diff --git a/.github/workflows/generate_docs.yaml b/.github/workflows/generate_docs.yaml index f817c019c..2350d5ba7 100644 --- a/.github/workflows/generate_docs.yaml +++ b/.github/workflows/generate_docs.yaml @@ -35,7 +35,7 @@ jobs: touch docs/.nojekyll gen-doc -d docs linkml-schema/purple_boxes.yaml mv docs/index.md docs/index_purple.md - gen-doc -d docs linkml-schema/kbmodel.yaml + gen-doc -d docs linkml-schema/gars.yaml mv docs/index.md docs/index_gars.md mv docs/index_main.md docs/index.md diff --git a/linkml-schema/bican_biolink.yaml b/linkml-schema/bican_biolink.yaml index 52fb6622e..d372ce127 100644 --- a/linkml-schema/bican_biolink.yaml +++ b/linkml-schema/bican_biolink.yaml @@ -530,274 +530,274 @@ types: typeof: string base: str uri: xsd:string - string: - name: string - definition_uri: https://w3id.org/linkml/String - description: A character string - notes: - - In RDF serializations, a slot with range of string is treated as a literal or - type xsd:string. If you are authoring schemas in LinkML YAML, the type is - referenced with the lower case "string". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Text - base: str - uri: xsd:string - integer: - name: integer - definition_uri: https://w3id.org/linkml/Integer - description: An integer - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "integer". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Integer - base: int - uri: xsd:integer - boolean: - name: boolean - definition_uri: https://w3id.org/linkml/Boolean - description: A binary (true or false) value - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "boolean". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Boolean - base: Bool - uri: xsd:boolean - repr: bool - float: - name: float - definition_uri: https://w3id.org/linkml/Float - description: A real number that conforms to the xsd:float specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "float". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Float - base: float - uri: xsd:float - double: - name: double - definition_uri: https://w3id.org/linkml/Double - description: A real number that conforms to the xsd:double specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "double". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - close_mappings: - - schema:Float - base: float - uri: xsd:double - decimal: - name: decimal - definition_uri: https://w3id.org/linkml/Decimal - description: A real number with arbitrary precision that conforms to the xsd:decimal - specification - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "decimal". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - broad_mappings: - - schema:Number - base: Decimal - uri: xsd:decimal - time: - name: time - definition_uri: https://w3id.org/linkml/Time - description: A time object represents a (local) time of day, independent of any - particular day - notes: - - URI is dateTime because OWL reasoners do not work with straight date or time - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "time". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Time - base: XSDTime - uri: xsd:time - repr: str - date: - name: date - definition_uri: https://w3id.org/linkml/Date - description: a date (year, month and day) in an idealized calendar - notes: - - URI is dateTime because OWL reasoners don't work with straight date or time - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "date". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:Date - base: XSDDate - uri: xsd:date - repr: str - datetime: - name: datetime - definition_uri: https://w3id.org/linkml/Datetime - description: The combination of a date and time - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "datetime". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - exact_mappings: - - schema:DateTime - base: XSDDateTime - uri: xsd:dateTime - repr: str - date_or_datetime: - name: date_or_datetime - definition_uri: https://w3id.org/linkml/DateOrDatetime - description: Either a date or a datetime - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "date_or_datetime". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: str - uri: linkml:DateOrDatetime - repr: str - uriorcurie: - name: uriorcurie - definition_uri: https://w3id.org/linkml/Uriorcurie - description: a URI or a CURIE - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "uriorcurie". