From da5302ad556c7656ddc7cc8ecdde1bc48c571382 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Wed, 20 May 2026 17:22:52 +0100 Subject: [PATCH 1/6] update schema-context script & regen context --- docs/_specification/1.3-DRAFT/context.jsonld | 8 ++++---- scripts/schema-context.py | 10 +++++----- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/_specification/1.3-DRAFT/context.jsonld b/docs/_specification/1.3-DRAFT/context.jsonld index 9fde7852..96b198b6 100644 --- a/docs/_specification/1.3-DRAFT/context.jsonld +++ b/docs/_specification/1.3-DRAFT/context.jsonld @@ -2874,10 +2874,10 @@ "RepositoryCollection": "http://pcdm.org/models#Collection", "RepositoryObject": "http://pcdm.org/models#Object", "RepositoryFile": "http://pcdm.org/models#File", - "ComputationalWorkflow": "https://bioschemas.org/ComputationalWorkflow", - "input": "https://bioschemas.org/properties/input", - "output": "https://bioschemas.org/properties/output", - "FormalParameter": "https://bioschemas.org/FormalParameter", + "ComputationalWorkflow": "https://bioschemas.org/terms/ComputationalWorkflow", + "input": "https://bioschemas.org/terms/input", + "output": "https://bioschemas.org/terms/output", + "FormalParameter": "https://bioschemas.org/terms/FormalParameter", "wasDerivedFrom": "http://www.w3.org/ns/prov#wasDerivedFrom", "importedFrom": "http://purl.org/pav/importedFrom", "importedOn": "http://purl.org/pav/importedOn", diff --git a/scripts/schema-context.py b/scripts/schema-context.py index a24119e0..58147e07 100755 --- a/scripts/schema-context.py +++ b/scripts/schema-context.py @@ -21,7 +21,7 @@ adding our additional properties. Run as: -./schema-context.py 0.3-DRAFT > ../docs/0.3-DRAFT/context.jsonld +./schema-context.py 1.3-DRAFT > ../docs/_specification/1.3-DRAFT/context.jsonld """ import sys @@ -31,7 +31,7 @@ # Our own version -ROCRATE_VERSION="1.2-DRAFT" +ROCRATE_VERSION="1.3-DRAFT" # Update version from http://schema.org/docs/releases.html SCHEMA_VERSION="22.0" @@ -48,9 +48,9 @@ # Update from https://bioschemas.org/profiles/Workflow/ BIOSCHEMA_WORKFLOW_PROFILE = "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE" -BIOSCHEMA_WORKFLOW_NS = "https://bioschemas.org/ComputationalWorkflow" -BIOSCHEMA_PROPERTIES_NS = "https://bioschemas.org/properties/" -BIOSCHEMA_FORMAL_PARAMETER_NS = "https://bioschemas.org/FormalParameter" +BIOSCHEMA_WORKFLOW_NS = "https://bioschemas.org/terms/ComputationalWorkflow" +BIOSCHEMA_PROPERTIES_NS = "https://bioschemas.org/terms/" +BIOSCHEMA_FORMAL_PARAMETER_NS = "https://bioschemas.org/terms/FormalParameter" BIOSCHEMA_FORMAL_PARAMETER_PROFILE = "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE" # Update from https://github.com/codemeta/codemeta/#codemeta-schema From 3232118d6a0bf42c07b70285c30ebfc57db57d58 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Wed, 20 May 2026 17:31:55 +0100 Subject: [PATCH 2/6] update description of bioschemas terms in spec --- docs/_specification/1.3-DRAFT/metadata.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/_specification/1.3-DRAFT/metadata.md b/docs/_specification/1.3-DRAFT/metadata.md index 5e9e293a..3a3cb79e 100644 --- a/docs/_specification/1.3-DRAFT/metadata.md +++ b/docs/_specification/1.3-DRAFT/metadata.md @@ -135,12 +135,12 @@ From the [IANA link relations] registry: These terms are being proposed by [Bioschemas profile ComputationalWorkflow 1.0-RELEASE][ComputationalWorkflow profile 1.0] and [FormalParameter 1.0-RELEASE][FormalParameter profile 1.0] to be integrated into Schema.org: -* `ComputationalWorkflow` mapped to -* `FormalParameter` mapped to -* `input` mapped to -* `output` mapped to +* `ComputationalWorkflow` mapped to +* `FormalParameter` mapped to +* `input` mapped to +* `output` mapped to -{% include callout.html type="note" content="In this specification the proposed Bioschemas terms use the temporary namespace; future releases of RO-Crate may reflect mapping to the namespace." %} +{% include callout.html type="note" content="In version 1.3 of this specification the proposed Bioschemas terms use the namespace; previous versions 1.1 and 1.2 used the temporary namespace. Future releases of RO-Crate may reflect mapping to the namespace." %} To support geometry in [Places](contextual-entities#places), these terms from the [GeoSPARQL ontology]: From 51b962f6dd759f91268c517add9f535a096614f9 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Wed, 20 May 2026 17:32:10 +0100 Subject: [PATCH 3/6] update profile crate & regen preview --- .../1.3-DRAFT/ro-crate-metadata.json | 882 ++++++++++++------ .../1.3-DRAFT/ro-crate-preview.html | 84 +- 2 files changed, 658 insertions(+), 308 deletions(-) diff --git a/docs/_specification/1.3-DRAFT/ro-crate-metadata.json b/docs/_specification/1.3-DRAFT/ro-crate-metadata.json index 7971184a..ec520d08 100644 --- a/docs/_specification/1.3-DRAFT/ro-crate-metadata.json +++ b/docs/_specification/1.3-DRAFT/ro-crate-metadata.json @@ -228,21 +228,51 @@ { "@id": "https://orcid.org/0000-0003-3234-6762" }, - { "@id": "https://orcid.org/0000-0003-4216-302X"}, - { "@id": "https://orcid.org/0000-0002-1880-0597"}, - { "@id": "https://orcid.org/0000-0001-6712-6335"}, - { "@id": "https://orcid.org/0000-0002-5934-8998"}, - { "@id": "https://orcid.org/0000-0001-9261-8390"}, - { "@id": "https://orcid.org/0000-0002-0035-6475"}, - { "@id": "https://orcid.org/0000-0001-9447-460X"}, - { "@id": "https://orcid.org/0000-0001-7760-1240"}, - { "@id": "https://orcid.org/0000-0001-9925-1560"}, - { "@id": "https://orcid.org/0000-0003-4028-811X"}, - { "@id": "https://orcid.org/0000-0003-2196-5015"}, - { "@id": "https://orcid.org/0009-0002-6541-4637"}, - { "@id": "https://orcid.org/0009-0002-8209-1999"}, - { "@id": "https://orcid.org/0000-0001-7218-0176"}, - { "@id": "https://orcid.org/0000-0003-3482-0325"} + { + "@id": "https://orcid.org/0000-0003-4216-302X" + }, + { + "@id": "https://orcid.org/0000-0002-1880-0597" + }, + { + "@id": "https://orcid.org/0000-0001-6712-6335" + }, + { + "@id": "https://orcid.org/0000-0002-5934-8998" + }, + { + "@id": "https://orcid.org/0000-0001-9261-8390" + }, + { + "@id": "https://orcid.org/0000-0002-0035-6475" + }, + { + "@id": "https://orcid.org/0000-0001-9447-460X" + }, + { + "@id": "https://orcid.org/0000-0001-7760-1240" + }, + { + "@id": "https://orcid.org/0000-0001-9925-1560" + }, + { + "@id": "https://orcid.org/0000-0003-4028-811X" + }, + { + "@id": "https://orcid.org/0000-0003-2196-5015" + }, + { + "@id": "https://orcid.org/0009-0002-6541-4637" + }, + { + "@id": "https://orcid.org/0009-0002-8209-1999" + }, + { + "@id": "https://orcid.org/0000-0001-7218-0176" + }, + { + "@id": "https://orcid.org/0000-0003-3482-0325" + } ], "cite-as": "https://doi.org/DOI", "citation": { @@ -341,24 +371,24 @@ { "@id": "https://codemeta.github.io/terms/" }, - { - "@id": "https://bioschemas.org/FormalParameter" + { + "@id": "https://bioschemas.org/terms/FormalParameter" }, - { - "@id": "https://bioschemas.org/ComputationalWorkflow" + { + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" }, - { + { "@id": "http://schema.org/defaultValue" - }, - { + }, + { "@id": "http://schema.org/valueRequired" }, - { - "@id": "https://bioschemas.org/properties/input" + { + "@id": "https://bioschemas.org/terms/input" + }, + { + "@id": "https://bioschemas.org/terms/output" }, - { - "@id": "https://bioschemas.org/properties/output" - }, { "@id": "http://purl.org/dc/terms/conformsTo" }, @@ -366,7 +396,9 @@ "@id": "https://w3id.org/ro/terms#localPath" } ], - "identifier": {"@id": "https://doi.org/DOI"}, + "identifier": { + "@id": "https://doi.org/DOI" + }, "isBasedOn": { "@id": "https://w3id.org/ro/crate/1.1" }, @@ -441,7 +473,10 @@ }, { "@id": "http://pcdm.org/models#Collection", - "@type": ["DefinedTerm", "Class"], + "@type": [ + "DefinedTerm", + "Class" + ], "inDefinedTermSet": { "@id": "http://pcdm.org/models#" }, @@ -450,7 +485,10 @@ }, { "@id": "http://pcdm.org/models#File", - "@type": ["DefinedTerm", "Class"], + "@type": [ + "DefinedTerm", + "Class" + ], "inDefinedTermSet": { "@id": "http://pcdm.org/models#" }, @@ -459,7 +497,10 @@ }, { "@id": "http://pcdm.org/models#Object", - "@type": ["DefinedTerm", "Class"], + "@type": [ + "DefinedTerm", + "Class" + ], "inDefinedTermSet": { "@id": "http://pcdm.org/models#" }, @@ -468,7 +509,10 @@ }, { "@id": "http://pcdm.org/models#hasFile", - "@type": ["DefinedTerm", "Property"], + "@type": [ + "DefinedTerm", + "Property" + ], "inDefinedTermSet": { "@id": "http://pcdm.org/models#" }, @@ -477,14 +521,17 @@ }, { "@id": "http://pcdm.org/models#hasMember", - "@type": ["DefinedTerm", "Property"], + "@type": [ + "DefinedTerm", + "Property" + ], "inDefinedTermSet": { "@id": "http://pcdm.org/models#" }, "name": "has member", "termCode": "hasMember" }, - { + { "@id": "http://purl.org/vocab/vann/preferredNamespacePrefix", "@type": "DefinedTerm", "name": "preferred namespace prefix", @@ -500,7 +547,10 @@ }, { "@id": "https://schema.org/docs/releases.html#v22.0", - "@type": ["DefinedTermSet", "Standard"], + "@type": [ + "DefinedTermSet", + "Standard" + ], "name": "Schema.org vocabulary (http prefix)", "vann:preferredNamespaceUri": "http://schema.org/", "version": "22.0", @@ -508,7 +558,10 @@ }, { "@id": "http://www.iana.org/assignments/relation/cite-as", - "@type": ["DefinedTerm","Property"], + "@type": [ + "DefinedTerm", + "Property" + ], "inDefinedTermSet": { "@id": "https://www.iana.org/assignments/link-relations/" }, @@ -520,7 +573,9 @@ "@id": "https://www.w3.org/TR/rdf-schema/", "@type": "Standard", "name": "RDF Schema (rdfs)", - "hasPart": {"@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#"} + "hasPart": { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" + } }, { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", @@ -531,7 +586,10 @@ }, { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class", - "@type": ["DefinedTerm","rdfs:Class"], + "@type": [ + "DefinedTerm", + "rdfs:Class" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" }, @@ -542,7 +600,10 @@ }, { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", - "@type": ["DefinedTerm","rdfs:Class"], + "@type": [ + "DefinedTerm", + "rdfs:Class" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" }, @@ -553,25 +614,39 @@ }, { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#subPropertyOf", - "@type": ["DefinedTerm","rdfs:Property"], + "@type": [ + "DefinedTerm", + "rdfs:Property" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" }, "termCode": "rdfs:subPropertyOf", "name": "subPropertyOf (rdfs)", - "domainIncludes": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"}, - "rangeIncludes": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"}, + "domainIncludes": { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property" + }, + "rangeIncludes": { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property" + }, "description": "A subproperty is a specialisation of another property", "url": "https://www.w3.org/TR/rdf-schema/#ch_subpropertyof" }, { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#subClassOf", - "@type": ["DefinedTerm","rdfs:Property"], + "@type": [ + "DefinedTerm", + "rdfs:Property" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" }, - "domainIncludes": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class"}, - "rangeIncludes": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class"}, + "domainIncludes": { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class" + }, + "rangeIncludes": { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class" + }, "termCode": "rdfs:subClassOf", "name": "subClassOf (rdfs)", "description": "A subclass is a specialisation of another class", @@ -579,31 +654,49 @@ }, { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#label", - "@type": ["DefinedTerm","rdfs:Property"], + "@type": [ + "DefinedTerm", + "rdfs:Property" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" }, - "domainIncludes": [ - { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"}, - { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class"} + "domainIncludes": [ + { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property" + }, + { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class" + } ], - "rangeIncludes": { "@id": "http://schema.org/Text"}, + "rangeIncludes": { + "@id": "http://schema.org/Text" + }, "termCode": "rdfs:label", "name": "label (rdfs)", "description": "A human-readable name of the property/class defined with RDFS, equivalent to 'name' in schema.org", "url": "https://www.w3.org/TR/rdf-schema/#ch_label" - }, + }, { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#comment", - "@type": ["DefinedTerm","rdfs:Property"], + "@type": [ + "DefinedTerm", + "rdfs:Property" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#" }, - "domainIncludes": [ - { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"}, - { "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class"} + "domainIncludes": [ + { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property" + }, + { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class" + } ], - "rangeIncludes": { "@id": "http://schema.org/Text"}, + "rangeIncludes": { + "@id": "http://schema.org/Text" + }, "termCode": "rdfs:comment", "name": "comment (rdfs)", "description": "A human-readable description of the property/class defined with RDFS, equivalent to 'description' in schema.org", @@ -611,43 +704,68 @@ }, { "@id": "http://schema.org/domainIncludes", - "@type": ["DefinedTerm","rdfs:Property"], + "@type": [ + "DefinedTerm", + "rdfs:Property" + ], "inDefinedTermSet": { "@id": "https://schema.org/docs/releases.html#v22.0" }, "name": "domainIncludes", "termCode": "domainIncludes", "domainIncludes": [ - {"@id": "http://schema.org/Class"}, - {"@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class"} + { + "@id": "http://schema.org/Class" + }, + { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class" + } ], "rangeIncludes": [ - {"@id": "http://schema.org/Class"}, - {"@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class"} + { + "@id": "http://schema.org/Class" + }, + { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class" + } ], - "description": "The domain of a property includes the given classes, meaning the property may be used on instances of these classes. Equivalent to rdfs:domain but allowing multiple disjoint classes." + "description": "The domain of a property includes the given classes, meaning the property may be used on instances of these classes. Equivalent to rdfs:domain but allowing multiple disjoint classes." }, { "@id": "http://schema.org/rangeIncludes", - "@type": ["DefinedTerm","rdfs:Property"], + "@type": [ + "DefinedTerm", + "rdfs:Property" + ], "inDefinedTermSet": { "@id": "https://schema.org/docs/releases.html#v22.0" }, "domainIncludes": [ - {"@id": "http://schema.org/Class"}, - {"@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class"} + { + "@id": "http://schema.org/Class" + }, + { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class" + } ], "rangeIncludes": [ - {"@id": "http://schema.org/Class"}, - {"@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class"} - ], + { + "@id": "http://schema.org/Class" + }, + { + "@id": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Class" + } + ], "name": "rangeIncludes", "termCode": "rangeIncludes", "description": "The range of a property includes the given types, meaning instances of these types may be the target of this property. Equivalent to rdfs:range but allowing multiple disjoint types. For datatype properties, point to subclasses of http://schema.org/DataType e.g. for a string, http://schema.org/Text" - }, + }, { "@id": "http://schema.org/Class", - "@type": ["DefinedTerm","Class"], + "@type": [ + "DefinedTerm", + "Class" + ], "inDefinedTermSet": { "@id": "https://schema.org/docs/releases.html#v22.0" }, @@ -656,15 +774,17 @@ }, { "@id": "http://schema.org/Property", - "@type": ["DefinedTerm","Class"], + "@type": [ + "DefinedTerm", + "Class" + ], "inDefinedTermSet": { "@id": "https://schema.org/docs/releases.html#v22.0" }, "name": "Property (schema.org)", - "description": "Property reference, as indicated by @id url or inDefinedTermSet" + "description": "Property reference, as indicated by @id url or inDefinedTermSet" }, - - { + { "@id": "http://schema.org/MediaObject", "@type": "DefinedTerm", "inDefinedTermSet": { @@ -684,7 +804,10 @@ }, { "@id": "http://www.w3.org/ns/dx/prof#Profile", - "@type": ["DefinedTerm","Class"], + "@type": [ + "DefinedTerm", + "Class" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/ns/dx/prof" }, @@ -694,7 +817,10 @@ }, { "@id": "http://www.w3.org/ns/dx/prof#ResourceDescriptor", - "@type": ["DefinedTerm","Class"], + "@type": [ + "DefinedTerm", + "Class" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/ns/dx/prof" }, @@ -704,7 +830,10 @@ }, { "@id": "http://www.w3.org/ns/dx/prof#ResourceRole", - "@type": ["DefinedTerm","Class"], + "@type": [ + "DefinedTerm", + "Class" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/ns/dx/prof" }, @@ -714,7 +843,10 @@ }, { "@id": "http://www.w3.org/ns/dx/prof#hasArtifact", - "@type": ["DefinedTerm","Property"], + "@type": [ + "DefinedTerm", + "Property" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/ns/dx/prof" }, @@ -724,7 +856,10 @@ }, { "@id": "http://www.w3.org/ns/dx/prof#hasResource", - "@type": ["DefinedTerm","Property"], + "@type": [ + "DefinedTerm", + "Property" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/ns/dx/prof" }, @@ -734,7 +869,10 @@ }, { "@id": "http://www.w3.org/ns/dx/prof#hasRole", - "@type": ["DefinedTerm","Property"], + "@type": [ + "DefinedTerm", + "Property" + ], "inDefinedTermSet": { "@id": "http://www.w3.org/ns/dx/prof" }, @@ -776,56 +914,80 @@ }, { "@id": "http://www.w3.org/ns/dx/prof/role/constraints", - "@type": ["DefinedTerm","ResourceRole"], + "@type": [ + "DefinedTerm", + "ResourceRole" + ], "description": "Descriptions of obligations, limitations or extensions that the profile defines", "name": "Constraints", "sameAs": "https://www.w3.org/TR/2019/NOTE-dx-prof-20191218/#Role:constraints" }, { "@id": "http://www.w3.org/ns/dx/prof/role/example", - "@type": ["DefinedTerm","ResourceRole"], + "@type": [ + "DefinedTerm", + "ResourceRole" + ], "description": "Sample instance data conforming to the profile", "name": "Example", "sameAs": "https://www.w3.org/TR/2019/NOTE-dx-prof-20191218/#Role:example" }, { "@id": "http://www.w3.org/ns/dx/prof/role/guidance", - "@type": ["DefinedTerm","ResourceRole"], + "@type": [ + "DefinedTerm", + "ResourceRole" + ], "description": "Documents, in human-readable form, how to use the profile", "name": "Guidance", "sameAs": "https://www.w3.org/TR/2019/NOTE-dx-prof-20191218/#Role:guidance" }, { "@id": "http://www.w3.org/ns/dx/prof/role/mapping", - "@type": ["DefinedTerm","ResourceRole"], + "@type": [ + "DefinedTerm", + "ResourceRole" + ], "description": "Describes conversions between two specifications", "name": "Mapping", "sameAs": "https://www.w3.org/TR/2019/NOTE-dx-prof-20191218/#Role:mapping" }, { "@id": "http://www.w3.org/ns/dx/prof/role/schema", - "@type": ["DefinedTerm","ResourceRole"], + "@type": [ + "DefinedTerm", + "ResourceRole" + ], "description": "Machine-readable structural descriptions of data defined by the profile", "name": "Schema", "sameAs": "https://www.w3.org/TR/2019/NOTE-dx-prof-20191218/#Role:schema" }, { "@id": "http://www.w3.org/ns/dx/prof/role/specification", - "@type": ["DefinedTerm","ResourceRole"], + "@type": [ + "DefinedTerm", + "ResourceRole" + ], "description": "Defining the profile in human-readable form", "name": "Specification", "sameAs": "https://www.w3.org/TR/2019/NOTE-dx-prof-20191218/#Role:specification" }, { "@id": "http://www.w3.org/ns/dx/prof/role/validation", - "@type": ["DefinedTerm","ResourceRole"], + "@type": [ + "DefinedTerm", + "ResourceRole" + ], "description": "Supplies instructions about how to verify conformance of data to the profile", "name": "Validation", "sameAs": "https://www.w3.org/TR/2019/NOTE-dx-prof-20191218/#Role:validation" }, { "@id": "http://www.w3.org/ns/dx/prof/role/vocabulary", - "@type": ["DefinedTerm","ResourceRole"], + "@type": [ + "DefinedTerm", + "ResourceRole" + ], "description": "Defines terms used in the profile specification", "name": "Vocabulary", "sameAs": "https://www.w3.org/TR/2019/NOTE-dx-prof-20191218/#Role:vocabulary" @@ -847,7 +1009,9 @@ "description": "The WKT (Well-Known Text) serialization (ISO13249) of a Geometry.", "name": "Geometry", "termCode": "asWKT", - "citation": { "@id": "https://portal.ogc.org/files/?artifact_id=25355" }, + "citation": { + "@id": "https://portal.ogc.org/files/?artifact_id=25355" + }, "sameAs": "https://opengeospatial.github.io/ogc-geosparql/geosparql11/#asWKT", "inDefinedTermSet": { "@id": "http://www.opengis.net/ont/geosparql#" @@ -876,7 +1040,10 @@ }, { "@id": "https://codemeta.github.io/terms/", - "@type": ["DefinedTermSet", "Profile"], + "@type": [ + "DefinedTermSet", + "Profile" + ], "name": "Codemeta Terms", "isPartOf": { "@id": "https://w3id.org/codemeta/3.0" @@ -884,125 +1051,216 @@ "url": "https://codemeta.github.io/terms/", "version": "3.0", "hasDefinedTerm": [ - { "@id": "https://codemeta.github.io/terms/softwareSuggestions" }, - { "@id": "https://codemeta.github.io/terms/continuousIntegration" }, - { "@id": "https://codemeta.github.io/terms/buildInstructions" }, - { "@id": "https://codemeta.github.io/terms/developmentStatus" }, - { "@id": "https://codemeta.github.io/terms/embargoEndDate" }, - { "@id": "https://codemeta.github.io/terms/readme" }, - { "@id": "https://codemeta.github.io/terms/issueTracker" }, - { "@id": "https://codemeta.github.io/terms/referencePublication" }, - { "@id": "https://codemeta.github.io/terms/hasSourceCode" }, - { "@id": "https://codemeta.github.io/terms/isSourceCodeOf" } + { + "@id": "https://codemeta.github.io/terms/softwareSuggestions" + }, + { + "@id": "https://codemeta.github.io/terms/continuousIntegration" + }, + { + "@id": "https://codemeta.github.io/terms/buildInstructions" + }, + { + "@id": "https://codemeta.github.io/terms/developmentStatus" + }, + { + "@id": "https://codemeta.github.io/terms/embargoEndDate" + }, + { + "@id": "https://codemeta.github.io/terms/readme" + }, + { + "@id": "https://codemeta.github.io/terms/issueTracker" + }, + { + "@id": "https://codemeta.github.io/terms/referencePublication" + }, + { + "@id": "https://codemeta.github.io/terms/hasSourceCode" + }, + { + "@id": "https://codemeta.github.io/terms/isSourceCodeOf" + } ] }, { "@id": "https://codemeta.github.io/terms/softwareSuggestions", - "@type": ["DefinedTerm", "rdf:Property"], + "@type": [ + "DefinedTerm", + "rdf:Property" + ], "name": "softwareSuggestions", "termCode": "softwareSuggestions", "description": "Optional dependencies , e.g. for optional features, code development, etc. ", - "domainIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "rangeIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, + "domainIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "rangeIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, "sameAs": "https://w3id.org/codemeta/terms/softwareSuggestions" }, { "@id": "https://codemeta.github.io/terms/continuousIntegration", - "@type": ["DefinedTerm", "rdf:Property"], + "@type": [ + "DefinedTerm", + "rdf:Property" + ], "name": "continuousIntegration", "termCode": "continuousIntegration", "description": "Link to continuous integration service ", - "domainIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "rangeIncludes": {"@id": "http://schema.org/URL"}, + "domainIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "rangeIncludes": { + "@id": "http://schema.org/URL" + }, "sameAs": "https://w3id.org/codemeta/terms/continuousIntegration" - - }, - { - "@id": "https://codemeta.github.io/terms/buildInstructions", - "@type": ["DefinedTerm", "rdf:Property"], - "name": "buildInstructions", - "termCode": "buildInstructions", - "description": "Link to installation instructions/documentation", - "domainIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "rangeIncludes": {"@id": "http://schema.org/URL"}, - "sameAs": "https://w3id.org/codemeta/terms/buildInstructions" -}, - { - "@id": "https://codemeta.github.io/terms/developmentStatus", - "@type": ["DefinedTerm", "rdf:Property"], - "name": "developmentStatus", - "termCode": "developmentStatus", - "description": "Description of development status, e.g. Active, inactive, suspended. See repostatus.org", - "domainIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "rangeIncludes": {"@id": "http://schema.org/Text"}, - "sameAs": "https://w3id.org/codemeta/terms/developmentStatus" - }, - { - "@id": "https://codemeta.github.io/terms/embargoEndDate", - "@type": ["DefinedTerm", "rdf:Property"], - "name": "embargoEndDate", - "termCode": "embargoEndDate", - "description": "Software may be embargoed from public access until a specified date (e.g. pending publication, 1 year from publication)", - "domainIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "rangeIncludes": {"@id": "http://schema.org/Date"}, - "sameAs": "https://w3id.org/codemeta/terms/embargoEndDate" - }, - { - "@id": "https://codemeta.github.io/terms/readme", - "@type": ["DefinedTerm", "rdf:Property"], - "name": "readme", - "termCode": "readme", - "description": "Link to software Readme file", - "domainIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "rangeIncludes": {"@id": "http://schema.org/URL"}, - "sameAs": "https://w3id.org/codemeta/terms/readme" - }, - { - "@id": "https://codemeta.github.io/terms/issueTracker", - "@type": ["DefinedTerm", "rdf:Property"], - "name": "issueTracker", - "termCode": "issueTracker", - "description": "Link to software bug reporting or issue tracking system", - "domainIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "rangeIncludes": {"@id": "http://schema.org/URL"}, - "sameAs": "https://w3id.org/codemeta/terms/issueTracker" - }, - { - "@id": "https://codemeta.github.io/terms/referencePublication", - "@type": ["DefinedTerm", "rdf:Property"], - "name": "referencePublication", - "termCode": "referencePublication", - "description": "An academic publication related to the software", - "domainIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "rangeIncludes": {"@id": "http://schema.org/ScholarlyArticle"}, - "sameAs": "https://w3id.org/codemeta/terms/referencePublication" - }, - { - "@id": "https://codemeta.github.io/terms/hasSourceCode", - "@type": ["DefinedTerm", "rdf:Property"], - "name": "hasSourceCode", - "termCode": "hasSourceCode", - "description": "Link that states where the software code is for a given software. For example a software registry may indicate that one of its software entries hasSourceCode in a GitHub repository. ", - "domainIncludes": {"@id": "http://schema.org/SoftwareApplication"}, - "rangeIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "sameAs": "https://w3id.org/codemeta/terms/hasSourceCode" - }, - { - "@id": "https://codemeta.github.io/terms/isSourceCodeOf", - "@type": ["DefinedTerm", "rdf:Property"], - "name": "isSourceCodeOf", - "termCode": "isSourceCodeOf", - "description": "Link that states where software application is built from a given source code. This is the reverse property of 'hasSourceCode'. ", - "domainIncludes": {"@id": "http://schema.org/SoftwareSourceCode"}, - "rangeIncludes": {"@id": "http://schema.org/SoftwareApplication"}, - "sameAs": "https://w3id.org/codemeta/terms/isSourceCodeOf" + }, + { + "@id": "https://codemeta.github.io/terms/buildInstructions", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], + "name": "buildInstructions", + "termCode": "buildInstructions", + "description": "Link to installation instructions/documentation", + "domainIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "rangeIncludes": { + "@id": "http://schema.org/URL" + }, + "sameAs": "https://w3id.org/codemeta/terms/buildInstructions" + }, + { + "@id": "https://codemeta.github.io/terms/developmentStatus", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], + "name": "developmentStatus", + "termCode": "developmentStatus", + "description": "Description of development status, e.g. Active, inactive, suspended. See repostatus.org", + "domainIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "rangeIncludes": { + "@id": "http://schema.org/Text" + }, + "sameAs": "https://w3id.org/codemeta/terms/developmentStatus" + }, + { + "@id": "https://codemeta.github.io/terms/embargoEndDate", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], + "name": "embargoEndDate", + "termCode": "embargoEndDate", + "description": "Software may be embargoed from public access until a specified date (e.g. pending publication, 1 year from publication)", + "domainIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "rangeIncludes": { + "@id": "http://schema.org/Date" + }, + "sameAs": "https://w3id.org/codemeta/terms/embargoEndDate" + }, + { + "@id": "https://codemeta.github.io/terms/readme", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], + "name": "readme", + "termCode": "readme", + "description": "Link to software Readme file", + "domainIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "rangeIncludes": { + "@id": "http://schema.org/URL" + }, + "sameAs": "https://w3id.org/codemeta/terms/readme" + }, + { + "@id": "https://codemeta.github.io/terms/issueTracker", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], + "name": "issueTracker", + "termCode": "issueTracker", + "description": "Link to software bug reporting or issue tracking system", + "domainIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "rangeIncludes": { + "@id": "http://schema.org/URL" + }, + "sameAs": "https://w3id.org/codemeta/terms/issueTracker" + }, + { + "@id": "https://codemeta.github.io/terms/referencePublication", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], + "name": "referencePublication", + "termCode": "referencePublication", + "description": "An academic publication related to the