diff --git a/project/information_resource_registry.py b/project/information_resource_registry.py index 9c7ded4..77f2158 100644 --- a/project/information_resource_registry.py +++ b/project/information_resource_registry.py @@ -1,5 +1,5 @@ # Auto generated from information_resource_registry.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-11-05T19:14:19 +# Generation date: 2024-11-11T07:22:39 # Schema: Information-Resource-Registry-Schema # # id: https://w3id.org/biolink/information_resource_registry.yaml diff --git a/project/jsonld/information_resource_registry.context.jsonld b/project/jsonld/information_resource_registry.context.jsonld index 894201d..b58258a 100644 --- a/project/jsonld/information_resource_registry.context.jsonld +++ b/project/jsonld/information_resource_registry.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2024-11-05T19:14:18", + "generation_date": "2024-11-11T07:22:39", "source": "information_resource_registry.yaml" }, "@context": { diff --git a/project/jsonld/information_resource_registry.jsonld b/project/jsonld/information_resource_registry.jsonld index f562fd5..acbef96 100644 --- a/project/jsonld/information_resource_registry.jsonld +++ b/project/jsonld/information_resource_registry.jsonld @@ -702,9 +702,9 @@ ], "metamodel_version": "1.7.0", "source_file": "information_resource_registry.yaml", - "source_file_date": "2024-11-05T19:13:42", + "source_file_date": "2024-11-11T07:22:01", "source_file_size": 11116, - "generation_date": "2024-11-05T19:14:18", + "generation_date": "2024-11-11T07:22:39", "@type": "SchemaDefinition", "@context": [ "project/jsonld/information_resource_registry.context.jsonld", diff --git a/project/owl/information_resource.owl.ttl b/project/owl/information_resource.owl.ttl index 51b0ced..0b31c04 100644 --- a/project/owl/information_resource.owl.ttl +++ b/project/owl/information_resource.owl.ttl @@ -12,10 +12,10 @@ infores:InformationResourceContainer a owl:Class ; rdfs:label "InformationResourceContainer" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom infores:InformationResource ; owl:onProperty infores:information_resources ], [ a owl:Restriction ; - owl:allValuesFrom infores:InformationResource ; + owl:minCardinality 0 ; owl:onProperty infores:information_resources ], linkml:ClassDefinition ; skos:definition "A collection of information resources" ; @@ -158,83 +158,83 @@ infores:xref a owl:DatatypeProperty ; infores:InformationResource a owl:Class ; rdfs:label "InformationResource" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:description ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom infores:KnowledgeLevelEnum ; owl:onProperty infores:knowledge_level ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty infores:status ], + owl:allValuesFrom xsd:string ; + owl:onProperty infores:name ], [ a owl:Restriction ; owl:allValuesFrom infores:AgentTypeEnum ; owl:onProperty infores:agent_type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty infores:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:agent_type ], + owl:onProperty infores:consumes ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty infores:status ], + owl:allValuesFrom xsd:string ; + owl:onProperty infores:xref ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty infores:id ], + owl:minCardinality 0 ; + owl:onProperty infores:agent_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty infores:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty infores:knowledge_level ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty infores:agent_type ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty infores:consumed_by ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty infores:name ], + owl:allValuesFrom xsd:string ; + owl:onProperty infores:synonym ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty infores:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:synonym ], + owl:minCardinality 1 ; + owl:onProperty infores:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty infores:synonym ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty infores:consumed_by ], [ a owl:Restriction ; owl:allValuesFrom infores:InformationResourceStatusEnum ; owl:onProperty infores:status ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:consumes ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty infores:consumed_by ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty infores:consumes ], + owl:onProperty infores:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty infores:description ], + owl:onProperty infores:knowledge_level ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty infores:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:xref ], + owl:onProperty infores:agent_type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty infores:description ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty infores:consumes ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:consumed_by ], + owl:onProperty infores:xref ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty infores:status ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty infores:id ], + owl:onProperty infores:description ], [ a owl:Restriction ; - owl:allValuesFrom infores:KnowledgeLevelEnum ; - owl:onProperty infores:knowledge_level ], + owl:maxCardinality 1 ; + owl:onProperty