Skip to content

Swap label and exact synonym for UBERON:0002346: neuroectoderm preferred #3683

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
dragon-ai-agent wants to merge 1 commit into
base: master
Choose a base branch
from
+18 −17
Open

Swap label and exact synonym for UBERON:0002346: neuroectoderm preferred #3683

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
35 changes: 18 additions & 17 deletions src/ontology/uberon-edit.obo
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2195,7 +2195,7 @@ xref: NCIT:C34309
xref: UMLS:C1515087 {source="ncithesaurus:Surface_Ectoderm"}
xref: Wikipedia:External_ectoderm
is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium
relationship: mutually_spatially_disjoint_with UBERON:0002346 ! neurectoderm
relationship: mutually_spatially_disjoint_with UBERON:0002346 ! neuroectoderm
relationship: part_of UBERON:0000922 ! embryo
relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm
property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI
Expand Down Expand Up @@ -25851,7 +25851,7 @@ xref: Wikipedia:Iris_sphincter_muscle
is_a: UBERON:0004234 {source="BTO"} ! iris smooth muscle
intersection_of: UBERON:0004590 ! sphincter muscle
intersection_of: part_of UBERON:0001769 ! iris
relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm
relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neuroectoderm
relationship: has_muscle_antagonist UBERON:0001608 {source="dbpedia"} ! dilatator pupillae
relationship: has_muscle_insertion UBERON:0001769 {notes="encircles iris", source="dbpedia"} ! iris
relationship: has_muscle_origin UBERON:0001769 {notes="encircles iris", source="dbpedia"} ! iris
Expand Down Expand Up @@ -25892,7 +25892,7 @@ xref: SCTID:280890008
xref: UMLS:C0229190 {source="ncithesaurus:Dilator_Pupillae_Muscle"}
xref: Wikipedia:Iris_dilator_muscle
is_a: UBERON:0004234 {source="BTO"} ! iris smooth muscle
relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm
relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neuroectoderm
relationship: has_muscle_antagonist UBERON:0001607 {source="dbpedia"} ! sphincter pupillae
relationship: has_muscle_insertion UBERON:0001769 {notes="inner margins of iris", source="dbpedia"} ! iris
relationship: has_muscle_origin UBERON:0001769 {notes="outer margins of iris", source="dbpedia"} ! iris
Expand Down Expand Up @@ -30818,7 +30818,7 @@ xref: Wikipedia:Ciliary_body
xref: XAO:0000186
is_a: UBERON:0000481 ! multi-tissue structure
relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea
relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm
relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neuroectoderm
relationship: has_part UBERON:0001605 ! ciliary muscle
relationship: has_part UBERON:0010427 ! ciliary processes
relationship: part_of UBERON:0011892 ! anterior uvea
Expand Down Expand Up @@ -31606,7 +31606,7 @@ xref: SCTID:181170006
xref: UMLS:C0042905 {source="ncithesaurus:Vitreous_Body"}
is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue
relationship: composed_primarily_of UBERON:0001797 ! vitreous humor
relationship: has_developmental_contribution_from UBERON:0002346 {notes="neural ectoderm of optic cup", source="ISBN:0781772214"} ! neurectoderm
relationship: has_developmental_contribution_from UBERON:0002346 {notes="neural ectoderm of optic cup", source="ISBN:0781772214"} ! neuroectoderm
relationship: part_of UBERON:0001799 ! vitreous chamber of eyeball
property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI
property_value: editor_note "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string
Expand Down Expand Up @@ -44080,7 +44080,7 @@ xref: ZFA:0001271
is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ
relationship: capable_of GO:0001992 {source="Wikipedia"} ! regulation of systemic arterial blood pressure by vasopressin
relationship: capable_of GO:0030103 {source="Wikipedia"} ! vasopressin secretion
relationship: develops_from UBERON:0002346 ! neurectoderm
relationship: develops_from UBERON:0002346 ! neuroectoderm
relationship: in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata <vertebrates>
relationship: part_of UBERON:0000007 {source="ZFA"} ! pituitary gland
relationship: present_in_taxon NCBITaxon:117569 {source="Ariens, p. 1192"} ! Hyperoartia
Expand Down Expand Up @@ -47898,7 +47898,7 @@ relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fol
relationship: dubious_for_taxon NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} ! Myxini
relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage
relationship: in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata <chordates>
relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm
relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neuroectoderm
property_value: curator_notes "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string
property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI
property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI
Expand Down Expand Up @@ -47946,14 +47946,14 @@ relationship: part_of UBERON:0001515 ! thoracic aorta

