExO_0000004 - has exposure transport path - - - - - - - - - - Any relationship between an exposure event or process and any other entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes. - related via exposure to - - - - - - - - - g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background. - over-expressed in - - - - - - - - - g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background. - under-expressed in - - - - - - - - - - - - Any portion of roundup 'has active ingredient' some glyphosate - A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance. - has active substance - has active pharmaceutical ingredient - has active ingredient - - - - - - - - - inverse of has active ingredient - - active ingredient in - - - - - - - - - - - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. - b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - connecting branch of - - - - - - - - - - inverse of connecting branch of - - - has connecting branch - - - - - - - - - - - - - - - - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - - x has developmental contribution from y iff x has some part z such that z develops from y - - has developmental contribution from - - - - - - - - - - - - - - - inverse of has developmental contribution from - - - developmentally contributes to - - - - - - - - - - - - - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - developmentally induced by - - - - - - - - - - - Inverse of developmentally induced by - - developmentally induces - - - - - - - - - - - - - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p - false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one - This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from - developmentally preceded by - - - - - - - - - c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432) - has biological role - - - - - - - - - c has-application-role r iff c has-role r and r is an application role (CHEBI:33232) - has application role - - - - - - - - - c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086) - has chemical role - - - - - - - - - - - - - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. - c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. - - acts upstream of - - - - - - - - - - - - - - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. - c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. - affects - - acts upstream of or within - https://wiki.geneontology.org/Acts_upstream_of_or_within - - - - - - - - - - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else - This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - developmentally replaces - - - - - - - - - - Inverse of developmentally preceded by - - developmentally succeeded by - - - - - - - - - - - - - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - - part of developmental precursor of - - - - - - - - - - - x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x - Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part. - - ubiquitously expressed in - - - - - - - - - - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - - expresses - - - - - - - - - - inverse of ubiquiotously expressed in - - - ubiquitously expresses - - - - - - - - - - - - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). - This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - - results in developmental progression of - - - - - - - - - - - every flower development (GO:0009908) results in development of some flower (PO:0009046) - - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml - - - - results in development of - - - - - - - - - - - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 - - - - results in formation of anatomical entity - - - - - - - - - - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 - - - - results in morphogenesis of - - - - - - - - - - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 - - - - results in maturation of - - - - - - - - - foramen ovale closure SubClassOf results in disappearance of foramen ovale - - - May be merged into parent relation - results in disappearance of - - - - - - - - - every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890) - - - May be merged into parent relation - results in developmental regression of - - - - - - - - - - Inverse of 'is substance that treats' - - - is treated by substance - - - - - - - - - - - Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' -where -'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview - - x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - - adapted for living in - - A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. - has habitat - - - - - - - - - - p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - - - - holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y - causally upstream of, positive effect - - - - - - - - - - - p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - - - - - causally upstream of, negative effect - - - - - - - - - - A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. - - - - - 2017-06-05T17:35:04Z - has exposure stimulus - - - - - - - - - - evolutionary variant of - - - - - - - - - - Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. - - regulates localization of - - - - transports or maintains localization of - - - - - - - - - - - - - - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. - Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - - characteristic of part of - - - - - - - - - - true - - - - - - - - - - - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. - The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 - - - - results in acquisition of features of - - - - - - - - A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. - evolutionarily related to - - - - - - - - A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) - Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions - - ecologically related to - - - - - - - - - - An experimental relation currently used to connect a feature possessed by an organism (e.g. anatomical structure, biological process, phenotype or quality) to a habitat or environment in which that feature is well suited, adapted or provides a reproductive advantage for the organism. For example, fins to an aquatic environment. Usually this will mean that the structure is adapted for this environment, but we avoid saying this directly - primitive forms of the structure may not have evolved specifically for that environment (for example, early wings were not necessarily adapted for an aerial environment). Note also that this is a statement about the general class of structures - not every instance of a limb need confer an advantage for a terrestrial environment, e.g. if the limb is vestigial. - - adapted for - - confers advantage in - - - - - - - - A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - - mereotopologically related to - - - - - - - - A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development - developmentally related to - - - - - - - - - - - Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826) - a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO]. - - In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO] - - colocalizes with - - - - - - - - - - ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity. - Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity. - eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex - We would like to say - -if and only if - exists c', p' - c part_of c' and c' capable_of p - and - c capable_of p' and p' part_of p -then - c contributes_to p - -However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - - In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. - - contributes to - https://wiki.geneontology.org/Contributes_to - - - - - - - - - - - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity - c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - - enables - https://wiki.geneontology.org/Enables - - - - - - - - A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - functionally related to - - - - - - - - - - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false - part of structure that is capable of - - - - - - - - - true - - - - - - - - - - holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism - genomically related to - - - - - - - - - - - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of - involved in - https://wiki.geneontology.org/Involved_in - - - - - - - - - - - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid - p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) - regulates levels of - - - - - - - - - - inverse of enables - - - enabled by - https://wiki.geneontology.org/Enabled_by - - - - - - - - - - - - inverse of regulates - - regulated by (processual) - - regulated by - - - - - - - - - inverse of negatively regulates - - - negatively regulated by - - - - - - - - - inverse of positively regulates - - - positively regulated by - - - - - - - - - - A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. - related via localization to - - - - - - - - - - - - - This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - - - - - has target start location - - - - - - - - - - - - - This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - - - - - has target end location - - - - - - - - - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s. - - - imports - - - - - - - - - Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - - results in transport along - - - - - - - - - - Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - - - results in transport across - - - - - - - - - - 'pollen tube growth' results_in growth_of some 'pollen tube' - - results in growth of - - - - - - - - - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - - results in transport to from or in - - - - - - - - - Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the end location of c is part of the region that surrounds s. - - - exports - - - - - - - - - - an annotation of gene X to cell commitment with results_in_commitment_to CL:0000540 (neuron) means that at the end of the process an unspecified cell has been specified and determined to develop into a neuron. - p 'results in commitment to' c if and only if p is a developmental process and c is a cell and p results in the state of c changing such that is can only develop into a single cell type. - - - - - results in commitment to - - - - - - - - - - p 'results in determination of' c if and only if p is a developmental process and c is a cell and p results in the state of c changing to be determined. Once a cell becomes determined, it becomes committed to differentiate down a particular pathway regardless of its environment. - - - - - results in determination of - - - - - - - - - - An organism that is a member of a population of organisms - is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - - member of - - - - - - - - - - has member is a mereological relation between a collection and an item. - SIO - - has member - - - - - - - - - - inverse of has input - - - - input of - - - - - - - - - - inverse of has output - - - - output of - - - - - - - - - - formed as result of - - - - - - - - - - A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity. - - results in structural organization of - - - - - - - - - - The relationship linking a cell and its participation in a process that results in the fate of the cell being specified. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment. - - - - - results in specification of - - - - - - - - - p results in developmental induction of c if and only if p is a collection of cell-cell signaling processes that signal to a neighbouring tissue that is the precursor of the mature c, where the signaling results in the commitment to cell types necessary for the formation of c. - - results in developmental induction of - - - - - - - - - - http://neurolex.org/wiki/Property:DendriteLocation - has dendrite location - - - - - - - - - - - a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - - attached to - - - - - - - - - - - m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - has muscle origin - - - - - - - We need to import uberon muscle to create a stricter domain constraint - - - - - - - - - - - m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - has muscle insertion - - - - - - - We need to import uberon muscle into RO to use as a stricter domain constraint - - - - - - - - - false - - x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat - - - has fused element - A has_fused_element B does not imply that A has_part some B: rather than A has_part some B', where B' that has some evolutionary relationship to B. - derived from ancestral fusion of - - - - - - - - - - - - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - - in branching relationship with - - https://github.com/obophenotype/uberon/issues/170 - - - - - - - - - - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - - tributary of - - http://en.wikipedia.org/wiki/Tributary - - - - - - - - - - Deschutes River distributary_of Little Lava Lake - - x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - - branch of - distributary channel of - http://en.wikipedia.org/wiki/Distributary - - This is both a mereotopological relationship and a relationship defined in connection to processes. It concerns both the connecting structure, and how this structure is disposed to causally affect flow processes - distributary of - - - - - - - - - - - - - - - - - x anabranch_of y if x is a distributary of y (i.e. it channels a from a larger flow from y) and x ultimately channels the flow back into y. - - anastomoses with - - anabranch of - - - - - - - - - - - - - - - A lump of clay and a statue - x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios - spatially coextensive with - - - - - - - - - - - - - - - - - - - - - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S - x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - - branching part of - - FMA:85994 - - - - - - - - - - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, S is the main stem of T. There are no other main stems. If we were to slice off S to get a new tree T', rooted at the root of B1, then B1 would be the main stem of T'. - - x main_stem_of y if y is a branching structure and x is a channel that traces a linear path through y, such that x has higher capacity than any other such path. - - - main stem of - - - - - - - - - - - x proper_distributary_of y iff x distributary_of y and x does not flow back into y - - - proper distributary of - - - - - - - - - - x proper_tributary_of y iff x tributary_of y and x does not originate from y - - - proper tributary of - - - - - - - - - - - - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - - has developmental potential involving - - - - - - - - - - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - has potential to developmentally contribute to - - - - - - - - - - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - - has potential to developmentally induce - - - - - - - - - - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - This relation has a stronger meaning than merely indicating that X may develop into Y, in that the capability of developing into Y is always present, even if X does not always actually develop into Y. In particular, this means that if Y is restricted to a given taxon T, X is necessarily likewise restricted. - has potential to develop into - - - - - - - - - - - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - - has potential to directly develop into - - - - - - - - - - - - - 'protein catabolic process' SubClassOf has_direct_input some protein - - p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - directly consumes - This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate' - has direct input - - - - - - - - - - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect input - true - - - - - - - - translation SubClassOf has_direct_output some protein - - p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c. - - directly produces - obsolete has direct output - true - - - - - - - - - - - - - - Likely to be obsoleted. See: -https://docs.google.com/document/d/1QMhs9J-P_q3o_rDh-IX4ZEnz0PnXrzLRVkI3vvz8NEQ/edit - obsolete has indirect output - true - - - - - - - - - - - - inverse of upstream of - - causally downstream of - - - - - - - - - - - - - immediately causally downstream of - - - - - - - - - This term was obsoleted because it has the same meaning as 'directly positively regulates'. - obsolete directly activates - true - - - - - - - - - - - - - - - - - - - - - - - - - - - p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - - indirectly positively regulates - https://wiki.geneontology.org/Indirectly_positively_regulates - - - - - - - - - This term was obsoleted because it has the same meaning as 'directly negatively regulates'. - obsolete directly inhibits - true - - - - - - - - - - - - - - - - - - - - - - - p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - - indirectly negatively regulates - https://wiki.geneontology.org/Indirectly_negatively_regulates - - - - - - - - relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. - This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. - -To define causal relations in an activity-flow type network, we make use of 3 primitives: - - * Temporal: how do the intervals of the two occurrents relate? - * Is the causal relation regulatory? - * Is the influence positive or negative? - -The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. - -For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. - -For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. - -Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causally related to - - - - - relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. - https://en.wikipedia.org/wiki/Causality - - - - - - - - - - - p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - - - - causally upstream of - - - - - - - - - - p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - - immediately causally upstream of - - - - - - - - - - - - - - p provides input for q iff p is immediately causally upstream of q, and there exists some c such that p has_output c and q has_input c. - - directly provides input for - - directly provides input for (process to process) - provides input for - https://wiki.geneontology.org/Provides_input_for - - - - - - - - - - - - - transitive form of directly_provides_input_for - - This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'provides input for'. - transitively provides input for (process to process) - transitively provides input for - - - - - - - - - - - - - - - p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. - We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) - affects - causally upstream of or within - - - - - - - - false - - This is an exploratory relation - differs in - https://code.google.com/p/phenotype-ontologies/w/edit/PhenotypeModelCompetencyQuestions - - - - - - - - - - - - - - - - - - differs in attribute of - - - - - - - - - - - differs in attribute - - - - - - - - - - inverse of causally upstream of or within - - - - causally downstream of or within - - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - - involved in regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - - involved in positive regulation of - - - - - - - - - - - - - - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - - - involved in negative regulation of - - - - - - - - - - - c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p - OWL does not allow defining object properties via a Union - - involved in or reguates - involved in or involved in regulation of - - - - - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in - enables activity in - is active in - https://wiki.geneontology.org/Is_active_in - - - - - - - - - true - - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - - - - - - - - - - p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - contributes to morphology of - - - - - - - - - - - A relationship that holds between two entities in which the processes executed by the two entities are causally connected. - This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. - Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. - in pairwise interaction with - - interacts with - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 - - - - - - - - - - An interaction that holds between two genetic entities (genes, alleles) through some genetic interaction (e.g. epistasis) - - genetically interacts with - - http://purl.obolibrary.org/obo/MI_0208 - - - - - - - - - - An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with - molecularly