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: URIorCURIE - uri: xsd:anyURI - repr: str - curie: - name: curie - definition_uri: https://w3id.org/linkml/Curie - conforms_to: https://www.w3.org/TR/curie/ - description: a compact URI - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "curie". - comments: - - in RDF serializations this MUST be expanded to a URI - - in non-RDF serializations MAY be serialized as the compact representation - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: Curie - uri: xsd:string - repr: str - uri: - name: uri - definition_uri: https://w3id.org/linkml/Uri - conforms_to: https://www.ietf.org/rfc/rfc3987.txt - description: a complete URI - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "uri". - comments: - - in RDF serializations a slot with range of uri is treated as a literal or type - xsd:anyURI unless it is an identifier or a reference to an identifier, in which - case it is translated directly to a node - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - close_mappings: - - schema:URL - base: URI - uri: xsd:anyURI - repr: str - ncname: - name: ncname - definition_uri: https://w3id.org/linkml/Ncname - description: Prefix part of CURIE - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "ncname". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: NCName - uri: xsd:string - repr: str - objectidentifier: - name: objectidentifier - definition_uri: https://w3id.org/linkml/Objectidentifier - description: A URI or CURIE that represents an object in the model. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "objectidentifier". - comments: - - Used for inheritance and type checking - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: ElementIdentifier - uri: shex:iri - repr: str - nodeidentifier: - name: nodeidentifier - definition_uri: https://w3id.org/linkml/Nodeidentifier - description: A URI, CURIE or BNODE that represents a node in a model. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "nodeidentifier". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: NodeIdentifier - uri: shex:nonLiteral - repr: str - jsonpointer: - name: jsonpointer - definition_uri: https://w3id.org/linkml/Jsonpointer - conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 - description: A string encoding a JSON Pointer. The value of the string MUST conform - to JSON Point syntax and SHOULD dereference to a valid object within the current - instance document when encoded in tree form. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "jsonpointer". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: str - uri: xsd:string - repr: str - jsonpath: - name: jsonpath - definition_uri: https://w3id.org/linkml/Jsonpath - conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html - description: A string encoding a JSON Path. The value of the string MUST conform - to JSON Point syntax and SHOULD dereference to zero or more valid objects within - the current instance document when encoded in tree form. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "jsonpath". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: str - uri: xsd:string - repr: str - sparqlpath: - name: sparqlpath - definition_uri: https://w3id.org/linkml/Sparqlpath - conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths - description: A string encoding a SPARQL Property Path. The value of the string - MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects - within the current instance document when encoded as RDF. - notes: - - If you are authoring schemas in LinkML YAML, the type is referenced with the - lower case "sparqlpath". - from_schema: https://w3id.org/linkml/types - imported_from: linkml:types - base: str - uri: xsd:string - repr: str + # string: + # name: string + # definition_uri: https://w3id.org/linkml/String + # description: A character string + # notes: + # - In RDF serializations, a slot with range of string is treated as a literal or + # type xsd:string. If you are authoring schemas in LinkML YAML, the type is + # referenced with the lower case "string". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # exact_mappings: + # - schema:Text + # base: str + # uri: xsd:string + # integer: + # name: integer + # definition_uri: https://w3id.org/linkml/Integer + # description: An integer + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "integer". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # exact_mappings: + # - schema:Integer + # base: int + # uri: xsd:integer + # boolean: + # name: boolean + # definition_uri: https://w3id.org/linkml/Boolean + # description: A binary (true or false) value + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "boolean". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # exact_mappings: + # - schema:Boolean + # base: Bool + # uri: xsd:boolean + # repr: bool + # float: + # name: float + # definition_uri: https://w3id.org/linkml/Float + # description: A real number that conforms to the xsd:float specification + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "float". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # exact_mappings: + # - schema:Float + # base: float + # uri: xsd:float + # double: + # name: double + # definition_uri: https://w3id.org/linkml/Double + # description: A real number that conforms to the xsd:double specification + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "double". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # close_mappings: + # - schema:Float + # base: float + # uri: xsd:double + # decimal: + # name: decimal + # definition_uri: https://w3id.org/linkml/Decimal + # description: A real number with arbitrary precision that conforms to the xsd:decimal + # specification + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "decimal". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # broad_mappings: + # - schema:Number + # base: Decimal + # uri: xsd:decimal + # time: + # name: time + # definition_uri: https://w3id.org/linkml/Time + # description: A time object represents a (local) time of day, independent of any + # particular day + # notes: + # - URI is dateTime because OWL reasoners do not work with straight date or time + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "time". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # exact_mappings: + # - schema:Time + # base: XSDTime + # uri: xsd:time + # repr: str + # date: + # name: date + # definition_uri: https://w3id.org/linkml/Date + # description: a date (year, month and day) in an idealized calendar + # notes: + # - URI is dateTime because OWL reasoners don't work with straight date or time + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "date". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # exact_mappings: + # - schema:Date + # base: XSDDate + # uri: xsd:date + # repr: str + # datetime: + # name: datetime + # definition_uri: https://w3id.org/linkml/Datetime + # description: The combination of a date and time + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "datetime". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # exact_mappings: + # - schema:DateTime + # base: XSDDateTime + # uri: xsd:dateTime + # repr: str + # date_or_datetime: + # name: date_or_datetime + # definition_uri: https://w3id.org/linkml/DateOrDatetime + # description: Either a date or a datetime + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "date_or_datetime". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # base: str + # uri: linkml:DateOrDatetime + # repr: str + # uriorcurie: + # name: uriorcurie + # definition_uri: https://w3id.org/linkml/Uriorcurie + # description: a URI or a CURIE + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "uriorcurie". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # base: URIorCURIE + # uri: xsd:anyURI + # repr: str + # curie: + # name: curie + # definition_uri: https://w3id.org/linkml/Curie + # conforms_to: https://www.w3.org/TR/curie/ + # description: a compact URI + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "curie". + # comments: + # - in RDF serializations this MUST be expanded to a URI + # - in non-RDF serializations MAY be serialized as the compact representation + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # base: Curie + # uri: xsd:string + # repr: str + # uri: + # name: uri + # definition_uri: https://w3id.org/linkml/Uri + # conforms_to: https://www.ietf.org/rfc/rfc3987.txt + # description: a complete URI + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "uri". + # comments: + # - in RDF serializations a slot with range of uri is treated as a literal or type + # xsd:anyURI unless it is an identifier or a reference to an identifier, in which + # case it is translated directly to a node + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # close_mappings: + # - schema:URL + # base: URI + # uri: xsd:anyURI + # repr: str + # ncname: + # name: ncname + # definition_uri: https://w3id.org/linkml/Ncname + # description: Prefix part of CURIE + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "ncname". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # base: NCName + # uri: xsd:string + # repr: str + # objectidentifier: + # name: objectidentifier + # definition_uri: https://w3id.org/linkml/Objectidentifier + # description: A URI or CURIE that represents an object in the model. + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "objectidentifier". + # comments: + # - Used for inheritance and type checking + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # base: ElementIdentifier + # uri: shex:iri + # repr: str + # nodeidentifier: + # name: nodeidentifier + # definition_uri: https://w3id.org/linkml/Nodeidentifier + # description: A URI, CURIE or BNODE that represents a node in a model. + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "nodeidentifier". