diff --git a/src/examples/dataset-version/DatasetVersionObject-customproperties.json b/src/examples/dataset-version/DatasetVersionObject-customproperties.json new file mode 100644 index 0000000..45cf50d --- /dev/null +++ b/src/examples/dataset-version/DatasetVersionObject-customproperties.json @@ -0,0 +1,14 @@ +{ + "properties": [ + { + "label": "Planned Number of Female Subjects", + "range": "xsd:nonNegativeInteger", + "type": "http://purl.obolibrary.org/obo/NCIT_C90437", + "value": [ + "54" + ] + } + ], + "name": "growing-dataset", + "@type": "DatasetVersionObject" +} diff --git a/src/examples/dataset-version/DatasetVersionObject-customproperties.yaml b/src/examples/dataset-version/DatasetVersionObject-customproperties.yaml new file mode 100644 index 0000000..94af395 --- /dev/null +++ b/src/examples/dataset-version/DatasetVersionObject-customproperties.yaml @@ -0,0 +1,6 @@ +name: growing-dataset +properties: + - type: http://purl.obolibrary.org/obo/NCIT_C90437 + label: Planned Number of Female Subjects + range: xsd:nonNegativeInteger + value: 54 diff --git a/src/examples/dataset-version/DatasetVersionObject-dats.json b/src/examples/dataset-version/DatasetVersionObject-dats.json new file mode 100644 index 0000000..21af6dc --- /dev/null +++ b/src/examples/dataset-version/DatasetVersionObject-dats.json @@ -0,0 +1,108 @@ +{ + "properties": [ + { + "label": "Total number of sessions", + "value": [ + "521" + ] + }, + { + "label": "logo", + "value": [ + "logo.png" + ] + }, + { + "label": "CONP_status", + "value": [ + "CONP" + ] + }, + { + "label": "files", + "value": [ + "3771" + ] + }, + { + "label": "subjects", + "type": "http://purl.obolibrary.org/obo/NCIT_C98703", + "value": [ + "1" + ] + }, + { + "label": "origin_consortium", + "value": [ + "IBIS" + ] + }, + { + "label": "origin_institution", + "value": [ + "McGill Centre for Integrative Neuroscience" + ] + }, + { + "label": "origin_city", + "value": [ + "Montreal" + ] + }, + { + "label": "origin_province", + "value": [ + "Quebec" + ] + }, + { + "label": "origin_country", + "type": "http://purl.obolibrary.org/obo/HSO_0000360", + "value": [ + "Canada" + ] + } + ], + "license": "licenses:CC-BY-ND-4.0", + "was_attributed_to": [ + { + "meta_code": "MCIN", + "meta_type": "dlco:OrganizationObject", + "name": "McGill Center for Integrative Neuroscience" + }, + { + "meta_code": "ACEvans", + "meta_type": "dlco:ResearchContributorObject", + "name": "Alan C. Evans" + } + ], + "was_generated_by": [ + { + "at_location": { + "name": "North America", + "description": "13 scanners in 6 sites accross North America" + }, + "started_at": "2008-04-25T00:00:00", + "ended_at": "2019-04-15T00:00:00" + } + ], + "qualified_attribution": [ + { + "agent": "ACEvans", + "had_role": [ + "marcrel:ccp", + "marcrel:cre", + "marcrel:ldr", + "marcrel:rth" + ] + } + ], + "description": "Longitudinal brain scans of a single human phantom acquired on multiple MRI devices across North America over a period of 11 years. In addition to the human brain images, lego phantom scans have been acquired in parallel for quality assessments over time across sites.", + "keyword": [ + "phantom", + "MRI" + ], + "title": "Multicenter Single Subject Human MRI Phantom", + "version": "2.0", + "@type": "DatasetVersionObject" +} diff --git a/src/examples/dataset-version/DatasetVersionObject-dats.yaml b/src/examples/dataset-version/DatasetVersionObject-dats.yaml index ccfadb9..641d5ab 100644 --- a/src/examples/dataset-version/DatasetVersionObject-dats.yaml +++ b/src/examples/dataset-version/DatasetVersionObject-dats.yaml @@ -124,86 +124,26 @@ license: licenses:CC-BY-ND-4.0 keyword: - phantom - MRI -# "extraProperties": [ -# { -# "category": "Total number of sessions", -# "values": [ -# { -# "value": "521" -# } -# ] -# }, -# { -# "category": "logo", -# "values": [ -# { -# "value": "logo.png" -# } -# ] -# }, -# { -# "category": "CONP_status", -# "values": [ -# { -# "value": "CONP" -# } -# ] -# }, -# { -# "category": "files", -# "values": [ -# { -# "value": "3771" -# } -# ] -# }, -# { -# "category": "subjects", -# "values": [ -# { -# "value": "1" -# } -# ] -# }, -# { -# "category": "origin_consortium", -# "values": [ -# { -# "value": "IBIS" -# } -# ] -# }, -# { -# "category": "origin_institution", -# "values": [ -# { -# "value": "McGill Centre for Integrative Neuroscience" -# } -# ] -# }, -# { -# "category": "origin_city", -# "values": [ -# { -# "value": "Montreal" -# } -# ] -# }, -# { -# "category": "origin_province", -# "values": [ -# { -# "value": "Quebec" -# } -# ] -# }, -# { -# "category": "origin_country", -# "values": [ -# { -# "value": "Canada" -# } -# ] -# } -# ] - +properties: + - label: Total number of sessions + value: 521 + - label: logo + value: logo.png + - label: CONP_status + value: CONP + - label: files + value: 3771 + - label: subjects + type: http://purl.obolibrary.org/obo/NCIT_C98703 + value: 1 + - label: origin_consortium + value: IBIS + - label: origin_institution + value: McGill Centre for Integrative Neuroscience + - label: origin_city + value: Montreal + - label: origin_province + value: Quebec + - label: origin_country + type: http://purl.obolibrary.org/obo/HSO_0000360 + value: Canada diff --git a/src/linkml/ontology/datasets.yaml b/src/linkml/ontology/datasets.yaml index b4fb907..d26ea27 100644 --- a/src/linkml/ontology/datasets.yaml +++ b/src/linkml/ontology/datasets.yaml @@ -148,14 +148,6 @@ slots: todos: - Rename to `named_part`? See also todo for `QualifiedPart` - type: - slot_uri: dlco:type - description: >- - The nature of the resource. - range: string - exact_mappings: - - dcterms:type - keyword: slot_uri: dlco:keyword description: >- @@ -186,7 +178,6 @@ classes: - qualified_part - relation - title - - type - version - was_attributed_to - was_generated_by diff --git a/src/linkml/ontology/rdfs.yaml b/src/linkml/ontology/rdfs.yaml new file mode 100644 index 0000000..4c2b05a --- /dev/null +++ b/src/linkml/ontology/rdfs.yaml @@ -0,0 +1,67 @@ +id: https://concepts.datalad.org/ontology/rdfs +name: meta_utils +title: RDFS elements +description: >- + TODO +prefixes: + rdfs: http://www.w3.org/2000/01/rdf-schema# +emit_prefixes: + - rdfs +imports: + - ../ontology/types + + +slots: + comment: + slot_uri: rdfs:comment + description: >- + A human-readable description. + range: string + + label: + slot_uri: rdfs:label + description: >- + A human-readable version of a resource's name. + range: string + + range: + slot_uri: rdfs:range + description: >- + State that the values of a property are instances a class. + range: uriorcurie + + type: + slot_uri: rdfs:type + description: >- + State that the subject is an instance of a class. + range: uriorcurie + + value: + slot_uri: rdfs:value + description: >- + Value of a resource. + range: string + multivalued: true + relational_role: OBJECT + + properties: + slot_uri: rdfs:property + description: >- + Container for arbitrary (extra) properties that are not covered by + other dedicated properties. + range: Property + multivalued: true + relational_role: PREDICATE + + +classes: + Property: + class_uri: rdfs:Property + description: >- + RDFS based class to describe arbitrary properties. + slots: + - comment + - label + - range + - type + - value diff --git a/src/linkml/ontology/schema_utils.yaml b/src/linkml/ontology/schema_utils.yaml index a07236b..e2ee690 100644 --- a/src/linkml/ontology/schema_utils.yaml +++ b/src/linkml/ontology/schema_utils.yaml @@ -8,7 +8,9 @@ prefixes: dcterms: http://purl.org/dc/terms/ dlco: https://concepts.datalad.org/ontology/ linkml: https://w3id.org/linkml/ + rdfs: http://www.w3.org/2000/01/rdf-schema# imports: + - ../ontology/rdfs - ../ontology/types default_prefix: dlco @@ -48,6 +50,7 @@ slots: exact_mappings: - dcterms:type + classes: HasMetaTypeDesignator: mixin: true diff --git a/src/linkml/schemas/dataset-version.yaml b/src/linkml/schemas/dataset-version.yaml index 6ce3ee4..03ca715 100644 --- a/src/linkml/schemas/dataset-version.yaml +++ b/src/linkml/schemas/dataset-version.yaml @@ -21,6 +21,7 @@ prefixes: dpv: https://w3id.org/dpv# linkml: https://w3id.org/linkml/ prov: http://www.w3.org/ns/prov# + rdfs: http://www.w3.org/2000/01/rdf-schema# schema: http://schema.org/ spdx: http://spdx.org/rdf/terms# licenses: http://spdx.org/licenses/ @@ -126,6 +127,8 @@ classes: range: LicenseDocumentObject description: >- Container to declare custom licenses. + slots: + - properties slot_usage: distribution: inlined: true @@ -161,6 +164,8 @@ classes: inlined_as_list: true multivalued: true range: ActivityObject + properties: + inlined: true qualified_attribution: inlined: true inlined_as_list: true diff --git a/src/linkml/schemas/ontology.yaml b/src/linkml/schemas/ontology.yaml index 09d8bae..1ca2be8 100644 --- a/src/linkml/schemas/ontology.yaml +++ b/src/linkml/schemas/ontology.yaml @@ -22,6 +22,7 @@ imports: - ../ontology/common - ../ontology/projects - ../ontology/provenance + - ../ontology/rdfs - ../ontology/schema_utils - ../ontology/schema_objects - ../ontology/types