software", + "domainIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "rangeIncludes": { + "@id": "http://schema.org/ScholarlyArticle" + }, + "sameAs": "https://w3id.org/codemeta/terms/referencePublication" + }, + { + "@id": "https://codemeta.github.io/terms/hasSourceCode", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], + "name": "hasSourceCode", + "termCode": "hasSourceCode", + "description": "Link that states where the software code is for a given software. For example a software registry may indicate that one of its software entries hasSourceCode in a GitHub repository. ", + "domainIncludes": { + "@id": "http://schema.org/SoftwareApplication" + }, + "rangeIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "sameAs": "https://w3id.org/codemeta/terms/hasSourceCode" + }, + { + "@id": "https://codemeta.github.io/terms/isSourceCodeOf", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], + "name": "isSourceCodeOf", + "termCode": "isSourceCodeOf", + "description": "Link that states where software application is built from a given source code. This is the reverse property of 'hasSourceCode'. ", + "domainIncludes": { + "@id": "http://schema.org/SoftwareSourceCode" + }, + "rangeIncludes": { + "@id": "http://schema.org/SoftwareApplication" + }, + "sameAs": "https://w3id.org/codemeta/terms/isSourceCodeOf" }, { "@id": "https://w3id.org/codemeta/3.0", "@type": "Profile", "name": "CodeMeta Terms profile", "version": "3.0", - "license": { "@id": "https://creativecommons.org/licenses/by/4.0/" } + "license": { + "@id": "https://creativecommons.org/licenses/by/4.0/" + } }, { "@id": "http://www.w3.org/ns/json-ld#flattened", @@ -1020,7 +1278,9 @@ "name": "JSON-LD 1.0", "description": "A JSON-based Serialization for Linked Data", "version": "1.0", - "sameAs": {"@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/880"} + "sameAs": { + "@id": "https://www.nationalarchives.gov.uk/PRONOM/fmt/880" + } }, { "@id": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE", @@ -1028,7 +1288,9 @@ "description": "Bioschemas specification for describing a Computational Workflow", "name": "ComputationalWorkflow profile", "version": "1.0-RELEASE", - "about": { "@id": "https://bioschemas.org/ComputationalWorkflow" } + "about": { + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" + } }, { "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE", @@ -1036,68 +1298,108 @@ "description": "Bioschemas specification for describing a formal parameter in the Life Sciences", "name": "FormalParameter Profile", "version": "1.0-RELEASE", - "about": { "@id": "https://bioschemas.org/FormalParameter" } + "about": { + "@id": "https://bioschemas.org/terms/FormalParameter" + } }, - { - "@id": "https://bioschemas.org/FormalParameter", - "@type": ["DefinedTerm", "rdfs:Class"], + { + "@id": "https://bioschemas.org/terms/FormalParameter", + "@type": [ + "DefinedTerm", + "rdfs:Class" + ], "name": "FormalParameter" }, - { - "@id": "https://bioschemas.org/ComputationalWorkflow", - "@type": ["DefinedTerm", "rdfs:Class"], + { + "@id": "https://bioschemas.org/terms/ComputationalWorkflow", + "@type": [ + "DefinedTerm", + "rdfs:Class" + ], "name": "ComputationalWorkflow" }, - { + { "@id": "http://schema.org/defaultValue", - "@type": ["DefinedTerm", "rdf:Property"], + "@type": [ + "DefinedTerm", + "rdf:Property" + ], "name": "defaultValue", "domainIncludes": [ - {"@id": "https://bioschemas.org/ComputationalWorkflow"} + { + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" + } ], "rangeIncludes": [ - {"@id": "http://schema.org/Text"}, - {"@id": "http://schema.org/Thing"} + { + "@id": "http://schema.org/Text" + }, + { + "@id": "http://schema.org/Thing" + } ] - }, - { + }, + { "@id": "http://schema.org/valueRequired", - "@type": ["DefinedTerm", "rdf:Property"], + "@type": [ + "DefinedTerm", + "rdf:Property" + ], "name": "valueRequired", "domainIncludes": [ - {"@id": "https://bioschemas.org/ComputationalWorkflow"} + { + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" + } ], "rangeIncludes": [ - {"@id": "http://schema.org/Text"}, - {"@id": "http://schema.org/Thing"} + { + "@id": "http://schema.org/Text" + }, + { + "@id": "http://schema.org/Thing" + } ] }, - { - "@id": "https://bioschemas.org/properties/input", - "@type": ["DefinedTerm", "rdf:Property"], + { + "@id": "https://bioschemas.org/terms/input", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], "termCode": "input", "name": "input", "description": "Definition of an input parameter required to use the computational workflow", "domainIncludes": [ - {"@id": "https://bioschemas.org/ComputationalWorkflow"} + { + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" + } ], "rangeIncludes": [ - {"@id": "https://bioschemas.org/FormalParameter"} + { + "@id": "https://bioschemas.org/terms/FormalParameter" + } ] }, - { - "@id": "https://bioschemas.org/properties/output", - "@type": ["DefinedTerm", "rdf:Property"], + { + "@id": "https://bioschemas.org/terms/output", + "@type": [ + "DefinedTerm", + "rdf:Property" + ], "termCode": "output", "name": "output", "description": "Definition of an output produced by the workflow", "domainIncludes": [ - {"@id": "https://bioschemas.org/ComputationalWorkflow"} + { + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" + } ], "rangeIncludes": [ - {"@id": "https://bioschemas.org/FormalParameter"} + { + "@id": "https://bioschemas.org/terms/FormalParameter" + } ] - }, + }, { "@id": "http://purl.org/dc/terms/conformsTo", "@type": "DefinedTerm", @@ -1114,20 +1416,24 @@ { "@id": "https://creativecommons.org/publicdomain/zero/1.0/", "@type": "CreativeWork", - "identifier": { "@id": "http://spdx.org/licenses/CC0-1.0"}, + "identifier": { + "@id": "http://spdx.org/licenses/CC0-1.0" + }, "name": "Creative Commons Zero v1.0 Universal", "version": "1.0" }, { "@id": "https://creativecommons.org/licenses/by/4.0/", "@type": "CreativeWork", - "identifier": { "@id": "http://spdx.org/licenses/CC-BY-4.0"}, + "identifier": { + "@id": "http://spdx.org/licenses/CC-BY-4.0" + }, "name": "Creative Commons Attribution 4.0 International", "version": "4.0" }, { "@id": "https://doi.org/DOI", - "@type": "PropertyValue", + "@type": "PropertyValue", "propertyID": "https://registry.identifiers.org/registry/doi", "value": "doi:DOI", "url": "https://doi.org/DOI" @@ -1692,64 +1998,78 @@ "@type": "Person", "name": "Laura Rodríguez-Navas" }, - { + { "@id": "https://orcid.org/0000-0003-4216-302X", "@type": "Person", "name": "Martin Weise" }, - { "@id": "https://orcid.org/0000-0002-1880-0597", + { + "@id": "https://orcid.org/0000-0002-1880-0597", "@type": "Person", "name": "Vartika Bisht" }, - { "@id": "https://orcid.org/0000-0001-6712-6335", + { + "@id": "https://orcid.org/0000-0001-6712-6335", "@type": "Person", "name": "Toshiyuki Nishiyama Hiraki" }, - { "@id": "https://orcid.org/0000-0002-5934-8998", + { + "@id": "https://orcid.org/0000-0002-5934-8998", "@type": "Person", "name": "Bram Ulrichts" }, - { "@id": "https://orcid.org/0000-0001-9261-8390", + { + "@id": "https://orcid.org/0000-0001-9261-8390", "@type": "Person", "name": "Michael Falk" }, - { "@id": "https://orcid.org/0000-0002-0035-6475", + { + "@id": "https://orcid.org/0000-0002-0035-6475", "@type": "Person", "name": "Eli Chadwick" }, - { "@id": "https://orcid.org/0000-0001-9447-460X", + { + "@id": "https://orcid.org/0000-0001-9447-460X", "@type": "Person", "name": "Daniel Bauer" }, - { "@id": "https://orcid.org/0000-0001-7760-1240", + { + "@id": "https://orcid.org/0000-0001-7760-1240", "@type": "Person", "name": "James Love" }, - { "@id": "https://orcid.org/0000-0001-9925-1560", + { + "@id": "https://orcid.org/0000-0001-9925-1560", "@type": "Person", "name": "Eleni