infores:description ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty infores:xref ], + owl:maxCardinality 1 ; + owl:onProperty infores:status ], linkml:ClassDefinition ; skos:altLabel "knowledgebase" ; skos:definition "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb." ; diff --git a/project/shacl/information_resource_registry.shacl.ttl b/project/shacl/information_resource_registry.shacl.ttl index 3a46973..552b961 100644 --- a/project/shacl/information_resource_registry.shacl.ttl +++ b/project/shacl/information_resource_registry.shacl.ttl @@ -19,45 +19,29 @@ infores:InformationResource a sh:NodeShape ; sh:closed true ; sh:description "A database or knowledgebase and its supporting ecosystem of interfaces and services that deliver content to consumers (e.g. web portals, APIs, query endpoints, streaming services, data downloads, etc.). A single Information Resource by this definition may span many different datasets or databases, and include many access endpoints and user interfaces. Information Resources include project-specific resources such as a Translator Knowledge Provider, and community knowledgebases like ChemBL, OMIM, or DGIdb." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the status of the infores identifier, the default is \"released\"" ; - sh:in ( "released" "deprecated" "draft" "modified" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 0 ; - sh:path infores:status ], - [ sh:datatype xsd:string ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path infores:xref ], + sh:order 2 ; + sh:path infores:id ], [ sh:description "The level of knowledge that supports an edge or node. This is a general categorization of the type of evidence that supports a statement, and is not intended to be a comprehensive description of the evidence. For example, a statement may be supported by a single publication, but that publication may contain multiple types of evidence, such as a computational prediction and a manual curation. In this case, the knowledge level would be \"curated\", and the evidence would be described in more detail in the evidence graph." ; sh:in ( "knowledge_assertion" "statistical_association" "prediction" "observation" "not_provided" "logical_entailment" "mixed" "other" ) ; sh:maxCount 1 ; sh:order 6 ; sh:path infores:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path infores:id ], - [ sh:description "The type of agent that supports an edge or node. This is a general categorization of the type of agent that supports a statement, and is not intended to be a comprehensive description of the agent. For example, a statement may be supported by a single publication, but that publication may contain multiple types of evidence, such as a computational prediction and a manual curation. In this case, the agent type would be \"publication\", and the evidence would be described in more detail in the evidence graph." ; - sh:in ( "manual_agent" "not_provided" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path infores:agent_type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path infores:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:description "the status of the infores identifier, the default is \"released\"" ; + sh:in ( "released" "deprecated" "draft" "modified" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], + sh:minCount 1 ; + sh:order 0 ; + sh:path infores:status ], [ sh:datatype xsd:anyURI ; sh:description "A collection of information resources that consume this information resource" ; sh:nodeKind sh:Literal ; @@ -68,11 +52,27 @@ infores:InformationResource a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path infores:consumes ], + [ sh:description "The type of agent that supports an edge or node. This is a general categorization of the type of agent that supports a statement, and is not intended to be a comprehensive description of the agent. For example, a statement may be supported by a single publication, but that publication may contain multiple types of evidence, such as a computational prediction and a manual curation. In this case, the agent type would be \"publication\", and the evidence would be described in more detail in the evidence graph." ; + sh:in ( "manual_agent" "not_provided" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path infores:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path infores:xref ], [ sh:datatype xsd:string ; sh:description "A free-text description of an entity or attribute." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path rdfs:comment ] ; + sh:path rdfs:comment ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ] ; sh:targetClass infores:InformationResource . diff --git a/src/information_resource_registry/datamodel/information_resource_registry.py b/src/information_resource_registry/datamodel/information_resource_registry.py index a9053d1..d62f45d 100644 --- a/src/information_resource_registry/datamodel/information_resource_registry.py +++ b/src/information_resource_registry/datamodel/information_resource_registry.py @@ -1,5 +1,5 @@ # Auto generated from information_resource_registry.yaml by pythongen.py version: 0.0.1 -# Generation date: 2024-11-05T19:14:23 +# Generation date: 2024-11-11T07:22:43 # Schema: Information-Resource-Registry-Schema # # id: https://w3id.org/biolink/information_resource_registry.yaml