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # base: NodeIdentifier + # uri: shex:nonLiteral + # repr: str + # jsonpointer: + # name: jsonpointer + # definition_uri: https://w3id.org/linkml/Jsonpointer + # conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 + # description: A string encoding a JSON Pointer. The value of the string MUST conform + # to JSON Point syntax and SHOULD dereference to a valid object within the current + # instance document when encoded in tree form. + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "jsonpointer". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # base: str + # uri: xsd:string + # repr: str + # jsonpath: + # name: jsonpath + # definition_uri: https://w3id.org/linkml/Jsonpath + # conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html + # description: A string encoding a JSON Path. The value of the string MUST conform + # to JSON Point syntax and SHOULD dereference to zero or more valid objects within + # the current instance document when encoded in tree form. + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "jsonpath". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # base: str + # uri: xsd:string + # repr: str + # sparqlpath: + # name: sparqlpath + # definition_uri: https://w3id.org/linkml/Sparqlpath + # conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths + # description: A string encoding a SPARQL Property Path. The value of the string + # MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects + # within the current instance document when encoded as RDF. + # notes: + # - If you are authoring schemas in LinkML YAML, the type is referenced with the + # lower case "sparqlpath". + # from_schema: https://w3id.org/linkml/types + # imported_from: linkml:types + # base: str + # uri: xsd:string + # repr: str slots: has attribute: name: has attribute @@ -1220,6 +1220,24 @@ slots: domain_of: - entity range: narrative text + creation date: + name: creation date + definition_uri: https://w3id.org/biolink/vocab/creation_date + description: date on which an entity was created. This can be applied to nodes + or edges + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - publication date + exact_mappings: + - dct:createdOn + - WIKIDATA_PROPERTY:P577 + is_a: node property + domain: named thing + slot_uri: biolink:creation_date + owner: information content entity + domain_of: + - information content entity + range: date has taxonomic rank: name: has taxonomic rank definition_uri: https://w3id.org/biolink/vocab/has_taxonomic_rank @@ -1234,6 +1252,60 @@ slots: domain_of: - organism taxon range: taxonomic rank + version: + name: version + definition_uri: https://w3id.org/biolink/vocab/version + from_schema: https://w3id.org/biolink/biolink-model + broad_mappings: + - pav:version + - owl:versionInfo + is_a: node property + domain: dataset + slot_uri: biolink:version + owner: version + range: string + license: + name: license + definition_uri: https://w3id.org/biolink/vocab/license + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - dct:license + narrow_mappings: + - WIKIDATA_PROPERTY:P275 + is_a: node property + domain: information content entity + slot_uri: biolink:license + owner: information content entity + domain_of: + - information content entity + range: string + rights: + name: rights + definition_uri: https://w3id.org/biolink/vocab/rights + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - dct:rights + is_a: node property + domain: information content entity + slot_uri: biolink:rights + owner: information content entity + domain_of: + - information content entity + range: string + format: + name: format + definition_uri: https://w3id.org/biolink/vocab/format + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - dct:format + - WIKIDATA_PROPERTY:P2701 + is_a: node property + domain: information content entity + slot_uri: biolink:format + owner: information content entity + domain_of: + - information content entity + range: string has biological sequence: name: has biological sequence definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence @@ -1687,6 +1759,82 @@ classes: - synonym - has taxonomic rank class_uri: biolink:OrganismTaxon + information content entity: + name: information content entity + id_prefixes: + - doi + definition_uri: https://w3id.org/biolink/vocab/InformationContentEntity + description: a piece of information that typically describes some topic of discourse + or is used as support. + from_schema: https://w3id.org/biolink/biolink-model + aliases: + - information + - information artefact + - information entity + exact_mappings: + - IAO:0000030 + narrow_mappings: + - UMLSSG:CONC + - STY:T077 + - STY:T078 + - STY:T079 + - STY:T080 + - STY:T081 + - STY:T082 + - STY:T089 + - STY:T102 + - STY:T169 + - STY:T171 + - STY:T185 + is_a: named thing + abstract: true + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + - license + - rights + - format + - creation date + class_uri: biolink:InformationContentEntity + dataset: + name: dataset + definition_uri: https://w3id.org/biolink/vocab/Dataset + description: an item that refers to a collection of data from a data source. + from_schema: https://w3id.org/biolink/biolink-model + exact_mappings: + - IAO:0000100 + - dctypes:Dataset + - schema:dataset + - dcid:Dataset + is_a: information content entity + slots: + - id + - iri + - category + - type + - name + - description + - has attribute + - deprecated + - provided by + - xref + - full name + - synonym + - license + - rights + - format + - creation date + class_uri: biolink:Dataset physical essence or occurrent: name: physical essence or occurrent definition_uri: https://w3id.org/biolink/vocab/PhysicalEssenceOrOccurrent @@ -2051,6 +2199,6 @@ classes: - has biological sequence class_uri: biolink:Genome metamodel_version: 1.7.0 -source_file_size: 42695 -generation_date: '2024-03-20T11:42:00' +source_file_size: 44864 +generation_date: '2024-03-27T11:46:24' diff --git a/linkml-schema/gars.yaml b/linkml-schema/gars.yaml new file mode 100644 index 000000000..d5798c754 --- /dev/null +++ b/linkml-schema/gars.yaml @@ -0,0 +1,151 @@ +id: https://identifiers.org/brain-bican/gars-model +name: gars-model +prefixes: + linkml: https://w3id.org/linkml/ + bican: https://identifiers.org/brain-bican/vocab/ + spdx: http://spdx.org/rdf/terms# + schema: http://schema.org/ + ncbi: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id= + NCBIAssembly: https://www.ncbi.nlm.nih.gov/assembly/ + prov: http://www.w3.org/ns/prov# + +imports: + - linkml:types + - bican_biolink +default_range: string +default_prefix: bican + +classes: + gene annotation: + is_a: gene + description: >- + An annotation describing the location, boundaries, and functions of + individual genes within a genome annotation. + slots: + - molecular type + - source id + attributes: + referenced in: + description: The genome annotation that this gene annotation was referenced from. + required: true + inlined: true + any_of: + - range: genome annotation + - range: string + id_prefixes: + - ENSEMBL + - MGI + - NCBIGene + + genome annotation: + is_a: genome + description: >- + Location and nomenclature of genes and all of the coding regions in a genome assembly + and the classification of genes and transcripts into types. + slots: + - version + - digest + - content_url + - authority + attributes: + reference assembly: + description: The reference genome assembly that this genome annotation was created from. + required: true + inlined: true + any_of: + - range: genome assembly + - range: string + + genome assembly: + is_a: named thing + mixins: + - thing with taxon + description: >- + Genome assembly to contain version and label information + slots: + - version + - strain + + checksum: + is_a: entity + description: >- + Checksum values associated with digital entities. + slots: + - checksum algorithm + attributes: + value: + description: The checksum value obtained from a specific cryotographic hash function. + + annotation collection: + tree_root: true + attributes: + annotations: + multivalued: true + inlined_as_list: true + range: gene annotation + genome_annotations: + multivalued: true + inlined_as_list: true + range: genome annotation + genome_assemblies: + multivalued: true + inlined_as_list: true + range: genome assembly + + +slots: + molecular type: + any_of: + - range: BioType + - range: string + + digest: + description: Stores checksum information. + multivalued: true + inlined_as_list: true + any_of: + - range: checksum + - range: string + + content_url: + slot_uri: schema:url + multivalued: true + + authority: + description: The organization responsible for publishing the data. + range: AuthorityType + + checksum algorithm: + description: The type of cryptographic hash function used to calculate the checksum value. + range: DigestType + + source id: + description: The authority specific identifier. + slot_uri: schema:identifier + + strain: + description: The genetic variant or subtype of a species or organism. + + +enums: + DigestType: + permissible_values: + spdx:checksumAlgorithm_sha1: + title: SHA1 + meaning: spdx:checksumAlgorithm_sha1 + spdx:checksumAlgorithm_md5: + title: MD5 + meaning: spdx:checksumAlgorithm_md5 + spdx:checksumAlgorithm_sha256: + title: SHA256 + meaning: spdx:checksumAlgorithm_sha256 + + BioType: + permissible_values: + protein_coding: + noncoding: + + AuthorityType: + permissible_values: + ENSEMBL: + NCBI: \ No newline at end of file diff --git a/linkml-schema/kbmodel.yaml b/linkml-schema/kbmodel.yaml deleted file mode 100644 index 27be15b64..000000000 --- a/linkml-schema/kbmodel.yaml +++ /dev/null @@ -1,608 +0,0 @@ -id: https://identifiers.org/brain-bican/kb-model -name: kb-model -prefixes: - linkml: https://w3id.org/linkml/ - #biolink: https://w3id.org/biolink/vocab/ - biolink: https://raw.githubusercontent.com/biolink/biolink-model/master/ - bican: https://identifiers.org/brain-bican/vocab/ - spdx: http://spdx.org/rdf/terms# - schema: http://schema.org/ - ncbi: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id= - NCBIAssembly: https://www.ncbi.nlm.nih.gov/assembly/ - prov: http://www.w3.org/ns/prov# - - -imports: - - linkml:types - - biolink:biolink-model -default_range: string -default_prefix: bican - -classes: - gene annotation: - is_a: gene - description: >- - An annotation describing the location, boundaries, and functions of - individual genes within a genome annotation. - slots: - - molecular type - - source id - attributes: - referenced in: - description: The genome annotation that this gene annotation was referenced from. - required: true - inlined: true - any_of: - - range: genome annotation - - range: string - id_prefixes: - - ENSEMBL - - MGI - - NCBIGene - - genome annotation: - is_a: genome - description: >- - Location and nomenclature of genes and all of the coding regions in a genome assembly - and the classification of genes and transcripts into types. - slots: - - version - - digest - - content_url - - authority - attributes: - reference assembly: - description: The reference genome assembly that this genome annotation was created from. - required: true - inlined: true - any_of: - - range: genome assembly - - range: string - - genome assembly: - is_a: named thing - mixins: - - thing with taxon - description: >- - Genome assembly to contain version and label information - slots: - - version - - strain - - checksum: - is_a: entity - description: >- - Checksum values associated with digital entities. - slots: - - checksum algorithm - attributes: - value: - description: The checksum value obtained from a specific cryotographic hash function. - - annotation collection: - tree_root: true - attributes: - annotations: - multivalued: true - inlined_as_list: true - range: gene annotation - genome_annotations: - multivalued: true - inlined_as_list: true - range: genome annotation - genome_assemblies: - multivalued: true - inlined_as_list: true - range: genome assembly - - prov activity: - mixin: true - description: >- - Based off prov:Activity; an activity is something that occurs over a period of time and acts upon or with entities; - it may include consuming, processing, transforming, modifying, relocating, using, or generating entities. - slots: - - used - - generated - - wasAssociatedWith - - - brain extraction: - description: >- - A process that takes a brain sample from a donor and produces a brain segment. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: donor - generated: - range: brain segment - - brain segment sectioning: - description: >- - A process that takes a brain segment and produces a brain section. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: brain segment - generated: - range: brain section - - tissue dissecting: - description: >- - A process that takes a brain section and produces a tissue sample. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: brain section - generated: - range: tissue sample - - cell dissociation: - description: >- - A process that takes a tissue sample and produces a dissociated cell sample. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: tissue sample - generated: - range: dissociated cell sample - - cell enrichment: - description: >- - A process that takes a dissociated cell sample and produces an enriched cell sample. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: dissociated cell sample - generated: - range: enriched cell sample - - cell barcoding: - description: >- - A process that takes an enriched cell sample and produces a barcoded cell sample. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: enriched cell sample - generated: - range: barcoded cell sample - - cdna amplification: - description: >- - A process that takes a barcoded cell sample and produces an amplified cDNA sample. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: barcoded cell sample - generated: - range: amplified cdna - - library construction: - description: >- - A process that takes an amplified cDNA sample and produces a library. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: amplified cdna - generated: - range: library - - library aliquoting: - description: >- - A process that takes a library and produces an library aliquot. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: library - generated: - range: library aliquot - - library pooling: - description: >- - A process that takes a library aliquot and produces a library pool. - is_a: activity - mixins: - - prov activity - slot_usage: - used: - range: library aliquot - generated: - range: library pool - - - prov entity: - mixin: true - description: >- - Based off prov:Entity; an entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; - entities may be real or imaginary. - slots: - - wasDerivedFrom - - wasGeneratedBy - - wasAttributedTo - - - # 028 - donors.ipynb - # age_at_death -> death age, date_of_birth -> birth date, date_of_death -> death date, full_genotype -> full genotype, - # entity_type -> type/category, label -> name, ncbitaxonomyid -> in_taxon, sex -> sex - donor: - is_a: agent - mixins: - - thing with taxon - description: >- - A person or organism that is the source of a biological sample. - slots: - - sex - - birth date - - death date - - death age - - full genotype - - - # 027 - brain_extraction.ipynb - # mappings (notebook -> model): anatomical_division -> anatomical division, barcode -> id, - # (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, label -> name - brain segment: - is_a: entity - mixins: - - prov entity - attributes: - anatomical division: - slot_usage: - wasGeneratedBy: - range: brain extraction - wasDerivedFrom: - range: donor - - - # 026 - brain_segment_sectioning.ipynb - # mappings (notebook -> model): barcode -> id, (created_by_process_id & created_by_process_type) -> wasGeneratedBy, - # entity_type -> type/category, label -> name, ordinal -> ordinal - brain section: - is_a: entity - mixins: - - prov entity - attributes: - ordinal: - description: The ordinal number of the section. - range: integer - slot_usage: - wasGeneratedBy: - range: brain segment sectioning - wasDerivedFrom: - range: brain segment - - - # 025b - tissue_dissectioning.ipynb - # mappings (notebook -> model): (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, - # label -> name, roi_plan -> roi plan, roi_label -> roi label - tissue sample: - is_a: entity - mixins: - - prov entity - attributes: - roi plan: - roi label: - description: The label of the region of interest. - slot_usage: - wasGeneratedBy: - range: tissue dissecting - wasDerivedFrom: - range: brain section - - - # 024 - cell_dissociation.ipynb - # mappings (notebook -> model): cell_prep_type -> cell prep type, (created_by_process_id & created_by_process_type) -> wasGeneratedBy, - # entity_type -> type/category, facs_population_plan -> facs population plan, label -> name, number_of_cells_collected -> num cells collected - dissociated cell sample: - is_a: entity - mixins: - - prov entity - attributes: - cell prep type: - facs population plan: - num cells collected: - range: integer - slot_usage: - wasGeneratedBy: - range: cell dissociation - wasDerivedFrom: - range: tissue sample - - - enriched cell sample: - is_a: entity - mixins: - - prov entity - slot_usage: - wasGeneratedBy: - range: cell enrichment - wasDerivedFrom: - range: dissociated cell sample - - - # 023 - cell_barcoding.ipynb - # mappings (notebook -> model): (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, - # label -> name, port_well -> port well, sample_quality_count -> sample quality count - barcoded cell sample: - is_a: entity - mixins: - - prov entity - attributes: - port well: - sample quality count: - slot_usage: - wasGeneratedBy: - range: cell barcoding - wasDerivedFrom: - range: enriched cell sample - - - # 022 - cnda_amplification.ipynb - # amplified_quantity_ng -> input quantity, (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, - # label -> name, method -> method, pcr_cycles -> pcr cycles, percent_cdna_longer_than_400bp -> percent cdna longer than 400bp, rna_amplification_pass_fail -> process pass - amplified cdna: - is_a: entity - mixins: - - prov entity - slots: - - method - - input quantity - - process pass - attributes: - pcr cycles: - description: >- - Number of PCR cycles used to amplify the cDNA. - range: integer - percent cdna longer than 400bp: - description: >- - The percentage of cDNA fragments that are longer than 400bp. - range: float - slot_usage: - input quantity: - description: The amount of input cDNA (ng) amplified. - process pass: - description: Indicates whether the rna amplification process passed or failed. - wasGeneratedBy: - range: cdna amplification - wasDerivedFrom: - range: barcoded cell sample - - - # 021 - library_constructions.ipynb - # avg_size_bp -> avg size bp, (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, label -> name, - # library_creation_date -> creation date, library_input_ng -> input quantity, method -> method, process_pass -> process pass, - # quantification_fmole -> quantification fmol, quantification_ng -> quantification ng, quantification_nm -> quantification