Adamidi" }, - { "@id": "https://orcid.org/0000-0003-4028-811X", + { + "@id": "https://orcid.org/0000-0003-4028-811X", "@type": "Person", "name": "Josh Moore" }, - { "@id": "https://orcid.org/0000-0003-2196-5015", + { + "@id": "https://orcid.org/0000-0003-2196-5015", "@type": "Person", "name": "Lars Schöbitz" }, - { "@id": "https://orcid.org/0009-0002-6541-4637", + { + "@id": "https://orcid.org/0009-0002-6541-4637", "@type": "Person", "name": "Andreas Meier" }, - { "@id": "https://orcid.org/0009-0002-8209-1999", + { + "@id": "https://orcid.org/0009-0002-8209-1999", "@type": "Person", "name": "Juan Fuentes" }, - { "@id": "https://orcid.org/0000-0001-7218-0176", + { + "@id": "https://orcid.org/0000-0001-7218-0176", "@type": "Person", "name": "Edan Bainglass" }, - { "@id": "https://orcid.org/0000-0003-3482-0325", + { + "@id": "https://orcid.org/0000-0003-3482-0325", "@type": "Person", "name": "Balazs E. Pataki" }, @@ -1763,11 +2083,11 @@ { "@id": "http://spdx.org/licenses/CC-BY-4.0", "@type": "PropertyValue", - "propertyID": "http://spdx.org/rdf/terms#licenseId", + "propertyID": "http://spdx.org/rdf/terms#licenseId", "name": "spdx", "value": "CC-BY-4.0" }, - { + { "@id": "http://spdx.org/licenses/Apache-2.0", "@type": "PropertyValue", "propertyID": "http://spdx.org/rdf/terms#licenseId", @@ -1788,10 +2108,10 @@ }, { "@id": "https://w3id.org/ro/crate/1.1", - "@type": "Dataset", + "@type": "Dataset", "name": "RO-Crate specification 1.1", - "version": "1.1.2" - }, + "version": "1.1.2" + }, { "@id": "https://w3id.org/ro/crate/1.3-DRAFT/context", "@type": "File", @@ -1840,7 +2160,9 @@ "@type": "CreativeWork", "name": "Apache License 2.0", "version": "2.0", - "identifier": { "@id": "http://spdx.org/licenses/Apache-2.0"} + "identifier": { + "@id": "http://spdx.org/licenses/Apache-2.0" + } }, { "@id": "https://www.iana.org/assignments/link-relations/", @@ -1896,7 +2218,7 @@ }, { "@id": "https://www.researchobject.org/ro-crate/1.3-DRAFT/appendix/relative-uris.html" - } + } ] }, { @@ -1962,8 +2284,10 @@ { "@id": "https://github.com/ResearchObject/ro-crate/releases/download/TAG/ro-crate-TAG.pdf" } - ], - "identifier": {"@id": "https://doi.org/DOI"}, + ], + "identifier": { + "@id": "https://doi.org/DOI" + }, "name": "RO-Crate Metadata Specification 1.3-DRAFT", "sameAs": { "@id": "https://zenodo.org/record/ZENODO/files/ro-crate-TAG.html" @@ -2271,24 +2595,51 @@ { "@id": "https://orcid.org/0000-0003-3234-6762" }, - { "@id": "https://orcid.org/0000-0003-4216-302X"}, - { "@id": "https://orcid.org/0000-0002-1880-0597"}, - { "@id": "https://orcid.org/0000-0001-6712-6335"}, - { "@id": "https://orcid.org/0000-0002-5934-8998"}, - { "@id": "https://orcid.org/0000-0001-9261-8390"}, - { "@id": "https://orcid.org/0000-0002-0035-6475"}, - { "@id": "https://orcid.org/0000-0001-9447-460X"}, - { "@id": "https://orcid.org/0000-0001-7760-1240"}, - { "@id": "https://orcid.org/0000-0001-9925-1560"}, - { "@id": "https://orcid.org/0000-0003-4028-811X"}, - { "@id": "https://orcid.org/0000-0003-2196-5015"}, - { "@id": "https://orcid.org/0009-0002-6541-4637"}, - { "@id": "https://orcid.org/0009-0002-8209-1999"}, - { "@id": "https://orcid.org/0000-0001-7218-0176"}, - { "@id": "https://orcid.org/0000-0003-3482-0325"} - - - + { + "@id": "https://orcid.org/0000-0003-4216-302X" + }, + { + "@id": "https://orcid.org/0000-0002-1880-0597" + }, + { + "@id": "https://orcid.org/0000-0001-6712-6335" + }, + { + "@id": "https://orcid.org/0000-0002-5934-8998" + }, + { + "@id": "https://orcid.org/0000-0001-9261-8390" + }, + { + "@id": "https://orcid.org/0000-0002-0035-6475" + }, + { + "@id": "https://orcid.org/0000-0001-9447-460X" + }, + { + "@id": "https://orcid.org/0000-0001-7760-1240" + }, + { + "@id": "https://orcid.org/0000-0001-9925-1560" + }, + { + "@id": "https://orcid.org/0000-0003-4028-811X" + }, + { + "@id": "https://orcid.org/0000-0003-2196-5015" + }, + { + "@id": "https://orcid.org/0009-0002-6541-4637" + }, + { + "@id": "https://orcid.org/0009-0002-8209-1999" + }, + { + "@id": "https://orcid.org/0000-0001-7218-0176" + }, + { + "@id": "https://orcid.org/0000-0003-3482-0325" + } ], "name": "RO-Crate Community", "parentOrganization": { @@ -2387,6 +2738,5 @@ "@id": "http://www.w3.org/ns/dx/prof/role/vocabulary" } } - ] -} \ No newline at end of file +} diff --git a/docs/_specification/1.3-DRAFT/ro-crate-preview.html b/docs/_specification/1.3-DRAFT/ro-crate-preview.html index 89be7773..86c3a95a 100644 --- a/docs/_specification/1.3-DRAFT/ro-crate-preview.html +++ b/docs/_specification/1.3-DRAFT/ro-crate-preview.html @@ -381,10 +381,10 @@ "@id": "https://codemeta.github.io/terms/" }, { - "@id": "https://bioschemas.org/FormalParameter" + "@id": "https://bioschemas.org/terms/FormalParameter" }, { - "@id": "https://bioschemas.org/ComputationalWorkflow" + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" }, { "@id": "http://schema.org/defaultValue" @@ -393,10 +393,10 @@ "@id": "http://schema.org/valueRequired" }, { - "@id": "https://bioschemas.org/properties/input" + "@id": "https://bioschemas.org/terms/input" }, { - "@id": "https://bioschemas.org/properties/output" + "@id": "https://bioschemas.org/terms/output" }, { "@id": "http://purl.org/dc/terms/conformsTo" @@ -1658,7 +1658,7 @@ ] }, { - "@id": "https://bioschemas.org/FormalParameter", + "@id": "https://bioschemas.org/terms/FormalParameter", "@type": [ "DefinedTerm", "rdfs:Class" @@ -1666,7 +1666,7 @@ "name": "FormalParameter" }, { - "@id": "https://bioschemas.org/ComputationalWorkflow", + "@id": "https://bioschemas.org/terms/ComputationalWorkflow", "@type": [ "DefinedTerm", "rdfs:Class" @@ -1681,7 +1681,7 @@ ], "name": "defaultValue", "domainIncludes": { - "@id": "https://bioschemas.org/ComputationalWorkflow" + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" }, "rangeIncludes": [ { @@ -1700,7 +1700,7 @@ ], "name": "valueRequired", "domainIncludes": { - "@id": "https://bioschemas.org/ComputationalWorkflow" + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" }, "rangeIncludes": [ { @@ -1712,7 +1712,7 @@ ] }, { - "@id": "https://bioschemas.org/properties/input", + "@id": "https://bioschemas.org/terms/input", "@type": [ "DefinedTerm", "rdf:Property" @@ -1721,14 +1721,14 @@ "name": "input", "description": "Definition of an input parameter required to use the computational workflow", "domainIncludes": { - "@id": "https://bioschemas.org/ComputationalWorkflow" + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" }, "rangeIncludes": { - "@id": "https://bioschemas.org/FormalParameter" + "@id": "https://bioschemas.org/terms/FormalParameter" } }, { - "@id": "https://bioschemas.org/properties/output", + "@id": "https://bioschemas.org/terms/output", "@type": [ "DefinedTerm", "rdf:Property" @@ -1737,10 +1737,10 @@ "name": "output", "description": "Definition of an output produced by the workflow", "domainIncludes": { - "@id": "https://bioschemas.org/ComputationalWorkflow" + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" }, "rangeIncludes": { - "@id": "https://bioschemas.org/FormalParameter" + "@id": "https://bioschemas.org/terms/FormalParameter" } }, { @@ -2575,7 +2575,7 @@ "name": "ComputationalWorkflow profile", "version": "1.0-RELEASE", "about": { - "@id": "https://bioschemas.org/ComputationalWorkflow" + "@id": "https://bioschemas.org/terms/ComputationalWorkflow" } }, { @@ -2585,7 +2585,7 @@ "name": "FormalParameter Profile", "version": "1.0-RELEASE", "about": { - "@id": "https://bioschemas.org/FormalParameter" + "@id": "https://bioschemas.org/terms/FormalParameter" } }, { @@ -3073,17 +3073,17 @@