interacts with - - http://purl.obolibrary.org/obo/MI_0915 - - - - - - - - - - - - - An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - - interacts with on organism level - - biotically interacts with - - http://eol.org/schema/terms/interactsWith - - - - - - - - - lions trophically interact with the zebras that they eat - An interaction relationship in which the partners are related via a feeding relationship. - - - trophically interacts with - - - - - - - - - - - A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824] - Baleen whale preys on krill - An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members - - - - is subject of predation interaction with - preys upon - - preys on - http://eol.org/schema/terms/preysUpon - http://www.inaturalist.org/observations/2942824 - - - - - - - - - - - - - - - - - whales symbiotically interact with the barnacles that attach to them - A biotic interaction in which the two organisms live together in more or less intimate association. - - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - We follow GO and PAMGO in using 'symbiosis' as the broad term encompassing mutualism through parasitism - - symbiotically interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which one benefits and the other is unaffected (GO). - - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - commensually interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which both organisms benefit from each other (GO). - - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - - mutualistically interacts with - - - - - - - - - - - - - - - - An interaction relationship between two organisms living together in more or less intimate association in a relationship in which association is disadvantageous or destructive to one of the organisms (GO). - - http://www.ncbi.nlm.nih.gov/pubmed/19278549 - This relation groups a pair of inverse relations, parasite of and parasitized by - - interacts with via parasite-host interaction - - - - - - - - - - - - - - - - - - Pediculus humanus capitis parasite of human - A parasite-host relationship where an organism benefits at the expense of another. - - parasitizes - direct parasite of - - parasite of - http://eol.org/schema/terms/parasitizes - - - - - - - - - - Inverse of parasite of - - has parasite - parasitised by - directly parasitized by - - parasitized by - http://eol.org/schema/terms/hasParasite - - - - - - - - - Porifiera attaches to substrate - A biotic interaction relationship in which one partner is an organism and the other partner is inorganic. For example, the relationship between a sponge and the substrate to which is it anchored. - - semibiotically interacts with - - participates in a abiotic-biotic interaction with - - - - - - - - - - - - - - - Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. - phosphorylates - - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - - molecularly controls - directly regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits - molecularly decreases activity of - directly negatively regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates - molecularly increases activity of - directly positively regulates activity of - - - - - - - - - all dengue disease transmitted by some mosquito - A relationship that holds between a disease and organism - Add domain and range constraints - - transmitted by - - - - - - - - - - A relation that holds between a disease or an organism and a phenotype - - has symptom - - - - - - - - - - The term host is usually used for the larger (macro) of the two members of a symbiosis (GO) - - host of - - - - - - - - - X 'has host' y if and only if: x is an organism, y is an organism, and x can live on the surface of or within the body of y - - - has host - http://eol.org/schema/terms/hasHost - - - - - - - - - - Bees pollinate Flowers - This relation is intended to be used for biotic pollination - e.g. a bee pollinating a flowering plant. Some kinds of pollination may be semibiotic - e.g. wind can have the role of pollinator. We would use a separate relation for this. - - is subject of pollination interaction with - - pollinates - http://eol.org/schema/terms/pollinates - - - - - - - - - - has polinator - is target of pollination interaction with - - pollinated by - http://eol.org/schema/terms/hasPollinator - - - - - - - - - - Inverse of provides nutrients for - - Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. - - acquires nutrients from - - - - - - - - - inverse of preys on - - has predator - is target of predation interaction with - - - preyed upon by - http://eol.org/schema/terms/HasPredator - http://polytraits.lifewatchgreece.eu/terms/PRED - - - - - - - - - - Anopheles is a vector for Plasmodium - - a is a vector for b if a carries and transmits an infectious pathogen b into another living organism - - is vector for - - - - - - - - - - - has vector - - - - - - - - - - Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target - partner in - - - - - - - - - - Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed. - subject participant in - - - - - - - - - - Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed. - target participant in - - - - - - - - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property (not for use in curation) - - - - - - - - - - is symbiosis - - - - - - - - - - is commensalism - - - - - - - - - - is mutualism - - - - - - - - - - is parasitism - - - - - - - - - A biotic interaction where a material entity provides nutrition for an organism. - - - provides nutrients for - - - - - - - - - A biotic interaction where one organism consumes a material entity through a type of mouth or other oral opening. - - is subject of eating interaction with - - eats - - - - - - - - - Inverse of eats - - eaten by - is target of eating interaction with - - is eaten by - - - - - - - - - - A relationship between a piece of evidence a and some entity b, where b is an information content entity, material entity or process, and -the a supports either the existence of b, or the truth value of b. - - - is evidence for - - - - - - - - - - - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' - x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - - composed primarily of - - - - - - - - - - - ABal nucleus child nucleus of ABa nucleus (in C elegans) - c is a child nucleus of d if and only if c and d are both nuclei and parts of cells c' and d', where c' is derived from d' by mitosis and the genetic material in c is a copy of the generic material in d - - This relation is primarily used in the worm anatomy ontology for representing lineage at the level of nuclei. However, it is applicable to any organismal cell lineage. - child nucleus of - - - - - - - - - A child nucleus relationship in which the cells are part of a hermaphroditic organism - - child nucleus of in hermaphrodite - - - - - - - - - A child nucleus relationship in which the cells are part of a male organism - - child nucleus of in male - - - - - - - - - - - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - - - has part that occurs in - - - - - - - - - true - - - - - - - - - - - - - - An interaction relation between x and y in which x catalyzes a reaction in which one or more ubiquitin groups are added to y - Axiomatization to GO to be added later - - ubiquitinates - - - - - - - - - - is kinase activity - - - - - - - - - - is ubiquitination - - - - - - - - - - See notes for inverse relation - - receives input from - - - - - - - - - This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - - sends output to - - - - - - - - - - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. - relation between physical entity and a process or stage - - - - - - - - - - - - - - - - - - x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - existence starts during - - - - - - - - - x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - existence starts with - - - - - - - - - x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence overlaps - - - - - - - - - - x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - exists during - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts and ends during - - - - - - - - - - - - - - - - - - x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during - - - - - - - - - x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends with - - - - - - - - - - x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - transformation of - - - - - - - - - - x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - immediate transformation of - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence starts during or after - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. - existence ends during or before - - - - - - - - - - A relationship between a material entity and a process where the material entity has some causal role that influences the process - - causal agent in process - - - - - - - - - - - p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between processes - - - - - - - - - depends on - - - - - - - - - - q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 - This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. - - - towards - - - - - - - - - 'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate - p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c - - has intermediate product - - has intermediate - - - - - - - - - - - The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - causal relation between entities - - - - - - - - - - - - - - A coral reef environment is determined by a particular coral reef - s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. - The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - - - determined by (system to material entity) - - - - determined by - - - - - - - - - inverse of determined by - - determines (material entity to system) - - - determines - - - - - - - - - - - - - - - - s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - - - determined by part of - - - - - - - - - true - - - - - - - - - - - - - - - - - - - - - - - - - - x is transcribed from y if and only if x is synthesized from template y - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - transcribed from - - - - - - - - - inverse of transcribed from - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - transcribed to - - - - - - - - - - - - - - - - - - - - - - - - - - x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - ribosomal translation of - - - - - - - - - - - - - - - - - - - - - - - - - inverse of ribosomal translation of - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - ribosomally translates to - - - - - - - - - - A relation that holds between two entities that have the property of being sequences or having sequences. - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving cause and effect. - The domain and range of this relation include entities such as: information-bearing macromolecules such as DNA, or regions of these molecules; abstract information entities encoded as a linear sequence including text, abstract DNA sequences; Sequence features, entities that have a sequence or sequences. Note that these entities are not necessarily contiguous - for example, the mereological sum of exons on a genome of a particular gene. - - sequentially related to - - - - - - - - - Every UTR is adjacent to a CDS of the same transcript - Two consecutive DNA residues are sequentially adjacent - Two exons on a processed transcript that were previously connected by an intron are adjacent - x is sequentially adjacent to y iff x and y do not overlap and if there are no base units intervening between x and y - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - sequentially adjacent to - - - - - - - - - - - Every CDS has as a start sequence the start codon for that transcript - x has start sequence y if the start of x is identical to the start of y, and x has y as a subsequence - - started by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has start sequence - - - - - - - - - - inverse of has start sequence - - starts - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - - is start sequence of - - - - - - - - - - - Every CDS has as an end sequence the stop codon for that transcript (note this follows from the SO definition of CDS, in which stop codons are included) - x has end sequence y if the end of x is identical to the end of y, and x has y as a subsequence - - ended by - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has end sequence - - - - - - - - - - inverse of has end sequence - - ends - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - - is end sequence of - - - - - - - - - x is a consecutive sequence of y iff x has subsequence y, and all the parts of x are made of zero or more repetitions of y or sequences as the same type as y. - In the SO paper, this was defined as an instance-type relation - - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - is consecutive sequence of - - - - - - - - - - Human Shh and Mouse Shh are sequentially aligned, by cirtue of the fact that they derive from the same ancestral sequence. - x is sequentially aligned with if a significant portion bases of x and y correspond in terms of their base type and their relative ordering - - - is sequentially aligned with - - - - - - - - - - - The genomic exons of a transcript bound the sequence of the genomic introns of the same transcript (but the introns are not subsequences of the exons) - x bounds the sequence of y iff the upstream-most part of x is upstream of or coincident with the upstream-most part of y, and the downstream-most part of x is downstream of or coincident with the downstream-most part of y - - - bounds sequence of - - - - - - - - - - inverse of bounds sequence of - - - - is bound by sequence of - - - - - - - - - - - - - x has subsequence y iff all of the sequence parts of y are sequence parts of x - - contains - http://www.ncbi.nlm.nih.gov/pubmed/20226267 - - has subsequence - - - - - - - - - - - - inverse of has subsequence - - contained by - - - is subsequence of - - - - - - - - - - - - - - - x overlaps the sequence of y if and only if x has a subsequence z and z is a subsequence of y. - - - overlaps sequence of - - - - - - - - - - x does not overlap the sequence of y if and only if there is no z such that x has a subsequence z and z is a subsequence of y. - - disconnected from - - does not overlap sequence of - - - - - - - - - - inverse of downstream of sequence of - - - is upstream of sequence of - - - - - - - - - - - x is downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, or (2) x and y are sequence units, and x is either immediately downstream of y, or transitively downstream of y. - - - is downstream of sequence of - - - - - - - - - - A 3'UTR is immediately downstream of the sequence of the CDS from the same monocistronic transcript - x is immediately downstream of the sequence of y iff either (1) x and y have sequence units, and all units of x are downstream of all units of y, and x is sequentially adjacent to y, or (2) x and y are sequence units, in which case the immediately downstream relation is primitive and defined by context: for DNA bases, y would be adjacent and 5' to y - - - - is immediately downstream of sequence of - - - - - - - - - - A 5'UTR is immediately upstream of the sequence of the CDS from the same monocistronic transcript - inverse of immediately downstream of - - - is immediately upstream of sequence of - - - - - - - - - - - - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' - A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - has skeleton - - - - - - This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. - - - - - - - - - - p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded. - - results in ending of - - - - - - - - - - - - - - x is a hyperparasite of y iff x is a parasite of a parasite of the target organism y - Note that parasite-of is a diret relationship, so hyperparasite-of is not considered a sub-relation, even though hyperparasitism can be considered a form of parasitism - - http://eol.org/schema/terms/hyperparasitoidOf - https://en.wikipedia.org/wiki/Hyperparasite - hyperparasitoid of - epiparasite of - - hyperparasite of - - - - - - - - - - - - - inverse of hyperparasite of - - has epiparasite - has hyperparasite - hyperparasitoidized by - - - hyperparasitized by - - - - - - - - - - A relationship between organisms where one organism is influenced by the biochemicals produced by another. - - http://en.wikipedia.org/wiki/Allelopathy - - Allelopathy is a phenomenon in which one organism releases chemicals to positively or negatively influence the growth, survival or reproduction of other organisms in its vicinity. - allelopath of - http://eol.org/schema/terms/allelopathyYes - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172429/ - x is an allelopath of y if x produces one or more biochemicals that influence the growth, survival, and reproduction of y - - - - - - - - - - Inverse of has pathogen - - - pathogen of - - - - - - - - - A host interaction where the smaller of the two members of a symbiosis causes a disease in the larger member - - - has pathogen - - - - - - - - - inverse of is evidence for - - - - - x has evidence y iff , x is an information content entity, material entity or process, and y supports either the existence of x, or the truth value of x. - has evidence - - - - - - - - - - - - causally influenced by (entity-centric) - causally influenced by - - - - - - - - - - interaction relation helper property - - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - - molecular interaction relation helper property - - - - - - - - - Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - - - - results in movement of - - - - - - - - - - - - - - - - - - - - - The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) - causally influences - - - - - - - - - - - A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. - biomechanically related to - - - - - - - - - m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - has muscle antagonist - - - - - - - - - - - inverse of branching part of - - - - has branching part - - - - - - - - - - - x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - - conduit for - - - - - - - - - - x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - - lumen of - - - - - - - - - - s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - - luminal space of - - - - - - - - - - A relation that holds between an attribute or a qualifier and another attribute. - - - This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. - - has modifier - - - - - - - - - - - - - participates in a biotic-biotic interaction with - - - - - - - - - - - - inverse of has skeleton - - - skeleton of - - - - - - - - - - p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - - - - - directly regulates - - - - - - - - - holds between x and y if and only if the time point at which x starts is equivalent to the time point at which y ends. Formally: iff α(x) = ω(y). - existence starts at end of - - - - - - - - - - - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' - s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - - has part structure that is capable of - - - - - - - - - - p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed. - results in closure of - - - - - - - - - p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p - results in breakdown of - - - - - - - - - results in synthesis of - - - - - - - - - - - - - results in assembly of - - - - - - - - - p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released. - results in catabolism of - - - - - - - - - - results in disassembly of - - - - - - - - - - results in remodeling of - - - - - - - - - p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c - results in organization of - - - - - - - - - holds between x and y if and only if the time point at which x ends is equivalent to the time point at which y starts. Formally: iff ω(x) = α(y). - existence ends at start of - - - - - - - - - - - A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - - causal relation between material entity and a process - - - - - - - - - - - - - pyrethroid -> growth - Holds between c and p if and only if c is capable of some activity a, and a regulates p. - - capable of regulating - - - - - - - - - - - - - Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - - capable of negatively regulating - - - - - - - - - - - - - renin -> arteriolar smooth muscle contraction - Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - - capable of positively regulating - - - - - - - - - pazopanib -> pathological angiogenesis - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p. - treats - - The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber. - capable of inhibiting or preventing pathological process - - - - - treats - Usage of the term 'treats' applies when we believe there to be a an inhibitory relationship - - - - - - - - - benzene -> cancer [CHEBI] - Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p. - causes disease - - capable of upregulating or causing pathological process - - - - - - - - - c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d. - treats - - is substance that treats - - - - - - - - - - c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d. - May be ceded to OBI - is marker for - - - - - - - - - Inverse of 'causal agent in process' - - process has causal agent - - - - - - - - A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - obsolete related via dependence to - true - - - - - - - - A relationship that holds between two entities, where the entities exhibit a statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. - Groups both positive and negative correlation - correlated with - - - - - - - - - An instance of a sequence similarity evidence (ECO:0000044) that uses a homologous sequence UniProtKB:P12345 as support. - A relationship between a piece of evidence and an entity that plays a role in supporting that evidence. - In the Gene Ontology association model, this corresponds to the With/From field - is evidence with support from - - - - - - - - - Inverse of is-model-of - has model - - - - - - - - Do not use this relation directly. It is a grouping relation. - related via evidence or inference to - - - - - - - - - - visits - https://github.com/oborel/obo-relations/issues/74 - - - - - - - - - visited by - - - - - - - - - - visits flowers of - - - - - - - - - has flowers visited by - - - - - - - - - - - lays eggs in - - - - - - - - - - has eggs laid in by - - - - - - - - - - https://github.com/jhpoelen/eol-globi-data/issues/143 - kills - - - - - - - - - is killed by - - - - - - - - - - p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - - - - - directly positively regulates - https://wiki.geneontology.org/Directly_positively_regulates - - - - - - - - - - p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) - - - - - directly negatively regulates - https://wiki.geneontology.org/Directly_negatively_regulates - - - - - - - - - - A sub-relation of parasite-of in which the parasite lives on or in the integumental system of the host - - ectoparasite of - - - - - - - - - inverse of ectoparasite of - - has ectoparasite - - - - - - - - - - - A sub-relation of parasite-of in which the parasite lives inside the host, beneath the integumental system - lives inside of - endoparasite of - - - - - - - - - has endoparasite - - - - - - - - - - A sub-relation of parasite-of in which the parasite is partially an endoparasite and partially an ectoparasite - mesoparasite of - - - - - - - - - inverse of mesoparasite of - - has mesoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits the spaces between host cells. - - intercellular endoparasite of - - - - - - - - - inverse of intercellular endoparasite of - - has intercellular endoparasite - - - - - - - - - - A sub-relation of endoparasite-of in which the parasite inhabits host cells. - - intracellular endoparasite of - - - - - - - - - inverse of intracellular endoparasite of - - has intracellular endoparasite - - - - - - - - - - Two or more individuals sharing the same roost site (cave, mine, tree or tree hollow, animal burrow, leaf tent, rock crack, space in man-made structure, etc.). Individuals that are sharing a communal roost may be said to be co-roosting. The roost may be either a day roost where the individuals rest during daytime hours, or a night roost where individuals roost to feed, groom, or rest in between flights and/or foraging bouts. Communal roosting as thus defined is an umbrella term within which different specialized types -- which are not mutually exclusive -- may be recognized based on taxonomy and the temporal and spatial relationships of the individuals that are co-roosting. - - co-roosts with - - - - - - - - - - An individual of species Camelus dromedarius (commonly known as dromedary camels) is a reservoir host of an individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) since at least the 1980s. - A relation between a host organism and a hosted organism in which the hosted organism naturally occurs in an indefinitely maintained reservoir provided by the host. - - - - A reservoir is a population, species or community (assemblage of different species in a given geographic area) in which a microorganism naturally occurs and is indefinitely maintained. Some zoonotic pathogens, particularly bacterial pathogens, may also have environmental reservoirs. Microorganisms with multiple reservoir species may be indefinitely maintained across the community of species even if they are not always present in each individual reservoir species. In the reservoir species or community, the microorganism may cause either asymptomatic infection or disease and this may vary among individuals. A pathogen may also be more genetically diverse in its reservoir host than in other taxa, in part because the pathogen is endemic to reservoir hosts. - reservoir host of - - - - - - - - - An individual of Middle East respiratory syndrome–related coronavirus (MERS-CoV) has an individual of species Camelus dromedarius (commonly known as dromedary camels) as their reservoir host since at least the 1980s. - inverse of reservoir host of - - has reservoir host - - - - - - - - - - - - - - - - - - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - - - Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. - produces - - - - - - - - - - - a produced_by b iff some process that occurs_in b has_output a. - - - produced by - - - - - - - - - - - Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA. - - represses expression of - - - - - - - - - - - Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA. - - increases expression of - - - - - - - - - - A relation between a biological, experimental, or computational artifact and an entity it is used to study, in virtue of its replicating or approximating features of the studied entity. - - is used to study - The primary use case for this relation was to link a biological model system such as a cell line or model organism to a disease it is used to investigate, in virtue of the model system exhibiting features similar to that of the disease of interest. But the relation is defined more broadly to support other use cases, such as linking genes in which alterations are made to create model systems to the condition the system is used to interrogate, or computational models to real-world phenomena they are defined to simulate. - has role in modeling - - - - - - - - - The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. - -An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'. - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition. - Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'. - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - causes or contributes to condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition. - causes condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition. - contributes to condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual. - contributes to expressivity of condition - contributes to severity of condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population. - contributes to penetrance of condition - contributes to frequency of condition - - - - - - - - - A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition. - is preventative for condition - Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. - -Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions. - ameliorates condition - - - - - - - - - A relationship between an entity and a condition (phenotype or disease) with which it exhibits a statistical dependence relationship. - correlated with condition - - - - - - - - - A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition. - exacerbates condition - - - - - - - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. - condition ameliorated by - - - - - - - - - A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity. - condition exacerbated by - - - - - - - - - - - - - - - - - - - - Do not use this relation directly. It is intended as a grouping for a more specific relations - - 2017-11-05T02:38:20Z - condition has genetic basis in - - - - - - - - - - - 2017-11-05T02:45:20Z - has material basis in gain of function germline mutation in - - - - - - - - - - - - - 2017-11-05T02:45:37Z - has material basis in loss of function germline mutation in - - - - - - - - - - - 2017-11-05T02:45:54Z - has material basis in germline mutation in - - - - - - - - - - - - 2017-11-05T02:46:07Z - has material basis in somatic mutation in - - - - - - - - - - - - 2017-11-05T02:46:26Z - has major susceptibility factor - - - - - - - - - - - 2017-11-05T02:46:57Z - has partial material basis in germline mutation in - - - - - - - - - p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. - - 2018-12-13T11:26:17Z - - has primary input or output - - - - - - - - - - p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - - 2018-12-13T11:26:32Z - - has primary output - - - - - p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. - - GOC:dph - GOC:kva - GOC:pt - PMID:27812932 - - - - - - - - - - p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - - 2018-12-13T11:26:56Z - - has primary input - - - - - p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c. - - GOC:dph - GOC:kva - GOC:pt - PMID:27812932 - - - - - - - - - - Do not use this relation directly. It is intended as a grouping for a more specific relations - - 2017-11-05T02:53:08Z - is genetic basis for condition - - - - - - - - - Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - - 2017-11-05T02:55:51Z - is causal gain of function germline mutation of in - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - - 2017-11-05T02:56:06Z - is causal loss of function germline mutation of in - - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet]. - - 2017-11-05T02:56:40Z - is causal germline mutation in - - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet]. - - 2017-11-05T02:57:07Z - is causal somatic mutation in - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet]. - - 2017-11-05T02:57:43Z - is causal susceptibility factor for - - - - - - - - - - - Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet]. - - 2017-11-05T02:58:43Z - is causal germline mutation partially giving rise to - - - - - - - - - - - - 2017-11-05T03:20:01Z - realizable has basis in - - - - - - - - - - 2017-11-05T03:20:29Z - is basis for realizable - - - - - - - - - - - - 2017-11-05T03:26:47Z - disease has basis in - - - - - - - - - - A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. - disease has basis in dysfunction of (disease to anatomical structure) - - 2017-11-05T03:29:32Z - disease has basis in dysfunction of - - - - - - - - - - A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. - disease has basis in disruption of (disease to process) - - 2017-11-05T03:37:52Z - disease has basis in disruption of - - - - - - - - - - - - - - - - - - - A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. - - 2017-11-05T03:46:07Z - disease has basis in feature - - - - - - - - - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject. - - 2017-11-05T03:50:54Z - causal relationship with disease as subject - - - - - - - - - - - - - - - - - - - A relationship between a disease and a process where the disease process disrupts the execution of the process. - disease causes disruption of (disease to process) - - 2017-11-05T03:51:09Z - disease causes disruption of - - - - - - - - - - - - - - - disease causes dysfunction of (disease to anatomical entity) - - 2017-11-05T03:58:20Z - disease causes dysfunction of - - - - - - - - - - - - - - - - - - - A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. - TODO: complete range axiom once more of CARO has been mireoted in to this ontology - This relation is intentionally very general, and covers isolated diseases, where the disease is realized as a process occurring in the location, and syndromic diseases, where one or more of the features may be present in that location. Thus any given disease can have multiple locations in the sense defined here. - - 2017-11-05T04:06:02Z - disease has location - - - - - - - - - - - - - - - - - - - A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity - - 2017-12-26T19:37:31Z - disease has inflammation site - - - - - - - - - - - - - - - A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - - 2017-12-26T19:45:49Z - realized in response to stimulus - - - - - - - - - - - - - - - - - - A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. - - 2017-12-26T19:50:53Z - disease has feature - - - - - - - - - - A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. Anatomical structure includes cellular and sub-cellular entities, such as chromosome and organelles. - - 2017-12-26T19:58:44Z - disease arises from alteration in structure - - - - - - - - - - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - - 2018-01-25T23:20:13Z - enables subfunction - - - - - - - - - - - - - - - 2018-01-26T23:49:30Z - - acts upstream of or within, positive effect - https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect - - - - - - - - - - - - - - - 2018-01-26T23:49:51Z - - acts upstream of or within, negative effect - https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect - - - - - - - - - - - - - - c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - - - 2018-01-26T23:53:14Z - - acts upstream of, positive effect - https://wiki.geneontology.org/Acts_upstream_of,_positive_effect - - - - - - - - - - - - - - c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - - - 2018-01-26T23:53:22Z - - acts upstream of, negative effect - https://wiki.geneontology.org/Acts_upstream_of,_negative_effect - - - - - - - - - - - 2018-03-13T23:55:05Z - causally upstream of or within, negative effect - https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect - - - - - - - - - - - 2018-03-13T23:55:19Z - causally upstream of or within, positive effect - - - - - - - - - DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. - DEPRECATED inheres in - true - - - - - - - - DEPRECATED bearer of - true - - - - - - - - A relation between two entities, in which one of the entities is any natural or human-influenced factor that directly or indirectly causes a change in the other entity. - - has driver - - - - - - - - - - A relation between an entity and a disease of a host, in which the entity is not part of the host itself, and the condition results in pathological processes. - - has disease driver - - - - - - - - - - - An interaction relationship wherein a plant or algae is living on the outside surface of another plant. - https://en.wikipedia.org/wiki/Epiphyte - epiphyte of - - - - - - - - - inverse of epiphyte of - - has epiphyte - - - - - - - - - - A sub-relation of parasite of in which a parasite steals resources from another organism, usually food or nest material - https://en.wikipedia.org/wiki/Kleptoparasitism - kleptoparasite of - - - - - - - - - inverse of kleptoparasite of - - kleptoparasitized by - - - - - - - - - - - An interaction relationship wherein one organism creates a structure or environment that is lived in by another organism. - creates habitat for - - - - - - - - - - - - An interaction relationship describing organisms that often occur together at the same time and space or in the same environment. - ecologically co-occurs with - - - - - - - - - - An interaction relationship in which organism a lays eggs on the outside surface of organism b. Organism b is neither helped nor harmed in the process of egg laying or incubation. - lays eggs on - - - - - - - - - inverse of lays eggs on - has eggs laid on by - - - - - - - - - - - Flying foxes (Pteropus giganteus) has_roost banyan tree (Ficus benghalensis) - x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x. - - 2023-01-18T14:28:21Z - - A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y. - has roost - - - - - - - - - frog symbiotrophically interacts with the pitcher plant it lives inside of - A trophic interaction in which one organism acquires nutrients through a symbiotic relationship with another organism - - 2023-07-17T14:39:56Z - - symbiotrophically interacts with - - - - - - - - - tapeworm is trophic parasite of the cow it lives inside of - A symbiotrophic interaction in which one organism acquires nutrients through a parasitic relationship with another organism - - 2023-07-17T14:41:07Z - - trophic parasite of - - - - - - - - - - - muffin 'has substance added' some 'baking soda' - - "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - - has substance added - - - - - - - - - - - 'egg white' 'has substance removed' some 'egg yolk' - - "has substance removed" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time. - - has substance removed - - - - - - - - - - - sardines 'immersed in' some 'oil and mustard' - - "immersed in" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance. - - immersed in - - - - - - - - - - sardine has consumer some homo sapiens - - 'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect. - - has consumer - - - - - - - - - - bread 'has primary substance added' some 'flour' - - 'has primary substance added' indicates that an entity has had the given substance added to it in a proportion greater than any other added substance. - - has primary substance added - - - - - - - - - - - A mass measurement assay measures an material's mass characteristic. A radioactivity detection assay measures the amount of radiation (alpha, beta or gamma ray emmissions) coming from a material. - A relation between an assay and a characteristic, in which the assay generates a data item which is a measure of a characteristic. - - 2023-05-23T15:24:15Z - assay measures characteristic - - - - - - - - - - Inverse of 'assay measures characteristic' - - 2023-05-23T15:29:50Z - characteristic measured by assay - - - - - - - - - - - - - - - A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions. - An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) - Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. - r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - - - - - triggered by process - realized in response to - https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit - - - - - triggered by process - - - - - - - - - - - - - - - - Genetic information generically depend on molecules of DNA. - The novel *War and Peace* generically depends on this copy of the novel. - The pattern shared by chess boards generically depends on any chess board. - The score of a symphony g-depends on a copy of the score. - This pdf file generically depends on this server. - A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. - [072-ISO] - g-depends on - generically depends on - - - - - - - - - - - - - - Molecules of DNA are carriers of genetic information. - This copy of *War and Peace* is carrier of the novel written by Tolstoy. - This hard drive is carrier of these data items. - *b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t* - [072-ISO] - is carrier of - - - - - - - - - - - The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - - regulates activity of - - - - - - - - - - - The entity A has an activity that regulates the quantity or abundance or concentration of the entity B. - - regulates quantity of - - - - - - - - - - - The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B. - - indirectly regulates activity of - - - - - - - - - - - The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. - -For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B. - - decreases by repression quantity of - - - - - - - - - - - The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. - -For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B. - - increases by expression quantity of - - - - - - - - - - - The entity A has an activity that directly positively regulates the quantity of B. - - directly positively regulates quantity of - - - - - - - - - - - The entity A has an activity that directly negatively regulates the quantity of B. - - directly negatively regulates quantity of - - - - - - - - - - - The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B. - - indirectly activates - indirectly positively regulates activity of - - - - - - - - - - - AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844) - An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it. - - destabilizes quantity of - - - - - - - - - - - AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488) - An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it. - - stabilizes quantity of - - - - - - - - - The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B. - - indirectly inhibits - indirectly negatively regulates activity of - - - - - - - - - The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B. - - directly regulates quantity of - - - - - - - - - The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B. - - indirectly regulates quantity of - - - - - - - - - The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B. - - indirectly negatively regulates quantity of - - - - - - - - - The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B. - - indirectly positively regulates quantity of - - - - - - - - - - a relation between a process and a continuant, in which the process is regulated by the small molecule continuant - - 2020-04-22T20:27:26Z - has small molecule regulator - - - - - - - - - - a relation between a process and a continuant, in which the process is activated by the small molecule continuant - - 2020-04-22T20:28:37Z - has small molecule activator - - - - - - - - - - a relation between a process and a continuant, in which the process is inhibited by the small molecule continuant - - 2020-04-22T20:28:54Z - has small molecule inhibitor - - - - - - - - - p acts on population of c iff c' is a collection, has members of type c, and p has participant c - - 2020-06-08T17:21:33Z - - - - acts on population of - - - - - - - - - a relation between a continuant and a process, in which the continuant is a small molecule that regulates the process - - 2020-06-24T13:15:17Z - is small molecule regulator of - - - - - - - - - - a relation between a continuant and a process, in which the continuant is a small molecule that activates the process - - 2020-06-24T13:15:26Z - is small molecule activator of - https://wiki.geneontology.org/Is_small_molecule_activator_of - - - - - - - - - - a relation between a continuant and a process, in which the continuant is a small molecule that inhibits the process - - 2020-06-24T13:15:35Z - is small molecule inhibitor of - https://wiki.geneontology.org/Is_small_molecule_inhibitor_of - - - - - - - - - The relationship that links anatomical entities with a process that results in the adhesion of two or more entities via the non-covalent interaction of molecules expressed in, located in, and/or adjacent to, those entities. - - 2020-08-27T08:13:59Z - results in adhesion of - - - - - - - - - - 2021-02-26T07:28:29Z - - - - results in fusion of - - - - - - - - - p is constitutively upstream of q iff p is causally upstream of q, p is required for execution of q or a part of q, and the execution of p is approximately constant. - - 2022-09-26T06:01:01Z - - - constitutively upstream of - https://wiki.geneontology.org/Constitutively_upstream_of - - - - - - - - - p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. - - 2022-09-26T06:06:20Z - - - removes input for - https://wiki.geneontology.org/Removes_input_for - - - - - - - - - p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - - 2022-09-26T06:07:17Z - indirectly causally upstream of - - - - - - - - - - p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - - 2022-09-26T06:08:01Z - indirectly regulates - - - - - - - - - x 'positively regulates in other organism' y if and only if: (x is the realization of a function to increase the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - - - 2023-10-12T10:02:28Z - positively regulates in other organism - - positively regulates in another organism - - - - - - - - - x 'negatively regulates in other organism' y if and only if: (x is the realization of a function to reduce the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2). - - - 2023-10-12T10:02:42Z - negatively regulates in other organism - - negatively regulates in another organism - - - - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region. - - 2020-07-17T09:26:52Z - has synaptic input or output in - has synaptic IO in region - - - - - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses in that region. - - 2020-07-17T09:42:23Z - receives synaptic input in region - - - - - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of output synapses in that region. - - 2020-07-17T09:45:06Z - sends synaptic output to region - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses distributed throughout that region (rather than confined to a subregion). - - 2020-07-17T09:52:19Z - has synaptic IO throughout - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number of input synapses distributed throughout that region (rather than confined to a subregion). - - 2020-07-17T09:55:36Z - receives synaptic input throughout - - - - - - - - - - A relationship between a neuron and a region, where the neuron has a functionally relevant number output synapses distributed throughout that region (rather than confined to a subregion). - - 2020-07-17T09:57:27Z - sends synaptic output throughout - - - - - - - - - - - - - - Relation between a sensory neuron and some structure in which it receives sensory input via a sensory dendrite. - - 2020-07-20T12:10:09Z - has sensory dendrite location - has sensory terminal in - has sensory terminal location - has sensory dendrite in - - - - - - - - - - A relationship between an anatomical structure (including cells) and a neuron that has a functionally relevant number of chemical synapses to it. - - 2021-05-26T08:40:18Z - receives synaptic input from neuron - - - - - - - - - A relationship between a neuron and a cell that it has a functionally relevant number of chemical synapses to. - - 2021-05-26T08:41:07Z - Not restricting range to 'cell' - object may be a muscle containing a cell targeted by the neuron. - sends synaptic output to cell - - - - - - - - - - - - - An optic lobe intrinsic neuron has its synapses restricted to optic lobe neuropil. - A relationship between a neuron and a region, where all of the functionally relevant input and output synapses are in that region. - - 2023-08-17T12:17:24Z - intrinsic to - This relation may still be used if a very small number of synapses fall slightly outside the boundaries of the region, but any class using this relation should not have another restriction using this relation to another non-overlapping region. - synapses restricted to region - - - - - - - - - A relationship between a disease and an infectious agent where the material basis of the disease is an infection with some infectious agent. - - disease has infectious agent - - - - - - - - - - - - - - transcriptomically defined cell type X equivalent to ‘cell’ and (has_exemplar_data value [transcriptomic profile data]) - A relation between a material entity and some data in which the data is taken as exemplifying the material entity. - C has_exemplar_data y iff x is an instance of C and y is data about x that is taken as exemplifying of C. - - This relation is not meant to capture the relation between occurrents and data. - has exemplar data - - - - - - - - - - exemplar data of - - - - - - - - - - A relation between a group and another group it is part of but does not fully constitute. - X subcluster_of Y iff: X and Y are clusters/groups; X != Y; all members of X are also members of Y. - - This is used specifically for sets whose members are specified by some set-forming operator (method of grouping) such as clustering analyses in single cell transcriptomics. - subcluster of - - - - - - - - - 'Lamp5-like Egln3_1 primary motor cortex GABAergic interneuron (Mus musculus)' subClass_of: has_characterizing_marker_set some 'NS forest marker set of Lamp5-like Egln3_1 MOp (Mouse).'; NS forest marker set of Lamp5-like Egln3_1 SubClass_of: ('has part' some 'Mouse Fbn2') and ('has part' some 'Mouse Chrna7') and ('has part' some 'Mouse Fam19a1'). - transcriptomically defined cell type X subClass_of: (has_characterizing_marker_set some S1); S1 has_part some gene 1, S1 has_part some gene 2, S1 has_part some gene 3. - A relation that applies between a cell type and a set of markers that can be used to uniquely identify that cell type. - C has_characterizing_marker_set y iff: C is a cell type and y is a collection of genes or proteins whose expression is sufficient to distinguish cell type C from most or all other cell types. - This relation is not meant for cases where set of genes/proteins are only useful as markers in some specific context - e.g. in some specific location. In these cases it is recommended to make a more specific cell class restricted to the relevant context. - - has marker gene combination - has marker signature set - has characterizing marker set - - - - - - - - - - q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - different in magnitude relative to - - - - - q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - - - - q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. - increased in magnitude relative to - - - - - q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - - - - q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. - decreased in magnitude relative to - - - - - q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - similar in magnitude relative to - - - - - q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - has relative magnitude - - - - - - - - s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. - Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. - has cross section - - - - - s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. - There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. - reciprocal of - - - - - q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. - https://orcid.org/0000-0002-6601-2165 - - - - - - - - - - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') - A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - - - has high plasma membrane amount - - - - - A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. - PMID:19243617 - - - - - - - - - - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') - A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - - - has low plasma membrane amount - - - - - A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. - PMID:19243617 - - - - - - - - Do not use this relation directly. It is intended as a grouping for a set of relations regarding presentation of phenotypes and disease. - - 2021-11-05T17:30:14Z - has phenotype or disease - https://github.com/oborel/obo-relations/issues/478 - - - - - - - - - A relationship that holds between an organism and a disease. Here a disease is construed broadly as a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. - - 2021-11-05T17:30:44Z - has disease - https://github.com/oborel/obo-relations/issues/478 - - - - - - - - - X has exposure medium Y if X is an exposure event (process), Y is a material entity, and the stimulus for X is transmitted or carried in Y. - ExO:0000083 - - 2021-12-14T20:41:45Z - has exposure medium - - - - - - - - - - - - A diagnostic testing device utilizes a specimen. - X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 - - - 2021-11-08T12:00:00Z - utilizes - device utilizes material - - - - - - - - - - A relation between entities in which one increases or decreases as the other does the same. - directly correlated with - - positively correlated with - - - - - - - - - - - A relation between entities in which one increases as the other decreases. - inversely correlated with - - negatively correlated with - - - - - - - - - - anticoagulant-containing test tube contains measured amount 5 ml of blood specimen. - A relation between a container and measurement datum that specifies the actual amount of material in the container. - - - contains measured amount - - - - - - - - - - anticoagulant-containing test tube has maximum capacity 10 ml. - A relation that relates a container to a measurement datum that specifies the maximum capacity of the container. Capacity can refer to either weight or volume. - - - has maximum capacity - - - - - - - - - biobank organization owns a specimen - hospital owns a laboratory facility - A primitive relation that holds between entities x and y in which y is at x's full disposal. - - - - This primitive relation is the foundation of the owner's right to have the owned entity at his/her full disposal. - 2023-03-29T16:57:03Z - owns - - - - - - - - freezer is owned by a biobank organization - Inverse of the owns relation. - - - - 2023-03-29T17:06:06Z - - is owned by - - - - - - - - - - A thorax specimen was collected during the larval stage. - An oyster was collected during low tide. - A relation between a material entity and an occurrent in which the material entity is collected during the existence of the occurrent. - - 2023-09-13T04:12:32Z - collected during - - - - - - - - - Helper relation for OWL definition of RO:0018002 myristoylates - - is myristoyltransferase activity - - - - - - - - - - - - - - - A molecularly-interacts-with relationship between two entities, where the subject catalyzes a myristoylation activity that takes the object as input - - - myristoylates - - - - - - - - inverse of myristoylates - - myristoylated by - - - - - - - - - mibolerone (CHEBI:34849) is agonist of androgen receptor (PR:P10275) - a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor activates some activity of the receptor - - is agonist of - - - - - - - - - - pimavanserin (CHEBI:133017) is inverse agonist of HTR2A (PR:P28223) - a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor inhibits some activity of the receptor to below basal level - - is inverse agonist of - - - - - - - - - - tretinoin (CHEBI:15367) is antagonist of Nuclear receptor ROR-beta (PR:Q92753) - a relation between a ligand (material entity) and a receptor (material entity) that implies the binding of the ligand to the receptor reduces some activity of the receptor to basal level - - is antagonist of - - - - - - - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a chemical. - - chemical relationship - - - - - - - - - - pyruvate anion (CHEBI:15361) is the conjugate base of the neutral pyruvic acid (CHEBI:32816) - A is a direct conjugate base of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by receiving a particular proton transforms it into B. - - - is direct conjugate base of - - - - - - - - - - neutral pyruvic acid (CHEBI:32816) is the conjugate acid of the pyruvate anion (CHEBI:15361) - A is a direct conjugate acid of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing a particular proton transforms it into B. - - - is direct conjugate acid of - - - - - - - - - - - - (E)-cinnamoyl-CoA(4-) (CHEBI:57252) is a deprotonated form (E)-cinnamoyl-CoA (CHEBI:10956), which involves removing four protons. - A is a deprotonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Base (i.e., can receive a proton) and by adding some nonzero number of protons transforms it into B. - -This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. - - obo:chebi#is_conjugate_base_of - is deprotonated form of - - - - - - - - - - - (E)-cinnamoyl-CoA (CHEBI:10956) is a protonated form of (E)-cinnamoyl-CoA(4-) (CHEBI:57252), which involves adding four protons. - A is a protonated form of B if and only if A is chemical entity that is a Brønsted–Lowry Acid (i.e., can give up a proton) and by removing some nonzero number of protons transforms it into B. - -This is a transitive relationship and follows this design pattern: https://oborel.github.io/obo-relations/direct-and-indirect-relations. - - obo:chebi#is_conjugate_acid_of - is protonated form of - - - - - - - - - - - phenol (CHEBI:15882) and aniline (CHEBI:17296) are matched molecular pairs because they differ by one chemical transformation i.e., the replacement of aryl primary amine with aryl primary alcohol. - A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. - -While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. - -This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. - -This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. - - 2023-02-28T18:53:32Z - is MMP with - is matched molecular pair with - is matched small molecular pair with - - - - - A and B are a matched small molecular pair (MMP) if their chemical structures define by a single, relatively small, well-defined structural modification. - -While this is normally called "matched molecular pair" in the cheminformatics literaturel, it is labeled as "matched small molecular pair" so as to reduce confusion with peptides and other macromolecules, which are also referenced as "molecules" in some contexts. - -This relationship is symmetric, meaning if A is a MMP with B iff B is a MMP with A. - -This relationship is not transitive, meaning that A is a MMP with B and B is a MMP with C, then A is not necessarily an MMP with C. - - - - - - - - - - - - - 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. - Two chemicals are tautomers if they can be readily interconverted. - -This commonly refers to prototropy in which a hydrogen's position is changed, such as between ketones and enols. This is also often observed in heterocyclic rings, e.g., ones containing nitrogens and/or have aryl functional groups containing heteroatoms. - - 2023-03-18T23:49:31Z - obo:chebi#is_tautomer_of - is desmotrope of - is tautomer of - - - - - - 3-carboxy-3-mercaptopropanoate (CHEBI:38707) is tautomer of 1,2-dicarboxyethanethiolate (CHEBI:38709) because 3-carboxy-3-mercaptopropanoate is deprotonated on the carboxylic acid whereas 1,2-dicarboxyethanethiolate is deprotonated on the secondary thiol. - - - - - - - - - - - carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) - Group A is a substituent group from Chemical B if A represents the functional part of A and includes information about where it is connected. A is not itself a chemical with a fully formed chemical graph, but is rather a partial graph with one or more connection points that can be used to attach to another chemical graph, typically as a functionalization. - - 2023-03-18T23:49:31Z - obo:chebi#is_substituent_group_from - is substitutent group from - - - - - - carboxylatoacetyl group (CHEBI:58957) is substituent group from malonate(1-) (CHEBI:30795) - - - - - - - - - - - hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) - Chemical A has functional parent Chemical B if there is chemical transformation through which chemical B can be produced from chemical A. - -For example, the relationship between a salt and a freebased compound is a "has functional parent" relationship. - - 2023-03-18T23:49:31Z - obo:chebi#has_functional_parent - has functional parent - - - - - - hydrocortamate hydrochloride (CHEBI:50854) has parent hydride hydrocortamate (CHEBI:50851) - - - - - - - - - - - - dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. - Chemicals A and B are enantiomers if they share the same molecular graph except the change of the configuration of substituents around exactly one chiral center. - -A chemical with no chiral centers can not have an enantiomer. A chemical with multiple chiral centers can have multiple enantiomers, but its enantiomers are not themselves enantiomers (they are diastereomers). - - 2023-03-18T23:49:31Z - obo:chebi#is_enantiomer_of - is optical isomer of - is enantiomer of - - - - - - dexmedetomidine hydrochloride (CHEBI:31472) is enantiomer of levomedetomidine hydrochloride (CHEBI:48557) because the stereochemistry of the central chiral carbon is swapped. - - - - - - - - - - - pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. - Chemical A has parent hydride Chemical B if there exists a molecular graphical transformation where functional groups on A are replaced with hydrogens in order to yield B. - - 2023-03-18T23:49:31Z - obo:chebi#has_parent_hydride - has parent hydride - - - - - - pyranine (CHEBI:52083) has parent hydride pyrene (CHEBI:39106). Pyrene is molecule with four fused benzene rings, whereas pyranine has the same core ring structure with additional sulfates. - - - - - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. - - regulates characteristic - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. - - positively regulates characteristic - - - - - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. - - negatively regulates characteristic - - - - - - - - - Relates a gene to condition, such that a variation in this gene predisposes to the development of a condition. - - confers susceptibility to condition - - - - - - - - - - - brachial artery vessel supplies blood to brachialis muscle - x vessel supplies blood to y if and only if x is a vessel that supplies blood directly or indirectly to an anatomical structure y. - - 2024-02-01T10:09:22Z - vessel supplies blood to - - - - - - - - - - - cystic vein vessel drains blood from gallbladder - x vessel drains blood from y if and only if x is a vessel that drains blood directly or indirectly from an anatomical structure y. - - 2024-02-01T10:09:41Z - vessel drains blood from - - - - - - - - - - - - alveolar capillary directly supplies and drains some alveolus - x directly supplies and drains y if and only if x is a capillary, y is an anatomical entity, and x directly supplies and drains y. - - 2024-02-01T10:09:59Z - directly supplies and drains - - - - - - - - - This property only applies to neurons - - 2024-10-23T14:34:52Z - is neuron - - - - - - - - - This property only applies to anatomical entities. - - 2024-10-29T09:55:07Z - is anatomical entity - - - - - - - - - - - A relationship between a ratio or proportion and its dividend. - - has dividend - has numerator - - - - - - - - - - - A relationship between a ratio or proportion and its divisor. - - has divisor - has denominator - - - - - - - - - inverse of allelopath of - - has allelopath - https://en.wikipedia.org/wiki/Allelopathy - - - - - - - - This relation groups relations between diseases and any other kind of entity. - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease. - - 2018-09-26T00:00:32Z - disease relationship - - - - - - - - - p has anatomical participant c iff p has participant c, and c is an anatomical entity - - 2018-09-26T01:08:58Z - results in changes to anatomical or cellular structure - - - - - - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - TODO: Add homeomorphy axiom - - - - - ECO:0000041 - SO:similar_to - sameness - similar to - correspondence - resemblance - in similarity relationship with - - - - - - Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison. - - BGEE:curator - - - - - correspondence - - - - - - - - - - - - - Similarity that results from common evolutionary origin. - - - homologous to - This broad definition encompasses all the working definitions proposed so far in the literature. - in homology relationship with - - - - - - Similarity that results from common evolutionary origin. - - - - - - - - - - - - - - Similarity that results from independent evolution. - - - homoplasous to - analogy - in homoplasy relationship with - - - - - - Similarity that results from independent evolution. - - - - - - - - - - - - - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - - ECO:0000075 - homocracous to - Homology and homocracy are not mutually exclusive. The homology relationships of patterning genes may be unresolved and thus may include orthologues and paralogues. - in homocracy relationship with - - - - - - Similarity that is characterized by the organization of anatomical structures through the expression of homologous or identical patterning genes. - - - - - - - - - - - - - - Homoplasy that involves different underlying mechanisms or structures. - - - analogy - Convergence usually implies a notion of adaptation. - in convergence relationship with - - - - - - Homoplasy that involves different underlying mechanisms or structures. - - - - - - - - - - - - Homoplasy that involves homologous underlying mechanisms or structures. - - - parallel evolution - Can be applied for features present in closely related organisms but not present continuously in all the members of the lineage. - in parallelism relationship with - - - - - - Homoplasy that involves homologous underlying mechanisms or structures. - - - - - - - - - - - - Homology that is defined by similarity with regard to selected structural parameters. - - - ECO:0000071 - MI:2163 - structural homologous to - idealistic homology - in structural homology relationship with - - - - - - Homology that is defined by similarity with regard to selected structural parameters. - - - - ISBN:0123195837 - - - - - - - - - - Homology that is defined by common descent. - - - homology - ECO:0000080 - RO_proposed_relation:homologous_to - SO:0000330 - SO:0000853 - SO:0000857 - SO:homologous_to - TAO:homologous_to - cladistic homology - historical homologous to - phylogenetic homology - taxic homology - true homology - in historical homology relationship with - - - - - - Homology that is defined by common descent. - - - ISBN:0123195837 - - - - - - - - - - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - - ECO:0000067 - biological homologous to - transformational homology - Applicable only to morphology. A certain degree of ambiguity is accepted between biological homology and parallelism. - in biological homology relationship with - - - - - - Homology that is defined by sharing of a set of developmental constraints, caused by locally acting self-regulatory mechanisms of differentiation, between individualized parts of the phenotype. - - - - - - - - - - - - - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - - atavism - rudiment - reversion - in reversal relationship with - - - - - - Homoplasy that involves phenotypes similar to those seen in ancestors within the lineage. - - - - - - - - - - - - Structural homology that is detected by similarity in content and organization between chromosomes. - - - MeSH:Synteny - SO:0000860 - SO:0005858 - syntenic homologous to - synteny - in syntenic homology relationship with - - - - - - Structural homology that is detected by similarity in content and organization between chromosomes. - - MeSH:Synteny - - - - - - - - - - - Historical homology that involves genes that diverged after a duplication event. - - - SO:0000854 - SO:0000859 - SO:paralogous_to - paralogous to - in paralogy relationship with - - - - - - Historical homology that involves genes that diverged after a duplication event. - - - - - - - - - - - - - - - Paralogy that involves sets of syntenic blocks. - - - syntenic paralogous to - duplicon - paralogon - in syntenic paralogy relationship with - - - - - - Paralogy that involves sets of syntenic blocks. - - - DOI:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y - - - - - - - - - - Syntenic homology that involves chromosomes of different species. - - - syntenic orthologous to - in syntenic orthology relationship with - - - - - - Syntenic homology that involves chromosomes of different species. - - - - - - - - - - - - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - - fractional homology - partial homologous to - segmental homology - mixed homology - modular homology - partial correspondence - percent homology - in partial homology relationship with - - - - - - Structural homology that involves complex structures from which only a fraction of the elements that can be isolated are separately homologous. - - ISBN:0123195837 - ISBN:978-0471984931 - - - - - - - - - - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - - MeSH:Structural_Homology,_Protein - protein structural homologous to - in protein structural homology relationship with - - - - - - Structural homology that is detected at the level of the 3D protein structure, but maybe not at the level of the amino acid sequence. - - - - - - - - - - - - - Structural homology that involves a pseudogenic feature and its functional ancestor. - - - pseudogene - SO:non_functional_homolog_of - non functional homologous to - in non functional homology relationship with - - - - - - Structural homology that involves a pseudogenic feature and its functional ancestor. - - SO:non_functional_homolog_of - - - - - - - - - - Historical homology that involves genes that diverged after a speciation event. - - - ECO:00000060 - SO:0000855 - SO:0000858 - SO:orthologous_to - orthologous to - The term is sometimes also used for anatomical structures. - in orthology relationship with - - - - - - Historical homology that involves genes that diverged after a speciation event. - - - - - - - - - - - - - - - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - - xenologous to - The term is sometimes also used for anatomical structures (e.g. in case of a symbiosis). - in xenology relationship with - - - - - - Historical homology that is characterized by an interspecies (horizontal) transfer since the common ancestor. - - - - - - - - - - - - - Historical homology that involves two members sharing no other homologs in the lineages considered. - - - 1 to 1 homologous to - 1:1 homology - one-to-one homology - in 1 to 1 homology relationship with - - - - - - Historical homology that involves two members sharing no other homologs in the lineages considered. - - BGEE:curator - - - - - - - - - - - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - - 1 to 1 orthologous to - 1:1 orthology - one-to-one orthology - in 1 to 1 orthology relationship with - - - - - - Orthology that involves two genes that did not experience any duplication after the speciation event that created them. - - - - - - - - - - - - - Paralogy that results from a whole genome duplication event. - - - ohnologous to - homoeology - in ohnology relationship with - - - - - - Paralogy that results from a whole genome duplication event. - - - - - - - - - - - - - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - - in-paralogous to - inparalogy - symparalogy - in in-paralogy relationship with - - - - - - Paralogy that results from a lineage-specific duplication subsequent to a given speciation event. - - - - - - - - - - - - Paralogy that results from a duplication preceding a given speciation event. - - - alloparalogy - out-paralogous to - outparalogy - in out-paralogy relationship with - - - - - - Paralogy that results from a duplication preceding a given speciation event. - - - - - - - - - - - - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - - pro-orthologous to - in pro-orthology relationship with - - - - - - 1:many orthology that involves a gene in species A and one of its ortholog in species B, when duplications more recent than the species split have occurred in species B but not in species A. - - - - - - - - - - - - - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - - semi-orthologous to - The converse of pro-orthologous. - in semi-orthology relationship with - - - - - - 1:many orthology that involves a gene in species A and its ortholog in species B, when duplications more recent than the species split have occurred in species A but not in species B. - - - - - - - - - - - - - Iterative homology that involves structures arranged along the main body axis. - - - serial homologous to - homonomy - in serial homology relationship with - - - - - - Iterative homology that involves structures arranged along the main body axis. - - - - - - - - - - - - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - - heterochronous homologous to - heterochrony - in heterochronous homology relationship with - - - - - - Biological homology that is characterized by changes, over evolutionary time, in the rate or timing of developmental events of homologous structures. - - ISBN:978-0674639416 - - - - - - - - - - - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - - juvenification - pedomorphosis - in paedomorphorsis relationship with - - - - - - Heterochronous homology that is produced by a retention in adults of a species of traits previously seen only in juveniles. - - - ISBN:978-0674639416 - - - - - - - - - - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - in peramorphosis relationship with - - - - - - Heterochronous homology that is produced by a maturation of individuals of a species past adulthood, which take on hitherto unseen traits. - - - - - - - - - - - - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - in progenesis relationship with - - - - - - Paedomorphosis that is produced by precocious sexual maturation of an organism still in a morphologically juvenile stage. - - - ISBN:978-0674639416 - - - - - - - - - - Paedomorphosis that is produced by a retardation of somatic development. - - - juvenilization - neotenous to - in neoteny relationship with - - - - - - Paedomorphosis that is produced by a retardation of somatic development. - - - ISBN:978-0674639416 - - - - - - - - - - Convergence that results from co-evolution usually involving an evolutionary arms race. - - - mimicrous to - in mimicry relationship with - - - - - - Convergence that results from co-evolution usually involving an evolutionary arms race. - - - - - - - - - - - - - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - - 1 to many orthologous to - 1:many orthology - one-to-many orthology - co-orthology - many to 1 orthology - in 1 to many orthology relationship with - - - - - - Orthology that involves two genes when duplications more recent than the species split have occurred in one species but not the other. - - - - - - - - - - - - - Historical homology that involves two members of a larger set of homologs. - - - many to many homologous to - many-to-many homology - many:many homology - in many to many homology relationship with - - - - - - Historical homology that involves two members of a larger set of homologs. - - - - - - - - - - - - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - - 1 to many homologous to - one-to-many homology - 1:many homology - in 1 to many homology relationship with - - - - - - Historical homology that involves a structure that has no other homologs in the species in which it is defined, and several homologous structures in another species. - - BGEE:curator - - - - - - - - - - - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - - apomorphous to - synapomorphy - in apomorphy relationship with - - - - - - Historical homology that is based on recent shared ancestry, characterizing a monophyletic group. - - ISBN:978-0252068140 - - - - - - - - - - Historical homology that is based on distant shared ancestry. - - - plesiomorphous to - symplesiomorphy - This term is usually contrasted to apomorphy. - in plesiomorphy relationship with - - - - - - Historical homology that is based on distant shared ancestry. - - ISBN:978-0252068140 - - - - - - - - - - - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - - deep genetic homology - deep homologous to - generative homology - homoiology - Used for structures in distantly related taxa. - in deep homology relationship with - - - - - - Homocracy that involves morphologically and phylogenetically disparate structures that are the result of parallel evolution. - - - - - - - - - - - - - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - - hemiplasous to - in hemiplasy relationship with - - - - - - Historical homology that is characterized by topological discordance between a gene tree and a species tree attributable to the phylogenetic sorting of genetic polymorphisms across successive nodes in a species tree. - - - - - - - - - - - - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - - gametologous to - in gametology relationship with - - - - - - Historical homology that involves not recombining and subsequently differentiated sex chromosomes. - - - - - - - - - - - - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - - MeSH:Chromosome_Pairing - chromosomal homologous to - in chromosomal homology relationship with - - - - - - Historical homology that involves the chromosomes able to pair (synapse) during meiosis. - - ISBN:0195307615 - - - - - - - - - - - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - - many to many orthologous to - many-to-many orthology - many:many orthology - trans-orthology - co-orthology - trans-homology - in many to many orthology relationship with - - - - - - Orthology that involves two genes that experienced duplications more recent than the species split that created them. - - - - - - - - - - - - - - Paralogy that involves genes from the same species. - - - within-species paralogous to - in within-species paralogy relationship with - - - - - - Paralogy that involves genes from the same species. - - - - - - - - - - - - Paralogy that involves genes from different species. - - - between-species paralogous to - The genes have diverged before a speciation event. - in between-species paralogy relationship with - - - - - - Paralogy that involves genes from different species. - - - - - - - - - - - - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - - post-displacement - in postdisplacement relationship with - - - - - - Paedomorphosis that is produced by delayed growth of immature structures into the adult form. - - - - - - - - - - - - Peramorphosis that is produced by a delay in the offset of development. - - - in hypermorphosis relationship with - - - - - - Peramorphosis that is produced by a delay in the offset of development. - - - ISBN:978-0674639416 - - - - - - - - - - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - - synologous to - in synology relationship with - - - - - - Xenology that results, not from the transfer of a gene between two species, but from a hybridization of two species. - - - - - - - - - - - - - - Orthology that involves functional equivalent genes with retention of the ancestral function. - - - ECO:0000080 - isoorthologous to - in isoorthology relationship with - - - - - - Orthology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - - tandem paralogous to - iterative paralogy - serial paralogy - in tandem paralogy relationship with - - - - - - Paralogy that is characterized by duplication of adjacent sequences on a chromosome segment. - - - ISBN:978-0878932665 - - - - - - - - - - - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - - apomorphic tendency - cryptic homology - latent homologous to - underlying synapomorphy - homoiology - homoplastic tendency - re-awakening - Used for structures in closely related taxa. - in latent homology relationship with - - - - - - Parallelism that involves morphologically very similar structures, occurring only within some members of a taxon and absent in the common ancestor (which possessed the developmental basis to develop this character). - - - - - ISBN:0199141118 - - - - - - - - - - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - - generative homology - syngenous to - Cannot be used when orthologous patterning gene are organizing obviously non-homologous structures in different organisms due for example to pleiotropic functions of these genes. - in syngeny relationship with - - - - - - Homocracy that involves recognizably corresponding characters that occurs in two or more taxa, or as a repeated unit within an individual. - - - DOI:10.1002/1521-1878(200009)22:9<846::AID-BIES10>3.0.CO;2-R - - - - - - - - - - - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - - 1:1 paralogy - apparent 1:1 orthology - apparent orthologous to - pseudoorthology - The genes are actually paralogs but appear to be orthologous due to differential, lineage-specific gene loss. - in apparent orthology relationship with - - - - - - Between-species paralogy that involves single copy paralogs resulting from reciprocal gene loss. - - - - - - - - - - - - - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - - pseudoparalogous to - These genes may come out as paralogs in a single-genome analysis. - in pseudoparalogy relationship with - - - - - - Xenology that involves genes that ended up in a given genome as a result of a combination of vertical inheritance and horizontal gene transfer. - - - - - - - - - - - - - Historical homology that involves functional equivalent genes with retention of the ancestral function. - - - equivalogous to - This may include examples of orthology, paralogy and xenology. - in equivalogy relationship with - - - - - - Historical homology that involves functional equivalent genes with retention of the ancestral function. - - - - - - - - - - - - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - - interologous to - in interology relationship with - - - - - - Historical homology that involves orthologous pairs of interacting molecules in different organisms. - - - - - - - - - - - - - Similarity that is characterized by interchangeability in function. - - - functional similarity - in functional equivalence relationship with - - - - - - Similarity that is characterized by interchangeability in function. - - - - - - - - - - - - - Biological homology that involves parts of the same organism. - - - iterative homologous to - in iterative homology relationship with - - - - - - Biological homology that involves parts of the same organism. - - - - - - - - - - - - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - - duplicate xenology - multiple xenology - paraxenologous to - in paraxenology relationship with - - - - - - Xenology that is characterized by multiple horizontal transfer events, resulting in the presence of two or more copies of the foreign gene in the host genome. - - - - - - - - - - - - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - - plerologous to - This phenomenon is usually due to gene conversion process. - in plerology relationship with - - - - - - Paralogy that is characterized by extra similarity between paralogous sequences resulting from concerted evolution. - - - - - - - - - - - - - Structural homology that involves structures with the same or similar relative positions. - - - homotopous to - Theissen (2005) mentions that some authors may consider homotopy to be distinct from homology, but this is not the standard use. - in homotopy relationship with - - - - - - Structural homology that involves structures with the same or similar relative positions. - - - - ISBN:0123195837 - - - - - - - - - - Biological homology that involves an ectopic structure and the normally positioned structure. - - - heterotopy - in homeosis relationship with - - - - - - Biological homology that involves an ectopic structure and the normally positioned structure. - - - - - - - - - - - - - - Synology that results from allopolyploidy. - - - homoeologous to - On a long term, it is hard to distinguish allopolyploidy from whole genome duplication. - in homoeology relationship with - - - - - - Synology that results from allopolyploidy. - - - - - - - - - - - - - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - - axis paramorphism - in paramorphism relationship with - - - - - - Iterative homology that involves two structures, one of which originated as a duplicate of the other and co-opted the expression of patterning genes of the ancestral structure. - - - - - - - - - - - - - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - - regulogous to - in regulogy relationship with - - - - - - Historical homology that involves orthologous pairs of transcription factors and downstream regulated genes in different organisms. - - - - - - - - - - - - - - - - - - - - 0 - - - 100 - - - - - Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - - 2018-05-22T16:43:28Z - This could be used to record the increased infant morality rate in some population compared to wild-type. For examples of usage see http://purl.obolibrary.org/obo/FBcv_0000351 and subclasses. - has increased age-specific mortality rate - - - - - Then percentage of organisms in a population that die during some specified age range (age-specific mortality rate), minus the percentage that die in during the same age range in a wild-type population. - PMID:24138933 - Wikipedia:Infant_mortality - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - continuant - - - - - - - - - - - - - - - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. - occurrent - - - - - - - - - - - - - - - - - b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - independent continuant - - - - - - - - - spatial region - - - - - - - - - - - - - - - p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - process - - - - - - - - - - disposition - - - - - - - - - - - - - - - - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - realizable entity - - - - - - - - - - - - - - - quality - - - - - - - - - - - - - - - - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - specifically dependent continuant - - - - - - - - - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - role - - - - - - - - - - - - - - - b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - generically dependent continuant - - - - - - - - - function - - - - - - - - - - - - - - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity - - - - - - - - - - - - - - - immaterial entity - - - - - - - - - - - - - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. - We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. - CALOHA:TS-2035 - FMA:68646 - GO:0005623 - KUPO:0000002 - MESH:D002477 - VHOG:0001533 - WBbt:0004017 - XAO:0003012 - The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). - cell - - - - - A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. - CARO:mah - - - - - - - - - Any neuron having a sensory function; an afferent neuron conveying sensory impulses. - - BTO:0001037 - FMA:84649 - MESH:D011984 - WBbt:0005759 - sensory neuron - - - - - Any neuron having a sensory function; an afferent neuron conveying sensory impulses. - ISBN:0721662544 - - - - - - - - - - - true - - - - The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. - - BTO:0000938 - CALOHA:TS-0683 - FMA:54527 - VHOG:0001483 - WBbt:0003679 - nerve cell - These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. - neuron - - - - - The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. - MESH:D009474 - http://en.wikipedia.org/wiki/Neuron - - - - - - - - - - - - - - - A process during which an organism comes into contact with another entity. - exposure of organism - - - - - - - - - A system which has the disposition to environ one or more material entities. - 2013-09-23T16:04:08Z - EcoLexicon:environment - environment - In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. - environmental system - - - - - A system which has the disposition to environ one or more material entities. - DOI:10.1186/2041-1480-4-43 - - - - - - - - - An environmental system which can sustain and allow the growth of an ecological population. - - - EcoLexicon:habitat - LTER:238 - SWEETRealm:Habitat - A habitat's specificity to an ecological population differentiates it from other environment classes. See Buttigieg et al. (2016; https://doi.org/10.1186/s13326-016-0097-6) for an explanation of ENVO's treatement of habitats. 3,849 of such habitat classes are available here: https://github.com/EnvironmentOntology/envo-habitats - habitat - - - - - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - This is the same as GO molecular function - molecular function - GO:0003674 - Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. - gene product or complex activity - molecular_function - - - - - A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. - GOC:pdt - - - - - - - - - - - - true - - - Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. - E2 - E3 - KEGG_REACTION:R03876 - Reactome:R-HSA-1169394 - Reactome:R-HSA-1169395 - Reactome:R-HSA-1169397 - Reactome:R-HSA-1169398 - Reactome:R-HSA-1169402 - Reactome:R-HSA-1169405 - Reactome:R-HSA-1169406 - Reactome:R-HSA-1234163 - Reactome:R-HSA-1234172 - Reactome:R-HSA-1253282 - Reactome:R-HSA-1358789 - Reactome:R-HSA-1358790 - Reactome:R-HSA-1358792 - Reactome:R-HSA-1363331 - Reactome:R-HSA-168915 - Reactome:R-HSA-173542 - Reactome:R-HSA-173545 - Reactome:R-HSA-174057 - Reactome:R-HSA-174104 - Reactome:R-HSA-174144 - Reactome:R-HSA-174159 - Reactome:R-HSA-174195 - Reactome:R-HSA-174227 - Reactome:R-HSA-179417 - Reactome:R-HSA-180540 - Reactome:R-HSA-180597 - Reactome:R-HSA-182986 - Reactome:R-HSA-182993 - Reactome:R-HSA-183051 - Reactome:R-HSA-183084 - Reactome:R-HSA-183089 - Reactome:R-HSA-1852623 - Reactome:R-HSA-187575 - Reactome:R-HSA-1912357 - Reactome:R-HSA-1912386 - Reactome:R-HSA-1918092 - Reactome:R-HSA-1918095 - Reactome:R-HSA-1977296 - Reactome:R-HSA-1980074 - Reactome:R-HSA-1980118 - Reactome:R-HSA-201425 - Reactome:R-HSA-202453 - Reactome:R-HSA-202534 - Reactome:R-HSA-205118 - Reactome:R-HSA-209063 - Reactome:R-HSA-211734 - Reactome:R-HSA-2169050 - Reactome:R-HSA-2172172 - Reactome:R-HSA-2179276 - Reactome:R-HSA-2186747 - Reactome:R-HSA-2186785 - Reactome:R-HSA-2187368 - Reactome:R-HSA-2213017 - Reactome:R-HSA-264444 - Reactome:R-HSA-2682349 - Reactome:R-HSA-2730904 - Reactome:R-HSA-2737728 - Reactome:R-HSA-2769007 - Reactome:R-HSA-2900765 - Reactome:R-HSA-3000335 - Reactome:R-HSA-3134804 - Reactome:R-HSA-3134946 - Reactome:R-HSA-3249386 - Reactome:R-HSA-3780995 - Reactome:R-HSA-3781009 - Reactome:R-HSA-3788724 - Reactome:R-HSA-3797226 - Reactome:R-HSA-400267 - Reactome:R-HSA-4332236 - Reactome:R-HSA-446877 - Reactome:R-HSA-450358 - Reactome:R-HSA-451418 - Reactome:R-HSA-5357757 - Reactome:R-HSA-5362412 - Reactome:R-HSA-5483238 - Reactome:R-HSA-5607725 - Reactome:R-HSA-5607728 - Reactome:R-HSA-5607756 - Reactome:R-HSA-5607757 - Reactome:R-HSA-5610742 - Reactome:R-HSA-5610745 - Reactome:R-HSA-5610746 - Reactome:R-HSA-5652009 - Reactome:R-HSA-5655170 - Reactome:R-HSA-5660753 - Reactome:R-HSA-5667107 - Reactome:R-HSA-5667111 - Reactome:R-HSA-5668454 - Reactome:R-HSA-5668534 - Reactome:R-HSA-5675470 - Reactome:R-HSA-5684250 - Reactome:R-HSA-5691108 - Reactome:R-HSA-5693108 - Reactome:R-HSA-68712 - Reactome:R-HSA-69598 - Reactome:R-HSA-741386 - Reactome:R-HSA-75824 - Reactome:R-HSA-870449 - Reactome:R-HSA-8948709 - Reactome:R-HSA-8956106 - Reactome:R-HSA-9013069 - Reactome:R-HSA-9013974 - Reactome:R-HSA-9014342 - Reactome:R-HSA-918224 - Reactome:R-HSA-936412 - Reactome:R-HSA-936942 - Reactome:R-HSA-936986 - Reactome:R-HSA-9628444 - Reactome:R-HSA-9645394 - Reactome:R-HSA-9645414 - Reactome:R-HSA-9688831 - Reactome:R-HSA-9701000 - Reactome:R-HSA-9750946 - Reactome:R-HSA-975118 - Reactome:R-HSA-975147 - Reactome:R-HSA-9758604 - Reactome:R-HSA-9793444 - Reactome:R-HSA-9793485 - Reactome:R-HSA-9793679 - Reactome:R-HSA-9796346 - Reactome:R-HSA-9796387 - Reactome:R-HSA-9796626 - Reactome:R-HSA-9815507 - Reactome:R-HSA-9817362 - Reactome:R-HSA-983140 - Reactome:R-HSA-983153 - Reactome:R-HSA-983156 - Reactome:R-HSA-9833155 - Reactome:R-HSA-9833973 - Reactome:R-HSA-9834070 - Reactome:R-HSA-9861563 - Reactome:R-HSA-9861640 - ubiquitin conjugating enzyme activity - ubiquitin ligase activity - ubiquitin protein ligase activity - ubiquitin protein-ligase activity - ubiquitin-conjugating enzyme activity - GO:0004842 - ubiquitin-protein transferase activity - - - - - Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y = Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages. - GOC:BioGRID - GOC:jh2 - PMID:9635407 - - - - - Reactome:R-HSA-1169394 - ISGylation of IRF3 - - - - - Reactome:R-HSA-1169395 - ISGylation of viral protein NS1 - - - - - Reactome:R-HSA-1169397 - Activation of ISG15 by UBA7 E1 ligase - - - - - Reactome:R-HSA-1169398 - ISGylation of host protein filamin B - - - - - Reactome:R-HSA-1169402 - ISGylation of E2 conjugating enzymes - - - - - Reactome:R-HSA-1169405 - ISGylation of protein phosphatase 1 beta (PP2CB) - - - - - Reactome:R-HSA-1169406 - ISGylation of host proteins - - - - - Reactome:R-HSA-1234163 - Cytosolic VBC complex ubiquitinylates hydroxyprolyl-HIF-alpha - - - - - Reactome:R-HSA-1234172 - Nuclear VBC complex ubiquitinylates HIF-alpha - - - - - Reactome:R-HSA-1253282 - ERBB4 ubiquitination by WWP1/ITCH - - - - - Reactome:R-HSA-1358789 - Self-ubiquitination of RNF41 - - - - - Reactome:R-HSA-1358790 - RNF41 ubiquitinates ERBB3 - - - - - Reactome:R-HSA-1358792 - RNF41 ubiquitinates activated ERBB3 - - - - - Reactome:R-HSA-1363331 - Ubiquitination of p130 (RBL2) by SCF (Skp2) - - - - - Reactome:R-HSA-168915 - K63-linked ubiquitination of RIP1 bound to the activated TLR complex - - - - - Reactome:R-HSA-173542 - SMURF2 ubiquitinates SMAD2 - - - - - Reactome:R-HSA-173545 - Ubiquitin-dependent degradation of the SMAD complex terminates TGF-beta signaling - - - - - Reactome:R-HSA-174057 - Multiubiquitination of APC/C-associated Cdh1 - - - - - Reactome:R-HSA-174104 - Ubiquitination of Cyclin A by APC/C:Cdc20 complex - - - - - Reactome:R-HSA-174144 - Ubiquitination of Securin by phospho-APC/C:Cdc20 complex - - - - - Reactome:R-HSA-174159 - Ubiquitination of Emi1 by SCF-beta-TrCP - - - - - Reactome:R-HSA-174195 - Ubiquitination of cell cycle proteins targeted by the APC/C:Cdh1complex - - - - - Reactome:R-HSA-174227 - Ubiquitination of Cyclin B by phospho-APC/C:Cdc20 complex - - - - - Reactome:R-HSA-179417 - Multiubiquitination of Nek2A - - - - - Reactome:R-HSA-180540 - Multi-ubiquitination of APOBEC3G - - - - - Reactome:R-HSA-180597 - Ubiquitination of CD4 by Vpu:CD4:beta-TrCP:SKP1 complex - - - - - Reactome:R-HSA-182986 - CBL-mediated ubiquitination of CIN85 - - - - - Reactome:R-HSA-182993 - Ubiquitination of stimulated EGFR (CBL) - - - - - Reactome:R-HSA-183051 - CBL ubiquitinates Sprouty - - - - - Reactome:R-HSA-183084 - CBL escapes CDC42-mediated inhibition by down-regulating the adaptor molecule Beta-Pix - - - - - Reactome:R-HSA-183089 - CBL binds and ubiquitinates phosphorylated Sprouty - - - - - Reactome:R-HSA-1852623 - Ubiquitination of NICD1 by FBWX7 - - - - - Reactome:R-HSA-187575 - Ubiquitination of phospho-p27/p21 - - - - - Reactome:R-HSA-1912357 - ITCH ubiquitinates DTX - - - - - Reactome:R-HSA-1912386 - Ubiquitination of NOTCH1 by ITCH in the absence of ligand - - - - - Reactome:R-HSA-1918092 - CHIP (STUB1) mediates ubiquitination of ERBB2 - - - - - Reactome:R-HSA-1918095 - CUL5 mediates ubiquitination of ERBB2 - - - - - Reactome:R-HSA-1977296 - NEDD4 ubiquitinates ERBB4jmAcyt1s80 dimer - - - - - Reactome:R-HSA-1980074 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 - - - - - Reactome:R-HSA-1980118 - ARRB mediates NOTCH1 ubiquitination - - - - - Reactome:R-HSA-201425 - Ubiquitin-dependent degradation of the Smad complex terminates BMP2 signalling - - - - - Reactome:R-HSA-202453 - Auto-ubiquitination of TRAF6 - - - - - Reactome:R-HSA-202534 - Ubiquitination of NEMO by TRAF6 - - - - - Reactome:R-HSA-205118 - TRAF6 polyubiquitinates NRIF - - - - - Reactome:R-HSA-209063 - Beta-TrCP ubiquitinates NFKB p50:p65:phospho IKBA complex - - - - - Reactome:R-HSA-211734 - Ubiquitination of PAK-2p34 - - - - - Reactome:R-HSA-2169050 - SMURFs/NEDD4L ubiquitinate phosphorylated TGFBR1 and SMAD7 - - - - - Reactome:R-HSA-2172172 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH2 - - - - - Reactome:R-HSA-2179276 - SMURF2 monoubiquitinates SMAD3 - - - - - Reactome:R-HSA-2186747 - Ubiquitination of SKI/SKIL by RNF111/SMURF2 - - - - - Reactome:R-HSA-2186785 - RNF111 ubiquitinates SMAD7 - - - - - Reactome:R-HSA-2187368 - STUB1 (CHIP) ubiquitinates SMAD3 - - - - - Reactome:R-HSA-2213017 - Auto-ubiquitination of TRAF3 - - - - - Reactome:R-HSA-264444 - Autoubiquitination of phospho-COP1(Ser-387 ) - - - - - Reactome:R-HSA-2682349 - RAF1:SGK:TSC22D3:WPP ubiquitinates SCNN channels - - - - - Reactome:R-HSA-2730904 - Auto-ubiquitination of TRAF6 - - - - - Reactome:R-HSA-2737728 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD domain mutants - - - - - Reactome:R-HSA-2769007 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 PEST domain mutants - - - - - Reactome:R-HSA-2900765 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH1 HD+PEST domain mutants - - - - - Reactome:R-HSA-3000335 - SCF-beta-TrCp1/2 ubiquitinates phosphorylated BORA - - - - - Reactome:R-HSA-3134804 - STING ubiquitination by TRIM32 or TRIM56 - - - - - Reactome:R-HSA-3134946 - DDX41 ubiquitination by TRIM21 - - - - - Reactome:R-HSA-3249386 - DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:dsDNA:ZBP1:TBK1 - - - - - Reactome:R-HSA-3780995 - NHLRC1 mediated ubiquitination of EPM2A (laforin) and PPP1RC3 (PTG) associated with glycogen-GYG2 - - - - - Reactome:R-HSA-3781009 - NHLRC1 mediated ubiquitination of EPM2A and PPP1RC3 associated with glycogen-GYG1 - - - - - Reactome:R-HSA-3788724 - Cdh1:APC/C ubiquitinates EHMT1 and EHMT2 - - - - - Reactome:R-HSA-3797226 - Defective NHLRC1 does not ubiquitinate EPM2A (laforin) and PPP1R3C (PTG) (type 2B disease) - - - - - Reactome:R-HSA-400267 - BTRC:CUL1:SKP1 (SCF-beta-TrCP1) ubiquitinylates PER proteins - - - - - Reactome:R-HSA-4332236 - CBL neddylates TGFBR2 - - - - - Reactome:R-HSA-446877 - TRAF6 is K63 poly-ubiquitinated - - - - - Reactome:R-HSA-450358 - Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR stimulation - - - - - Reactome:R-HSA-451418 - Pellino ubiquitinates IRAK1 - - - - - Reactome:R-HSA-5357757 - BIRC(cIAP1/2) ubiquitinates RIPK1 - - - - - Reactome:R-HSA-5362412 - SYVN1 ubiquitinates Hh C-terminal fragments - - - - - Reactome:R-HSA-5483238 - Hh processing variants are ubiquitinated - - - - - Reactome:R-HSA-5607725 - SCF-beta-TRCP ubiquitinates p-7S-p100:RELB in active NIK:p-176,S180-IKKA dimer:p-7S-p100:SCF-beta-TRCP - - - - - Reactome:R-HSA-5607728 - beta-TRCP ubiquitinates IkB-alpha in p-S32,33-IkB-alpha:NF-kB complex - - - - - Reactome:R-HSA-5607756 - TRAF6 oligomer autoubiquitinates - - - - - Reactome:R-HSA-5607757 - K63polyUb-TRAF6 ubiquitinates TAK1 - - - - - Reactome:R-HSA-5610742 - SCF(beta-TrCP) ubiquitinates p-GLI1 - - - - - Reactome:R-HSA-5610745 - SCF(beta-TrCP) ubiquitinates p-GLI2 - - - - - Reactome:R-HSA-5610746 - SCF(beta-TrCP) ubiquitinates p-GLI3 - - - - - Reactome:R-HSA-5652009 - RAD18:UBE2B or RBX1:CUL4:DDB1:DTL monoubiquitinates PCNA - - - - - Reactome:R-HSA-5655170 - RCHY1 monoubiquitinates POLH - - - - - Reactome:R-HSA-5660753 - SIAH1:UBE2L6:Ubiquitin ubiquitinates SNCA - - - - - Reactome:R-HSA-5667107 - SIAH1, SIAH2 ubiquitinate SNCAIP - - - - - Reactome:R-HSA-5667111 - PARK2 K63-Ubiquitinates SNCAIP - - - - - Reactome:R-HSA-5668454 - K63polyUb-cIAP1,2 ubiquitinates TRAF3 - - - - - Reactome:R-HSA-5668534 - cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK - - - - - Reactome:R-HSA-5675470 - BIRC2/3 (cIAP1/2) is autoubiquitinated - - - - - Reactome:R-HSA-5684250 - SCF betaTrCP ubiquitinates NFKB p105 within p-S927, S932-NFkB p105:TPL2:ABIN2 - - - - - Reactome:R-HSA-5691108 - SKP1:FBXL5:CUL1:NEDD8 ubiquitinylates IREB2 - - - - - Reactome:R-HSA-5693108 - TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains - - - - - Reactome:R-HSA-68712 - The geminin component of geminin:Cdt1 complexes is ubiquitinated, releasing Cdt1 - - - - - Reactome:R-HSA-69598 - Ubiquitination of phosphorylated Cdc25A - - - - - Reactome:R-HSA-741386 - RIP2 induces K63-linked ubiquitination of NEMO - - - - - Reactome:R-HSA-75824 - Ubiquitination of Cyclin D1 - - - - - Reactome:R-HSA-870449 - TRIM33 monoubiquitinates SMAD4 - - - - - Reactome:R-HSA-8948709 - DTX4 ubiquitinates p-S172-TBK1 within NLRP4:DTX4:STING:TBK1:IRF3 - - - - - Reactome:R-HSA-8956106 - VHL:EloB,C:NEDD8-CUL2:RBX1 complex ubiquitinylates HIF-alpha - - - - - Reactome:R-HSA-9013069 - Ubiquitination of DLL/JAG ligands upon binding to NOTCH3 - - - - - Reactome:R-HSA-9013974 - Auto-ubiquitination of TRAF3 within activated TLR3 complex - - - - - Reactome:R-HSA-9014342 - K63-linked ubiquitination of RIP1 bound to the activated TLR complex - - - - - Reactome:R-HSA-918224 - DDX58 is K63 polyubiquitinated - - - - - Reactome:R-HSA-936412 - RNF125 mediated ubiquitination of DDX58, IFIH1 and MAVS - - - - - Reactome:R-HSA-936942 - Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 - - - - - Reactome:R-HSA-936986 - Activated TRAF6 synthesizes unanchored polyubiquitin chains - - - - - Reactome:R-HSA-9628444 - Activated TRAF6 synthesizes unanchored polyubiquitin chains upon TLR3 stimulation - - - - - Reactome:R-HSA-9645394 - Activated TRAF6 synthesizes unanchored polyubiquitin chains upon ALPK1:ADP-heptose stimulation - - - - - Reactome:R-HSA-9645414 - Auto ubiquitination of TRAF6 bound to ALPK1:ADP-heptose:TIFA oligomer - - - - - Reactome:R-HSA-9688831 - STUB1 ubiquitinates RIPK3 at K55, K363 - - - - - Reactome:R-HSA-9701000 - BRCA1:BARD1 heterodimer autoubiquitinates - - - - - Reactome:R-HSA-9750946 - TRAF2,6 ubiquitinates NLRC5 - - - - - Reactome:R-HSA-975118 - TRAF6 ubiquitinqtes IRF7 within the activated TLR7/8 or 9 complex - - - - - Reactome:R-HSA-975147 - Auto ubiquitination of oligo-TRAF6 bound to p-IRAK2 at endosome membrane - - - - - Reactome:R-HSA-9758604 - Ubiquitination of IKBKG by TRAF6 - - - - - Reactome:R-HSA-9793444 - ITCH polyubiquitinates MLKL at K50 - - - - - Reactome:R-HSA-9793485 - PRKN polyubiquitinates RIPK3 - - - - - Reactome:R-HSA-9793679 - LUBAC ubiquitinates RIPK1 at K627 - - - - - Reactome:R-HSA-9796346 - MIB2 ubiquitinates RIPK1 at K377, K604, K634 - - - - - Reactome:R-HSA-9796387 - STUB1 ubiquitinates RIPK1 at K571, K604, K627 - - - - - Reactome:R-HSA-9796626 - MIB2 ubiquitinates CFLAR - - - - - Reactome:R-HSA-9815507 - MIB2 ubiquitinates CYLD at K338, K530 - - - - - Reactome:R-HSA-9817362 - SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex - - - - - Reactome:R-HSA-983140 - Transfer of Ub from E2 to substrate and release of E2 - - - - - Reactome:R-HSA-983153 - E1 mediated ubiquitin activation - - - - - Reactome:R-HSA-983156 - Polyubiquitination of substrate - - - - - Reactome:R-HSA-9833155 - Ubiquitination of STAT2 - - - - - Reactome:R-HSA-9833973 - ISGylation of PKR - - - - - Reactome:R-HSA-9834070 - PRKN ubiquitinates MOM substrates - - - - - Reactome:R-HSA-9861563 - CTLH E3 ligase ubiquitinates LDHA - - - - - Reactome:R-HSA-9861640 - CTLH E3 ligase ubiquitinates