[Term]
id: UBERON:0002346
name: neurectoderm
name: neuroectoderm
def: "Embryonic ectoderm that gives rise to nervous tissue." [Wikipedia:Neuroectoderm]
subset: uberon_slim
subset: vertebrate_core
synonym: "epithelium tubi neuralis; neuroectoderma" RELATED OMO:0003011 [Wikipedia:Neuroectoderm]
synonym: "neuaral ectoderm" RELATED []
synonym: "neural ectoderm" EXACT []
synonym: "neuroectoderm" EXACT []
synonym: "neurectoderm" EXACT []
synonym: "presumptive central nervous system" RELATED []
synonym: "ventral neurogenic region" RELATED [VHOG:0000150]
xref: AAO:0011074
Expand All @@ -47979,7 +47979,8 @@ relationship: develops_from UBERON:0000924 {source="https://github.com/obophenot
relationship: has_part CL:0000133 ! neurectodermal cell
property_value: has_relational_adjective "neurectodermal" xsd:string
property_value: homology_notes "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"}
property_value: terminology_notes "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string
property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3682" xsd:string
property_value: terminology_notes "we prefer neuroectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string

[Term]
id: UBERON:0002347
Expand Down Expand Up @@ -65252,7 +65253,7 @@ xref: Wikipedia:Nasal_placode
xref: XAO:0000005
xref: ZFA:0000048
is_a: UBERON:0009955 {contradicted_by="NCBIBook:NBK53171", source="ZFA"} ! neurogenic placode
relationship: develops_from UBERON:0002346 ! neurectoderm
relationship: develops_from UBERON:0002346 ! neuroectoderm
relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm
relationship: part_of UBERON:0000922 ! embryo
property_value: homology_notes "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000186", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"}
Expand Down Expand Up @@ -82168,7 +82169,7 @@ xref: XAO:0000228
xref: ZFA:0000050
is_a: UBERON:0000479 ! tissue
relationship: developmentally_induced_by UBERON:0004880 ! chordamesoderm
relationship: develops_from UBERON:0002346 {source="GO-def"} ! neurectoderm
relationship: develops_from UBERON:0002346 {source="GO-def"} ! neuroectoderm
relationship: develops_from UBERON:0003071 {source="ZFA"} ! eye primordium
relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye
property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI
Expand Down Expand Up @@ -102529,7 +102530,7 @@ xref: XAO:0004091
xref: ZFA:0001178
is_a: UBERON:0000479 {source="ZFA"} ! tissue
relationship: develops_from UBERON:0000924 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! ectoderm
relationship: mutually_spatially_disjoint_with UBERON:0002346 ! neurectoderm
relationship: mutually_spatially_disjoint_with UBERON:0002346 ! neuroectoderm
property_value: development_notes "After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm." xsd:string
property_value: editor_note "todo - epidermis? todo - track down EHDAA2 class in new release" xsd:string
property_value: homology_notes "In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001372", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"}
Expand Down Expand Up @@ -109911,7 +109912,7 @@ xref: TAO:0000146
xref: ZFA:0000146
is_a: UBERON:0005423 ! developing anatomical structure
relationship: has_potential_to_develop_into UBERON:0000955 ! brain
relationship: part_of UBERON:0002346 ! neurectoderm
relationship: part_of UBERON:0002346 ! neuroectoderm
property_value: external_definition "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"}

[Term]
Expand Down Expand Up @@ -120269,7 +120270,7 @@ xref: ZFA:0000063
is_a: UBERON:0016879 ! future central nervous system
intersection_of: UBERON:0006598 ! presumptive structure
intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate
relationship: develops_from UBERON:0002346 ! neurectoderm
relationship: develops_from UBERON:0002346 ! neuroectoderm
relationship: part_of UBERON:0004734 ! gastrula
property_value: editor_note "consider merging" xsd:string
property_value: external_definition "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"}
Expand Down Expand Up @@ -168925,7 +168926,7 @@ synonym: "presumptive central nervous system" EXACT []
intersection_of: UBERON:0006598 ! presumptive structure
intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system
relationship: develops_from UBERON:0000924 ! ectoderm
relationship: develops_from UBERON:0002346 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! neurectoderm
relationship: develops_from UBERON:0002346 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! neuroectoderm
relationship: part_of UBERON:0016880 ! future nervous system

[Term]
Expand Down Expand Up @@ -219662,7 +219663,7 @@ synonym: "P2 iVenEp" RELATED [https://orcid.org/0000-0002-7073-9172]
synonym: "venEpiP2" RELATED []
is_a: UBERON:0001048 ! primordium
is_a: UBERON:6025993 ! insect ventral ectoderm derivative
relationship: develops_from UBERON:0002346 ! neurectoderm
relationship: develops_from UBERON:0002346 ! neuroectoderm
relationship: part_of UBERON:0000922 ! embryo

[Term]
Expand Down
Loading