Go to: RO-Crate specifica
  • Codemeta Terms
    • -
  • FormalParameter
    • +
  • FormalParameter
    • -
  • ComputationalWorkflow
    • +
  • ComputationalWorkflow
  • defaultValue
  • valueRequired
    • -
  • input
    • +
  • input
    • -
  • output
    • +
  • output
  • conformsTo
    • @@ -7216,17 +7216,17 @@

    Go to: Codemeta Terms



    -

    Go to: FormalParameter

    +

    Go to: FormalParameter

    -
    +
    - + @@ -7246,9 +7246,9 @@

    Go to: FormalParameter

    @idhttps://bioschemas.org/FormalParameterhttps://bioschemas.org/terms/FormalParameter
    name [?] FormalParameter
    rangeIncludes [?]
    @@ -7256,17 +7256,17 @@

    Go to: FormalParameter



    -

    Go to: ComputationalWorkflow

    +

    Go to: ComputationalWorkflow

    -
    +
    - + @@ -7290,9 +7290,9 @@

    Go to: Computati
  • valueRequired
    • -
  • input
    • +
  • input
    • -
  • output
    • +
  • output

    • @idhttps://bioschemas.org/ComputationalWorkflowhttps://bioschemas.org/terms/ComputationalWorkflow
    name [?] ComputationalWorkflow
    @@ -7323,7 +7323,7 @@

    Go to: defaultValue

    domainIncludes [?] - ComputationalWorkflow + ComputationalWorkflow rangeIncludes [?]
      @@ -7363,7 +7363,7 @@

      Go to: valueRequired

    domainIncludes [?] - ComputationalWorkflow + ComputationalWorkflow rangeIncludes [?]
      @@ -7380,17 +7380,17 @@