nm, - # r1_index -> r1 index, r1_sequence -> r1 sequence, r2_index -> r2 index, r2_sequence -> r2 sequence - library: - is_a: entity - mixins: - - prov entity - slots: - - method - - creation date - - input quantity - - process pass - - avg size bp - attributes: - quantification fmol: - range: float - quantification ng: - range: float - quantification nm: - range: float - r1 index: - r1 sequence: - r2 index: - r2 sequence: - slot_usage: - creation date: - description: The date and time the object was created. - range: datetime - input quantity: - description: The amount of input material (ng) used to create the library. - process pass: - description: Indicates whether the library prep process passed or failed. - avg size bp: - description: The average size (bp) of the library fragments. - wasGeneratedBy: - range: library construction - wasDerivedFrom: - range: amplified cdna - - - # 020 - aliquoting_and_pooling.ipynb - # mappings (notebook -> model): label -> name, input_quantity_fmol -> input quantity, library_label -> xref, - # (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, - library aliquot: - is_a: entity - mixins: - - prov entity - slots: - - input quantity - slot_usage: - wasGeneratedBy: - range: library aliquoting - wasDerivedFrom: - range: library - input quantity: - description: The amount of input material (fmol) used to create the library aliquot. - range: integer - - - # 020 - aliquoting_and_pooling.ipynb - # mappings (notebook -> model): label -> name, tube_avg_size_bp -> avg size bp, tube_contents_nm -> tube contents nm, tube_internal_label -> xref, - # (created_by_process_id & created_by_process_type) -> wasGeneratedBy, entity_type -> type/category, - library pool: - is_a: entity - mixins: - - prov entity - slots: - - avg size bp - attributes: - tube contents: - description: The content concentration (nm). - range: float - slot_usage: - avg size bp: - description: The average size (bp) of the library fragments in the tube. - wasGeneratedBy: - range: library pooling - wasDerivedFrom: - range: library aliquot - - -slots: - used: - slot_uri: prov:used - domain: activity - range: entity - multivalued: true - inlined_as_list: true - - generated: - slot_uri: prov:generated - domain: activity - range: entity - multivalued: true - inlined_as_list: true - - wasGeneratedBy: - slot_uri: prov:wasGeneratedBy - domain: entity - range: activity - multivalued: true - inlined_as_list: true - - wasDerivedFrom: - slot_uri: prov:wasDerivedFrom - domain: entity - range: entity - multivalued: true - inlined_as_list: true - - wasAssociatedWith: - slot_uri: prov:wasAssociatedWith - domain: activity - range: agent - multivalued: true - inlined_as_list: true - - wasAttributedTo: - slot_uri: prov:wasAttributedTo - domain: entity - range: agent - multivalued: true - inlined_as_list: true - - molecular type: - any_of: - - range: BioType - - range: string - - digest: - description: Stores checksum information. - multivalued: true - inlined_as_list: true - any_of: - - range: checksum - - range: string - - content_url: - slot_uri: schema:url - multivalued: true - - authority: - description: The organization responsible for publishing the data. - range: AuthorityType - - checksum algorithm: - description: The type of cryptographic hash function used to calculate the checksum value. - range: DigestType - - source id: - description: The authority specific identifier. - slot_uri: schema:identifier - - strain: - description: The genetic variant or subtype of a species or organism. - - sex: - range: SexType - - birth date: - description: The date of birth of the donor. - range: date - - death date: - description: The date of death of the donor. - range: date - - death age: - description: The age of the donor at the time of death (ISO 8601 format). - range: string - - full genotype: - description: The full genotype of the donor. - range: string - - method: - description: - slot_uri: schema:name - - input quantity: - description: The amount of input material used for an activity. - range: float - - process pass: - description: Indicates whether the process passed or failed. - range: boolean - - avg size bp: - description: The average size (bp = base pairs) of an entity. - range: integer - - -enums: - DigestType: - permissible_values: - spdx:checksumAlgorithm_sha1: - title: SHA1 - meaning: spdx:checksumAlgorithm_sha1 - spdx:checksumAlgorithm_md5: - title: MD5 - meaning: spdx:checksumAlgorithm_md5 - spdx:checksumAlgorithm_sha256: - title: SHA256 - meaning: spdx:checksumAlgorithm_sha256 - - SexType: - permissible_values: - female: - male: - - BioType: - permissible_values: - protein_coding: - noncoding: - - AuthorityType: - permissible_values: - ENSEMBL: - NCBI: \ No newline at end of file