PKM-1 - - - - - - - - A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. - NIF_Subcellular:sao1702920020 - Wikipedia:Cell_nucleus - cell nucleus - horsetail nucleus - GO:0005634 - nucleus - - - - - A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. - GOC:go_curators - - - - - horsetail nucleus - GOC:al - GOC:mah - GOC:vw - PMID:15030757 - - - - - - - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - jl - 2012-09-19T15:05:24Z - Wikipedia:Biological_process - biological process - physiological process - single organism process - single-organism process - GO:0008150 - Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. - biological process - biological_process - - - - - A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - GOC:pdt - - - - - - - - - - - - true - - - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - Reactome:R-HSA-6788855 - Reactome:R-HSA-6788867 - phosphokinase activity - GO:0016301 - Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. - kinase activity - - - - - Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. - ISBN:0198506732 - - - - - Reactome:R-HSA-6788855 - FN3KRP phosphorylates PsiAm, RibAm - - - - - Reactome:R-HSA-6788867 - FN3K phosphorylates ketosamines - - - - - - - - - - - - true - - - Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. - Reactome:R-HSA-141367 - Reactome:R-HSA-162914 - GO:0019107 - myristoyltransferase activity - - - - - Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule. - GOC:ai - - - - - Reactome:R-HSA-141367 - Myristoylation of tBID by NMT1 - - - - - Reactome:R-HSA-162914 - Myristoylation of Nef - - - - - - - - - - - - - - - - - - - - - - - curation status specification - - The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) - PERSON:Bill Bug - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> - OBI_0000266 - curation status specification - - - - - - - - - planned process - Injecting mice with a vaccine in order to test its efficacy - - A process that realizes a plan which is the concretization of a plan specification. - 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) - We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some -objectives is a planned process. - Bjoern Peters - branch derived - 6/11/9: Edited at workshop. Used to include: is initiated by an agent - This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) - planned process - - - - - - - - - processed material - Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples - - Is a material entity that is created or changed during material processing. - PERSON: Alan Ruttenberg - processed material - - - - - - - - - assay - Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. - - A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. - 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. - Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683. - PlanAndPlannedProcess Branch - measuring - scientific observation - OBI branch derived - assay - - - - - - - - - container - - A device that can be used to restrict the location of material entities over time - 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) - PERSON: Bjoern Peters - container - - - - - - - - - device - A voltmeter is a measurement device which is intended to perform some measure function. - An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. - - A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. - 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. - -2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: - -(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. - -(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. - -(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. - -In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. - PERSON: Helen Parkinson - instrument - OBI development call 2012-12-17. - device - - - - - - - - - organism - animal - fungus - plant - virus - - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') - 13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI. - GROUP: OBI Biomaterial Branch - WEB: http://en.wikipedia.org/wiki/Organism - organism - - - - - - - - - A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. - disease - - - - - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATO:0000001 - quality - - - - - A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities - PATOC:GVG - - - - - - - - - A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - - ramified - ramiform - PATO:0000402 - branched - - - - - A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - WordNet:WordNet - - - - - - - - - A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. - PATO:0001199 - linear - - - - - A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. - ISBN:0881923214 - - - - - - - - - A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity. - proportion - proportionality - proportionality to - quotient - rate - PATO:0001470 - Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio. - ratio - - - - - A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity. - https://orcid.org/0000-0001-8314-2140 - - - - - Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio. - https://orcid.org/0000-0001-8314-2140 - - - - - - - - - A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. - - 2009-10-06T04:37:14Z - PATO:0002124 - laminar - - - - - A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. - PATOC:GVG - - - - - - - - An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human, - An exposure event in which a plant is provided with fertilizer. The exposure receptor is the root system of the plant, the stimulus is the fertilizing chemical, the route is via the soil, possibly mediated by symbotic microbes. - OBSOLETE A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism. - This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions. - - - 2017-06-05T17:55:39Z - obsolete exposure event or process - https://github.com/oborel/obo-relations/pull/173 - true - - - - - - - - - - - - - - Any entity that is ordered in discrete units along a linear axis. - - sequentially ordered entity - - - - - - - - - Any individual unit of a collection of like units arranged in a linear order - - An individual unit can be a molecular entity such as a base pair, or an abstract entity, such as the abstraction of a base pair. - sequence atomic unit - - - - - - - - - Any entity that can be divided into parts such that each part is an atomical unit of a sequence - - Sequence bearers can be molecular entities, such as a portion of a DNA molecule, or they can be abstract entities, such as an entity representing all human sonic hedgehog regions of the genome with a particular DNA sequence. - sequence bearer - - - - - - - - - A material entity consisting of multiple components that are causally integrated. - May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 - - http://www.jbiomedsem.com/content/4/1/43 - system - - - - - - - - - Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. - - - AAO:0010825 - AEO:0000003 - BILA:0000003 - CARO:0000003 - EHDAA2:0003003 - EMAPA:0 - FMA:305751 - FMA:67135 - GAID:781 - HAO:0000003 - MA:0003000 - MESH:D000825 - SCTID:362889002 - TAO:0000037 - TGMA:0001823 - VHOG:0001759 - XAO:0003000 - ZFA:0000037 - http://dbpedia.org/ontology/AnatomicalStructure - biological structure - connected biological structure - UBERON:0000061 - - - - - anatomical structure - - - - - Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. - CARO:0000003 - - - - - connected biological structure - CARO:0000003 - - - - - - - - - A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. - CARO:0001001 - NLX:147821 - funiculus - nerve fiber bundle - neural fiber bundle - UBERON:0000122 - - - neuron projection bundle - - - - - A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. - CARO:0001001 - FBC:DOS - FBbt:00005099 - - - - - nerve fiber bundle - FBbt:00005099 - - - - - - - - - - - Anatomical entity that has mass. - - - AAO:0010264 - AEO:0000006 - BILA:0000006 - CARO:0000006 - EHDAA2:0003006 - FMA:67165 - HAO:0000006 - TAO:0001836 - TGMA:0001826 - VHOG:0001721 - UBERON:0000465 - - - - - material anatomical entity - - - - - Anatomical entity that has mass. - http://orcid.org/0000-0001-9114-8737 - - - - - - - - - - Anatomical entity that has no mass. - - - AAO:0010265 - AEO:0000007 - BILA:0000007 - CARO:0000007 - EHDAA2:0003007 - FMA:67112 - HAO:0000007 - TAO:0001835 - TGMA:0001827 - VHOG:0001727 - immaterial physical anatomical entity - UBERON:0000466 - - - - - immaterial anatomical entity - - - - - Anatomical entity that has no mass. - http://orcid.org/0000-0001-9114-8737 - - - - - immaterial physical anatomical entity - FMA:67112 - - - - - - - - - - - true - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - - - AAO:0010841 - AEO:0000000 - BFO:0000004 - BILA:0000000 - BIRNLEX:6 - CARO:0000000 - EHDAA2:0002229 - FMA:62955 - HAO:0000000 - MA:0000001 - NCIT:C12219 - TAO:0100000 - TGMA:0001822 - UMLS:C1515976 - WBbt:0000100 - XAO:0000000 - ZFA:0100000 - UBERON:0001062 - - - - - anatomical entity - - - - - Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. - FMA:62955 - http://orcid.org/0000-0001-9114-8737 - - - - - UMLS:C1515976 - ncithesaurus:Anatomic_Structure_System_or_Substance - - - - - - - - - A vessel through which blood circulates in the body. - consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - vascular element - AAO:0011004 - AEO:0000207 - BTO:0001102 - CALOHA:TS-0080 - EFO:0000817 - EHDAA2:0003252 - EHDAA:240 - EMAPA:32743 - EMAPA:35993 - FMA:50722 - FMA:63183 - GAID:169 - MA:0000060 - MAT:0000393 - MESH:D001808 - NCIT:C12679 - NLXANAT:090901 - SCTID:361097006 - TAO:0002137 - UMLS:C0005847 - VHOG:0001250 - Wikipedia:Blood_vessel - XAO:0001011 - ZFA:0005314 - region of vascular tree organ - vascular tree organ region - UBERON:0001981 - - - - - - - - blood vessel - - - - - A vessel through which blood circulates in the body. - BTO:0001102 - Wikipedia:Blood_vessel - - - - - vascular element - EMAPA:35993 - - - - - UMLS:C0005847 - ncithesaurus:Blood_Vessel - - - - - region of vascular tree organ - FMA:50722 - - - - - vascular tree organ region - FMA:50722 - - - - - - - - - Any of the smallest blood vessels connecting arterioles with venules. - not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element - AAO:0010252 - BTO:0002045 - CALOHA:TS-2006 - EFO:0001906 - EMAPA:35198 - EV:0100035 - FMA:63194 - MA:0000065 - MESH:D002196 - NCIT:C12685 - NLXANAT:090902 - TAO:0005250 - UMLS:C0935624 - VHOG:0001253 - Wikipedia:Capillary - XAO:0000116 - ZFA:0005250 - blood capillary - capillary vessel - UBERON:0001982 - - - - - - - - capillary - https://github.com/obophenotype/uberon/issues/2186 - - - - - Any of the smallest blood vessels connecting arterioles with venules. - ISBN:0073040584 - Wikipedia:Capillary - https://github.com/obophenotype/uberon/issues/137 - - - - - UMLS:C0935624 - ncithesaurus:Capillary - - - - - - - - - An anatomical structure that has more than one cell as a part. - - - CARO:0010000 - multicellular structure - UBERON:0010000 - - - - - multicellular anatomical structure - - - - - An anatomical structure that has more than one cell as a part. - CARO:0010000 - - - - - multicellular structure - FBbt:00100313 - - - - - - - - - phenotype - - - - - - - - - - - - - - - - - - - example to be eventually removed - example to be eventually removed - - - - - - - - metadata complete - Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. - metadata complete - - - - - - - - organizational term - Term created to ease viewing/sort terms for development purpose, and will not be included in a release - organizational term - - - - - - - - ready for release - - Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." - ready for release - - - - - - - - metadata incomplete - Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. - metadata incomplete - - - - - - - - uncurated - Nothing done yet beyond assigning a unique class ID and proposing a preferred term. - uncurated - - - - - - - - - pending final vetting - - All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. - pending final vetting - - - - - - - - to be replaced with external ontology term - Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI - to be replaced with external ontology term - - - - - - - - - requires discussion - - A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI - requires discussion - - - - - - - - ## Elucidation - -This is used when the statement/axiom is assumed to hold true &apos;eternally&apos; - -## How to interpret (informal) - -First the &quot;atemporal&quot; FOL is derived from the OWL using the standard -interpretation. This axiom is temporalized by embedding the axiom -within a for-all-times quantified sentence. The t argument is added to -all instantiation predicates and predicates that use this relation. - -## Example - - Class: nucleus - SubClassOf: part_of some cell - - forall t : - forall n : - instance_of(n,Nucleus,t) - implies - exists c : - instance_of(c,Cell,t) - part_of(n,c,t) - -## Notes - -This interpretation is *not* the same as an at-all-times relation - axiom holds for all times - - - - - - - - ## Elucidation - -This is used when the first-order logic form of the relation is -binary, and takes no temporal argument. - -## Example: - - Class: limb - SubClassOf: develops_from some lateral-plate-mesoderm - - forall t, t2: - forall x : - instance_of(x,Limb,t) - implies - exists y : - instance_of(y,LPM,t2) - develops_from(x,y) - relation has no temporal argument - - - - - - - - Researcher ORCID=0000-0001-6677-8489 - Aleix Puig-Barbé - - - - - Researcher ORCID=0000-0001-6677-8489 - - - - - - Aleix Puig-Barbé - - - - - - - - - Researcher - Austin Meier - - - - - Researcher - - - - - - Austin Meier - - - - - - - - - researcher - Shawn Zheng Kai Tan - - - - - researcher - - - - - - Shawn Zheng Kai Tan - - - - - - - - - researcher - Raymund Stefancsik - - - - - researcher - - - - - - Raymund Stefancsik - - - - - - - - - researcher, metadata, diseases, University of Maryland - Lynn Schriml - - - - - researcher, metadata, diseases, University of Maryland - - - - - - Lynn Schriml - - - - - - - - - researcher - William D Duncan - - - - - researcher - - - - - - William D Duncan - - - - - - - - - researcher (ORCID 0000-0002-1373-1705) - Clare Pilgrim - - - - - researcher (ORCID 0000-0002-1373-1705) - - - - - - Clare Pilgrim - - - - - - - - - data scientist - Anne Thessen - - - - - data scientist - - - - - - Anne Thessen - - - - - - - - - researcher (ORCID 0000-0002-2999-0103) - Jie Zheng - - - - - researcher (ORCID 0000-0002-2999-0103) - - - - - - Jie Zheng - - - - - - - - - researcher - Pier Luigi Buttigieg - - - - - researcher - - - - - - Pier Luigi Buttigieg - - - - - - - - - researcher - Christian J Stoeckert - - - - - researcher - - - - - - Christian J Stoeckert - - - - - - - - - bioinformatics researcher - Christopher J. Mungall - - - - - bioinformatics researcher - - - - - - Christopher J. Mungall - - - - - - - - - researcher - David Osumi-Sutherland - - - - - researcher - - - - - - David Osumi-Sutherland - - - - - - - - - researcher - Lauren E. Chan - - - - - researcher - - - - - - Lauren E. Chan - - - - - - - - - researcher - Marie-Angélique Laporte - - - - - researcher - - - - - - Marie-Angélique Laporte - - - - - - - - - researcher - James P. Balhoff - - - - - researcher - - - - - - James P. Balhoff - - - - - - - - - researcher - Damion M Dooley - - - - - researcher - - - - - - Damion M Dooley - - - - - - - - - researcher - Lindsay G Cowell - - - - - researcher - - - - - - Lindsay G Cowell - - - - - - - - - Canadian biocurator - Pascale Gaudet - - - - - Canadian biocurator - - - - - - Pascale Gaudet - - - - - - - - - researcher - Mathias Brochhausen - - - - - researcher - - - - - - Mathias Brochhausen - - - - - - - - - Researcher ORCID=0000-0003-1909-9269 - S. Clint Dowland - - - - - Researcher ORCID=0000-0003-1909-9269 - - - - - - S. Clint Dowland - - - - - - - - - researcher - Anna Maria Masci - - - - - researcher - - - - - - Anna Maria Masci - - - - - - - - - Researcher ORCID=0000-0003-2620-0345 - Asiyah Yu Lin - - - - - Researcher ORCID=0000-0003-2620-0345 - - - - - - Asiyah Yu Lin - - - - - - - - - software/data engineer - Jorrit Poelen - - - - - software/data engineer - - - - - - Jorrit Poelen - - - - - - - - - American chemist - Charles Tapley Hoyt - - - - - American chemist - - - - - - Charles Tapley Hoyt - - - - - - - - - - - - data item - data item - - - information content entity - information content entity - - - data about an ontology part - Data about an ontology part is a data item about a part of an ontology, for example a term - Person:Alan Ruttenberg - data about an ontology part - - - failed exploratory term - The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg - failed exploratory term - - - in branch - An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. - GROUP:OBI - OBI_0000277 - in branch - - - Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolete_core - - - obsolescence reason specification - - The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. - The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. - PERSON: Alan Ruttenberg - PERSON: Melanie Courtot - obsolescence reason specification - - - placeholder removed - placeholder removed - - - terms merged - An editor note should explain what were the merged terms and the reason for the merge. - terms merged - - - term imported - This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. - term imported - - - term split - This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. - term split - - - has obsolescence reason - Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot - has obsolescence reason - - - ontology term requester - - The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - The 'term requester' can credit the person, organization or project who request the ontology term. - ontology term requester - - - denotator type - The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. - A denotator type indicates how a term should be interpreted from an ontological perspective. - Alan Ruttenberg - Barry Smith, Werner Ceusters - denotator type - - - universal - Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf - universal - - - is denotator type - Relates an class defined in an ontology, to the type of it's denotator - In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') - Alan Ruttenberg - is denotator type - - - defined class - A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal - "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg - defined class - - - named class expression - A named class expression is a logical expression that is given a name. The name can be used in place of the expression. - named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg - named class expression - - - antisymmetric property - part_of antisymmetric property xsd:true - Use boolean value xsd:true to indicate that the property is an antisymmetric property - Alan Ruttenberg - antisymmetric property - - - has ID digit count - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) - Person:Alan Ruttenberg - has ID digit count - - - has ID range allocated - Datatype: idrange:1 -Annotations: 'has ID range allocated to': "Chris Mungall" -EquivalentTo: xsd:integer[> 2151 , <= 2300] - - Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms - Person:Alan Ruttenberg - has ID range allocated to - - - has ID policy for - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relating an ontology used to record id policy to the ontology namespace whose policy it manages - Person:Alan Ruttenberg - has ID policy for - - - has ID prefix - Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> - Annotations: - 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" - 'has ID digit count' : 7, - rdfs:label "RO id policy" - 'has ID policy for': "RO" - Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. - Person:Alan Ruttenberg - has ID prefix - - - has associated axiom(nl) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom associated with a term expressed using natural language - has associated axiom(nl) - - - has associated axiom(fol) - Person:Alan Ruttenberg - Person:Alan Ruttenberg - An axiom expressed in first order logic using CLIF syntax - has associated axiom(fol) - - - is allocated id range - Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" - PERSON:Alan Ruttenberg - Add as annotation triples in the granting ontology - is allocated id range - - - may be identical to - A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. - David Osumi-Sutherland - Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. - may be identical to - - - scheduled for obsoletion on or after - Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. - Chris Mungall, Jie Zheng - scheduled for obsoletion on or after - - - has axiom id - Person:Alan Ruttenberg - Person:Alan Ruttenberg - A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI - has axiom label - - - ontology module - I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. - ontology file - This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. - ontology module - - - base ontology module - An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. - base ontology module - - - - editors ontology module - An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. - source ontology module - editors ontology module - - - main release ontology module - An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. - TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module - main release ontology module - - - bridge ontology module - An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. - bridge ontology module - - - - import ontology module - A subset ontology module that is intended to be imported from another ontology. - TODO: add axioms that indicate this is the output of a module extraction process. - import file - import ontology module - - - - subset ontology module - An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. - ontology slim - subset ontology - subset ontology module - - - - - curation subset ontology module - A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. - curation subset ontology module - - - analysis ontology module - An ontology module that is intended for usage in analysis or discovery applications. - analysis subset ontology module - - - single layer ontology module - A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. - ribbon subset - single layer subset ontology module - - - exclusion subset ontology module - A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. - antislim - exclusion subset ontology module - - - external import ontology module - An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. - external import - external import ontology module - - - species subset ontology module - A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. - taxon subset - species subset ontology module - - - - reasoned ontology module - An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. - reasoned ontology module - - - - generated ontology module - An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. - TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process - generated ontology module - - - template generated ontology module - An ontology module that is automatically generated from a template specification and fillers for slots in that template. - template generated ontology module - - - - - - taxonomic bridge ontology module - taxonomic bridge ontology module - - - ontology module subsetted by expressivity - ontology module subsetted by expressivity - - - obo basic subset ontology module - A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. - -Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). - -An ontology is OBO Basic if and only if it has the following characteristics: -DAG -Unidirectional -No Dangling Clauses -Fully Asserted -Fully Labeled -No equivalence axioms -Singly labeled edges -No qualifier lists -No disjointness axioms -No owl-axioms header -No imports - obo basic subset ontology module - - - - ontology module subsetted by OWL profile - ontology module subsetted by OWL profile - - - EL++ ontology module - EL++ ontology module - - - The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. - This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - - out of scope - - - This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. - OBO Operations call - - logical characteristic of object property - - - The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality. - This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). - - domain entity does not exist - - - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) - A synonym type for describing abbreviations or initalisms - - abbreviation - - - A synonym type for describing ambiguous synonyms - - ambiguous synonym - - - A synonym type for describing dubious synonyms - - dubious synonym - - - EFO:0006346 (severe cutaneous adverse reaction) has an exact synonym (scar), which is of the type OMO:0003003 (layperson synonym) - A synonym type for describing layperson or colloquial synonyms - - layperson synonym - - - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) - A synonym type for describing pluralization synonyms - - plural form - - - CHEBI:16189 (sulfate) has an exact synonym (sulphate), which is of the type OMO:0003005 (UK spelling synonym) - A synonym type for describing UK spelling variants - - UK spelling synonym - - - A synonym type for common misspellings - - misspelling - - - A synonym type for misnomers, i.e., a synonym that is not technically correct but is commonly used anyway - - misnomer - - - MAPT, the gene that encodes the Tau protein, has a previous name DDPAC. Note: in this case, the name type is more specifically the gene symbol. - A synonym type for names that have been used as primary labels in the past. - - previous name - - - The legal name for Harvard University (https://ror.org/03vek6s52) is President and Fellows of Harvard College - A synonym type for the legal entity name - - legal name - - - CHEBI:46195 has been assigned the english International Nonproproprietary Name (INN) "paracetamol". In some cases such as this one, the INN might be the same as the ontology's primary label - The International Nonproprietary Name (INN) is a standardize name for a pharmaceutical drug or active ingredient issued by the World Health Organization (WHO) meant to address the issues with country- or language-specific brand names. These are issued in several languages, including English, Latin, French, Russian, Spanish, Arabic, and Chinese. - - INN - International Nonproprietary Name - - - nasopharynx (UBERON:0001728) has the latin name "pars nasalis pharyngis - A synonym type for describing Latin term synonyms. - - latin term - - - NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced. - A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms. - - acronym - - - A serial number such as "12324X"; a stop sign; a written proper name such as "OBI - An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. - - has symbol - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/src/ontology/tmp/run.sh b/src/ontology/tmp/run.sh deleted file mode 100644 index b8c88db..0000000 --- a/src/ontology/tmp/run.sh +++ /dev/null @@ -1,138 +0,0 @@ -set -e - -# Check for spaces in the current directory path -for item in $PWD ; do - if [ "$item" != "$PWD" ]; then - echo "${0##*/}: error: repository path must not contain whitespace characters" >&2 - exit 1 - fi -done - -if [ -f run.sh.conf ]; then - . ./run.sh.conf -fi - -# Look for a GitHub token -if [ -n "$GH_TOKEN" ]; then - : -elif [ -f ../../.github/token.txt ]; then - GH_TOKEN=$(cat ../../.github/token.txt) -elif [ -f $XDG_CONFIG_HOME/ontology-development-kit/github/token ]; then - GH_TOKEN=$(cat $XDG_CONFIG_HOME/ontology-development-kit/github/token) -elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/token" ]; then - GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token") -fi - -# SSH agent socket -# On macOS, we cannot use $SSH_AUTH_SOCK directly, -# we need to use a "magic" socket instead. -case "$(uname)" in -Darwin) - ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock - ;; -*) - ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK - ;; -esac -ODK_SSH_BIND= -if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then - ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock" -fi - -ODK_IMAGE=${ODK_IMAGE:-odkfull} -TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }') -if [ -n "$TAG_IN_IMAGE" ]; then - # Override ODK_TAG env var if IMAGE already includes a tag - ODK_TAG=$TAG_IN_IMAGE - ODK_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $1 }') -fi -ODK_TAG=${ODK_TAG:-latest} - -ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G} - -ODK_DEBUG=${ODK_DEBUG:-no} - -ODK_USER_ID=${ODK_USER_ID:-$(id -u)} -ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)} - -# Convert OWLAPI_* environment variables to the OWLAPI as Java options -# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html -# for a list of allowed options -OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions -for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do - ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}" -done - -# Proxy settings for Java applications -[ -z "$HTTP_PROXY" ] && [ -n "$http_proxy" ] && HTTP_PROXY=$http_proxy -if [ -n "$HTTP_PROXY" ]; then - proxy_host=$(echo $HTTP_PROXY | sed -E 's,^https?://,,; s,:[0-9]+$,,') - proxy_port=$(echo $HTTP_PROXY | sed -E 's,^.*:([0-9]+)$,\1,') - ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttp.proxyHost=$proxy_host" - [ "$proxy_port" != "$proxy_host" ] && ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttp.proxyPort=$proxy_port" -fi -[ -z "$HTTPS_PROXY" ] && [ -n "$https_proxy" ] && HTTPS_PROXY=$https_proxy -if [ -n "$HTTPS_PROXY" ]; then - proxy_host=$(echo $HTTPS_PROXY | sed -E 's,^https?://,,; s,:[0-9]+$,,') - proxy_port=$(echo $HTTPS_PROXY | sed -E 's,^.*:([0-9]+)$,\1,') - ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttps.proxyHost=$proxy_host" - [ "$proxy_port" != "$proxy_host" ] && ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttps.proxyPort=$proxy_port" -fi -[ -z "$NO_PROXY" ] && [ -n "$no_proxy" ] && NO_PROXY=$no_proxy -if [ -n "$NO_PROXY" ] ; then - no_proxy_hosts=$(echo $NO_PROXY | tr ',' '|') - ODK_JAVA_OPTS="$ODK_JAVA_OPTS -Dhttp.nonProxyHosts=$no_proxy_hosts" -fi - -TIMECMD= -if [ x$ODK_DEBUG = xyes ]; then - # If you wish to change the format string, take care of using - # non-breaking spaces (U+00A0) instead of normal spaces, to - # prevent the shell from tokenizing the format string. - echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps." - TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb" -fi -rm -f tmp/debug.log - -VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND -WORK_DIR=/work/src/ontology - -# Support for OAK cache sharing -if [ -n "$ODK_SHARE_OAK_CACHE" ]; then - case "$ODK_SHARE_OAK_CACHE" in - user) - # We assume the cache is in its default location; if it is not, - # ODK_SHARE_OAK_CACHE must point to the actual location. - ODK_SHARE_OAK_CACHE="$HOME/.data/oaklib" - ;; - repo) - ODK_SHARE_OAK_CACHE="$PWD/tmp/oaklib" - ;; - esac - [ $ODK_USER_ID -eq 0 ] && OAK_DEST=/root/.data/oaklib || OAK_DEST=/home/odkuser/.data/oaklib - VOLUME_BIND="$VOLUME_BIND,$ODK_SHARE_OAK_CACHE:$OAK_DEST" -fi - -if [ -n "$ODK_BINDS" ]; then - VOLUME_BIND="$VOLUME_BIND,$ODK_BINDS" -fi - -if [ -n "$USE_SINGULARITY" ]; then - - singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \ - --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \ - --bind $VOLUME_BIND \ - -W $WORK_DIR \ - docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" -else - BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /g')" - docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \ - -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \ - --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" -fi - -case "$@" in -*update_repo*|*release*) - echo "Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/." - ;; -esac \ No newline at end of file diff --git a/src/ontology/tmp/seed.txt b/src/ontology/tmp/seed.txt index 5aa9e09..d9670aa 100644 --- a/src/ontology/tmp/seed.txt +++ b/src/ontology/tmp/seed.txt @@ -1,4 +1,10 @@ +http://purl.obolibrary.org/obo/BFO_0000001 +http://purl.obolibrary.org/obo/BFO_0000015 +http://purl.obolibrary.org/obo/BFO_0000016 +http://purl.obolibrary.org/obo/BFO_0000019 http://purl.obolibrary.org/obo/BFO_0000020 +http://purl.obolibrary.org/obo/BFO_0000023 +http://purl.obolibrary.org/obo/BFO_0000031 http://purl.obolibrary.org/obo/BFO_0000040 http://purl.obolibrary.org/obo/BFO_0000050 http://purl.obolibrary.org/obo/BFO_0000051 @@ -6,6 +12,11 @@ http://purl.obolibrary.org/obo/BFO_0000054 http://purl.obolibrary.org/obo/BFO_0000055 http://purl.obolibrary.org/obo/BFO_0000066 http://purl.obolibrary.org/obo/BFO_0000067 +http://purl.obolibrary.org/obo/COB_0000022 +http://purl.obolibrary.org/obo/COB_0000035 +http://purl.obolibrary.org/obo/COB_0000110 +http://purl.obolibrary.org/obo/IAO_0000027 +http://purl.obolibrary.org/obo/IAO_0000030 http://purl.obolibrary.org/obo/IAO_0000111 http://purl.obolibrary.org/obo/IAO_0000112 http://purl.obolibrary.org/obo/IAO_0000114 @@ -25,15 +36,133 @@ http://purl.obolibrary.org/obo/IAO_0100001 http://purl.obolibrary.org/obo/IDO_0000504 http://purl.obolibrary.org/obo/IDO_0000586 http://purl.obolibrary.org/obo/IDO_0000630 -http://purl.obolibrary.org/obo/OBI_0000011 http://purl.obolibrary.org/obo/OBI_0000278 http://purl.obolibrary.org/obo/OBI_0000312 http://purl.obolibrary.org/obo/OBI_0000846 http://purl.obolibrary.org/obo/OBI_0001688 -http://purl.obolibrary.org/obo/OBI_0100026 http://purl.obolibrary.org/obo/OBI_0200000 +http://purl.obolibrary.org/obo/OBI_0600014 http://purl.obolibrary.org/obo/OBI_0600052 -http://purl.obolibrary.org/obo/OGMS_0000000 +http://purl.obolibrary.org/obo/OGMS_0000014 +http://purl.obolibrary.org/obo/OGMS_0000015 +http://purl.obolibrary.org/obo/OGMS_0000016 +http://purl.obolibrary.org/obo/OGMS_0000017 +http://purl.obolibrary.org/obo/OGMS_0000018 +http://purl.obolibrary.org/obo/OGMS_0000019 +http://purl.obolibrary.org/obo/OGMS_0000020 +http://purl.obolibrary.org/obo/OGMS_0000022 +http://purl.obolibrary.org/obo/OGMS_0000023 +http://purl.obolibrary.org/obo/OGMS_0000024 +http://purl.obolibrary.org/obo/OGMS_0000025 +http://purl.obolibrary.org/obo/OGMS_0000026 +http://purl.obolibrary.org/obo/OGMS_0000027 +http://purl.obolibrary.org/obo/OGMS_0000028 +http://purl.obolibrary.org/obo/OGMS_0000029 +http://purl.obolibrary.org/obo/OGMS_0000030 +http://purl.obolibrary.org/obo/OGMS_0000031 +http://purl.obolibrary.org/obo/OGMS_0000032 +http://purl.obolibrary.org/obo/OGMS_0000033 +http://purl.obolibrary.org/obo/OGMS_0000034 +http://purl.obolibrary.org/obo/OGMS_0000035 +http://purl.obolibrary.org/obo/OGMS_0000037 +http://purl.obolibrary.org/obo/OGMS_0000038 +http://purl.obolibrary.org/obo/OGMS_0000039 +http://purl.obolibrary.org/obo/OGMS_0000040 +http://purl.obolibrary.org/obo/OGMS_0000045 +http://purl.obolibrary.org/obo/OGMS_0000046 +http://purl.obolibrary.org/obo/OGMS_0000047 +http://purl.obolibrary.org/obo/OGMS_0000050 +http://purl.obolibrary.org/obo/OGMS_0000051 +http://purl.obolibrary.org/obo/OGMS_0000055 +http://purl.obolibrary.org/obo/OGMS_0000056 +http://purl.obolibrary.org/obo/OGMS_0000057 +http://purl.obolibrary.org/obo/OGMS_0000059 +http://purl.obolibrary.org/obo/OGMS_0000060 +http://purl.obolibrary.org/obo/OGMS_0000061 +http://purl.obolibrary.org/obo/OGMS_0000063 +http://purl.obolibrary.org/obo/OGMS_0000064 +http://purl.obolibrary.org/obo/OGMS_0000065 +http://purl.obolibrary.org/obo/OGMS_0000066 +http://purl.obolibrary.org/obo/OGMS_0000067 +http://purl.obolibrary.org/obo/OGMS_0000069 +http://purl.obolibrary.org/obo/OGMS_0000070 +http://purl.obolibrary.org/obo/OGMS_0000071 +http://purl.obolibrary.org/obo/OGMS_0000073 +http://purl.obolibrary.org/obo/OGMS_0000074 +http://purl.obolibrary.org/obo/OGMS_0000077 +http://purl.obolibrary.org/obo/OGMS_0000078 +http://purl.obolibrary.org/obo/OGMS_0000079 +http://purl.obolibrary.org/obo/OGMS_0000080 +http://purl.obolibrary.org/obo/OGMS_0000081 +http://purl.obolibrary.org/obo/OGMS_0000082 +http://purl.obolibrary.org/obo/OGMS_0000083 +http://purl.obolibrary.org/obo/OGMS_0000084 +http://purl.obolibrary.org/obo/OGMS_0000085 +http://purl.obolibrary.org/obo/OGMS_0000086 +http://purl.obolibrary.org/obo/OGMS_0000087 +http://purl.obolibrary.org/obo/OGMS_0000088 +http://purl.obolibrary.org/obo/OGMS_0000089 +http://purl.obolibrary.org/obo/OGMS_0000090 +http://purl.obolibrary.org/obo/OGMS_0000091 +http://purl.obolibrary.org/obo/OGMS_0000092 +http://purl.obolibrary.org/obo/OGMS_0000093 +http://purl.obolibrary.org/obo/OGMS_0000094 +http://purl.obolibrary.org/obo/OGMS_0000095 +http://purl.obolibrary.org/obo/OGMS_0000096 +http://purl.obolibrary.org/obo/OGMS_0000097 +http://purl.obolibrary.org/obo/OGMS_0000098 +http://purl.obolibrary.org/obo/OGMS_0000099 +http://purl.obolibrary.org/obo/OGMS_0000100 +http://purl.obolibrary.org/obo/OGMS_0000101 +http://purl.obolibrary.org/obo/OGMS_0000102 +http://purl.obolibrary.org/obo/OGMS_0000103 +http://purl.obolibrary.org/obo/OGMS_0000104 +http://purl.obolibrary.org/obo/OGMS_0000105 +http://purl.obolibrary.org/obo/OGMS_0000106 +http://purl.obolibrary.org/obo/OGMS_0000107 +http://purl.obolibrary.org/obo/OGMS_0000108 +http://purl.obolibrary.org/obo/OGMS_0000109 +http://purl.obolibrary.org/obo/OGMS_0000110 +http://purl.obolibrary.org/obo/OGMS_0000111 +http://purl.obolibrary.org/obo/OGMS_0000112 +http://purl.obolibrary.org/obo/OGMS_0000113 +http://purl.obolibrary.org/obo/OGMS_0000114 +http://purl.obolibrary.org/obo/OGMS_0000115 +http://purl.obolibrary.org/obo/OGMS_0000116 +http://purl.obolibrary.org/obo/OGMS_0000117 +http://purl.obolibrary.org/obo/OGMS_0000118 +http://purl.obolibrary.org/obo/OGMS_0000119 +http://purl.obolibrary.org/obo/OGMS_0000120 +http://purl.obolibrary.org/obo/OGMS_0000121 +http://purl.obolibrary.org/obo/OGMS_0000122 +http://purl.obolibrary.org/obo/OGMS_0000123 +http://purl.obolibrary.org/obo/OGMS_0000124 +http://purl.obolibrary.org/obo/OGMS_0000125 +http://purl.obolibrary.org/obo/OGMS_0000126 +http://purl.obolibrary.org/obo/OGMS_0000127 +http://purl.obolibrary.org/obo/OGMS_0000128 +http://purl.obolibrary.org/obo/OGMS_0000129 +http://purl.obolibrary.org/obo/OGMS_0000130 +http://purl.obolibrary.org/obo/OGMS_0000131 +http://purl.obolibrary.org/obo/OGMS_0000132 +http://purl.obolibrary.org/obo/OGMS_0000133 +http://purl.obolibrary.org/obo/OGMS_0000134 +http://purl.obolibrary.org/obo/OGMS_0000135 +http://purl.obolibrary.org/obo/OGMS_0000136 +http://purl.obolibrary.org/obo/OGMS_0000137 +http://purl.obolibrary.org/obo/OGMS_0000138 +http://purl.obolibrary.org/obo/OGMS_0000139 +http://purl.obolibrary.org/obo/OGMS_0000140 +http://purl.obolibrary.org/obo/OGMS_0000141 +http://purl.obolibrary.org/obo/OGMS_0000142 +http://purl.obolibrary.org/obo/OGMS_0000143 +http://purl.obolibrary.org/obo/OGMS_0000144 +http://purl.obolibrary.org/obo/OGMS_0000145 +http://purl.obolibrary.org/obo/OGMS_0000146 +http://purl.obolibrary.org/obo/OGMS_0000147 +http://purl.obolibrary.org/obo/OGMS_0000148 +http://purl.obolibrary.org/obo/OGMS_0000149 +http://purl.obolibrary.org/obo/OGMS_0000150 http://purl.obolibrary.org/obo/RO_0000052 http://purl.obolibrary.org/obo/RO_0000053 http://purl.obolibrary.org/obo/RO_0000056 @@ -54,9 +183,14 @@ http://purl.obolibrary.org/obo/RO_0002351 http://purl.obolibrary.org/obo/RO_0002353 http://purl.obolibrary.org/obo/RO_0002577 http://purl.obolibrary.org/obo/ogms.owl -http://purl.org/dc/terms/description +http://purl.org/dc/elements/1.1/contributor +http://purl.org/dc/elements/1.1/creator +http://purl.org/dc/elements/1.1/date +http://purl.org/dc/elements/1.1/description +http://purl.org/dc/elements/1.1/publisher +http://purl.org/dc/elements/1.1/title http://purl.org/dc/terms/license -http://purl.org/dc/terms/title +http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym +http://www.geneontology.org/formats/oboInOwl#hasExactSynonym http://www.w3.org/2002/07/owl#Thing -https://creativecommons.org/licenses/unspecified term diff --git a/src/templates/external_import.tsv b/src/templates/external_import.tsv index 5d82db6..fd9b882 100644 --- a/src/templates/external_import.tsv +++ b/src/templates/external_import.tsv @@ -9,6 +9,9 @@ BFO:0000054 owl:ObjectProperty BFO:0000055 owl:ObjectProperty BFO:0000066 owl:ObjectProperty BFO:0000067 owl:ObjectProperty +COB:0000022 owl:Class +COB:0000035 owl:Class +COB:0000110 owl:Class IAO:0000111 owl:AnnotationProperty IAO:0000112 owl:AnnotationProperty IAO:0000114 owl:AnnotationProperty @@ -29,13 +32,12 @@ IDO:0000504 owl:Class IDO:0000586 owl:Class IDO:0000630 owl:Class OBI:0000278 owl:Class -OBI:0000011 owl:ObjectProperty +OBI:0200000 owl:Class +OBI:0600052 owl:Class +OBI:0600014 owl:Class OBI:0000312 owl:ObjectProperty OBI:0000846 owl:ObjectProperty OBI:0001688 owl:ObjectProperty -OBI:0100026 owl:Class -OBI:0200000 owl:Class -OBI:0600052 owl:Class RO:0000052 owl:ObjectProperty RO:0000053 owl:ObjectProperty RO:0000056 owl:ObjectProperty