      Go to: valueRequired



    -

    Go to: input

    +

    Go to: input

    -
    +
    - + @@ -7409,10 +7409,10 @@

    Go to: input

    - + - + @@ -7422,17 +7422,17 @@

    Go to: input



    -

    Go to: output

    +

    Go to: output

    -
    +
    @idhttps://bioschemas.org/properties/inputhttps://bioschemas.org/terms/input
    name [?] input input
    domainIncludes [?]ComputationalWorkflowComputationalWorkflow
    rangeIncludes [?]FormalParameterFormalParameter
    Items that reference this one
    hasPart [?] RO-Crate specification 1.2
    - + @@ -7451,10 +7451,10 @@

    Go to: output

    - + - + From c74b4afe761d0d74f04a22aba0fcabc34531bb07 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Wed, 20 May 2026 17:38:12 +0100 Subject: [PATCH 4/6] update changelog --- docs/_specification/1.3-DRAFT/appendix/changelog.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/_specification/1.3-DRAFT/appendix/changelog.md b/docs/_specification/1.3-DRAFT/appendix/changelog.md index 94d0a8d6..e0712137 100644 --- a/docs/_specification/1.3-DRAFT/appendix/changelog.md +++ b/docs/_specification/1.3-DRAFT/appendix/changelog.md @@ -28,6 +28,14 @@ excerpt: List of changes in releases of this specifications # APPENDIX: Changelog {#changelog} +* RO-Crate 1.3.0 + * Updated the Bioschemas namespace to `https://bioschemas.org/terms/` for all types and properties (previously `https://bioschemas.org/` for types and `https://bioschemas.org/properties` for properties). This change affects the following terms in the [JSON-LD context](../ro-crate-metadata.json): + * `ComputationalWorkflow`: `https://bioschemas.org/ComputationalWorkflow` -> `https://bioschemas.org/terms/ComputationalWorkflow` + * `FormalParameter` : `https://bioschemas.org/FormalParameter` -> `https://bioschemas.org/terms/FormalParameter` + * `input`: `https://bioschemas.org/properties/input` -> `https://bioschemas.org/terms/input` + * `output` `https://bioschemas.org/properties/output` -> `https://bioschemas.org/terms/output` + + * [RO-Crate 1.2.0](https://github.com/ResearchObject/ro-crate/releases/tag/1.2.0) * Clarified that the [RO-Crate Metadata Descriptor MUST have `@id` of `ro-crate-metadata.json`](../root-data-entity#ro-crate-metadata-descriptor) by removing conflicting statements elsewhere in the specification [#365](https://github.com/ResearchObject/ro-crate/pull/365) * Updated the Bioschemas namespace for properties from `https://bioschemas.org/ComputationalWorkflow#` to `https://bioschemas.org/properties/`. This change affects only the `input` and `output` properties in the [JSON-LD context](../ro-crate-metadata.json). From 130e645adf8e6be61aacc553cbed7e12755bbb75 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Wed, 20 May 2026 17:44:15 +0100 Subject: [PATCH 5/6] improves changelog readability --- docs/_specification/1.3-DRAFT/appendix/changelog.md | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/docs/_specification/1.3-DRAFT/appendix/changelog.md b/docs/_specification/1.3-DRAFT/appendix/changelog.md index e0712137..bca45892 100644 --- a/docs/_specification/1.3-DRAFT/appendix/changelog.md +++ b/docs/_specification/1.3-DRAFT/appendix/changelog.md @@ -29,11 +29,14 @@ excerpt: List of changes in releases of this specifications # APPENDIX: Changelog {#changelog} * RO-Crate 1.3.0 - * Updated the Bioschemas namespace to `https://bioschemas.org/terms/` for all types and properties (previously `https://bioschemas.org/` for types and `https://bioschemas.org/properties` for properties). This change affects the following terms in the [JSON-LD context](../ro-crate-metadata.json): - * `ComputationalWorkflow`: `https://bioschemas.org/ComputationalWorkflow` -> `https://bioschemas.org/terms/ComputationalWorkflow` - * `FormalParameter` : `https://bioschemas.org/FormalParameter` -> `https://bioschemas.org/terms/FormalParameter` - * `input`: `https://bioschemas.org/properties/input` -> `https://bioschemas.org/terms/input` - * `output` `https://bioschemas.org/properties/output` -> `https://bioschemas.org/terms/output` + * Updated the Bioschemas namespace to `https://bioschemas.org/terms/` for all types and properties (previously `https://bioschemas.org/` for types and `https://bioschemas.org/properties` for properties). This change affects 4 terms in the [JSON-LD context](../ro-crate-metadata.json): `ComputationalWorkflow`, `FormalParameter`, `input`, and `output`. + +| Term | Previous URI | New URI | +| --- | --- | --- | +| ComputationalWorkflow |`https://bioschemas.org/ComputationalWorkflow` | `https://bioschemas.org/terms/ComputationalWorkflow` | +| FormalParameter | `https://bioschemas.org/FormalParameter` | `https://bioschemas.org/terms/FormalParameter` | +| input |`https://bioschemas.org/properties/input` | `https://bioschemas.org/terms/input` | +| output |`https://bioschemas.org/properties/output` | `https://bioschemas.org/terms/output` | * [RO-Crate 1.2.0](https://github.com/ResearchObject/ro-crate/releases/tag/1.2.0) From 2a63796f1d41f222848d9533de1bd8b97fc2cdfc Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Wed, 20 May 2026 17:45:15 +0100 Subject: [PATCH 6/6] add issue number --- docs/_specification/1.3-DRAFT/appendix/changelog.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_specification/1.3-DRAFT/appendix/changelog.md b/docs/_specification/1.3-DRAFT/appendix/changelog.md index bca45892..a74d77d2 100644 --- a/docs/_specification/1.3-DRAFT/appendix/changelog.md +++ b/docs/_specification/1.3-DRAFT/appendix/changelog.md @@ -29,7 +29,7 @@ excerpt: List of changes in releases of this specifications # APPENDIX: Changelog {#changelog} * RO-Crate 1.3.0 - * Updated the Bioschemas namespace to `https://bioschemas.org/terms/` for all types and properties (previously `https://bioschemas.org/` for types and `https://bioschemas.org/properties` for properties). This change affects 4 terms in the [JSON-LD context](../ro-crate-metadata.json): `ComputationalWorkflow`, `FormalParameter`, `input`, and `output`. + * Updated the Bioschemas namespace to `https://bioschemas.org/terms/` for all types and properties (previously `https://bioschemas.org/` for types and `https://bioschemas.org/properties` for properties). This change affects 4 terms in the [JSON-LD context](../ro-crate-metadata.json): `ComputationalWorkflow`, `FormalParameter`, `input`, and `output`. [#529](https://github.com/ResearchObject/ro-crate/issues/529) | Term | Previous URI | New URI | | --- | --- | --- |
    @idhttps://bioschemas.org/properties/outputhttps://bioschemas.org/terms/output
    name [?] output output
    domainIncludes [?]ComputationalWorkflowComputationalWorkflow
    rangeIncludes [?]FormalParameterFormalParameter
    Items that reference this one
    hasPart [?] RO-Crate specification 1.2