diff --git a/project/information_resource_registry.py b/project/information_resource_registry.py index aed3c4f..a4754a4 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: 2024-10-10T04:58:57 +# Generation date: 2024-10-10T05:07:24 # 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 8ac15b1..da6fe16 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": "2024-10-10T04:58:57", + "generation_date": "2024-10-10T05:07:24", "source": "information_resource_registry.yaml" }, "@context": { diff --git a/project/jsonld/information_resource_registry.jsonld b/project/jsonld/information_resource_registry.jsonld index 289b740..be96d27 100644 --- a/project/jsonld/information_resource_registry.jsonld +++ b/project/jsonld/information_resource_registry.jsonld @@ -647,9 +647,9 @@ ], "metamodel_version": "1.7.0", "source_file": "information_resource_registry.yaml", - "source_file_date": "2024-10-10T04:57:56", + "source_file_date": "2024-10-10T05:06:25", "source_file_size": 11239, - "generation_date": "2024-10-10T04:58:57", + "generation_date": "2024-10-10T05:07:24", "@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 9500f14..0b1a97c 100644 --- a/project/owl/information_resource.owl.ttl +++ b/project/owl/information_resource.owl.ttl @@ -64,71 +64,71 @@ biolink:information_resource_registry.yaml.owl.ttl a owl:Ontology ; infores:InformationResource a owl:Class ; rdfs:label "InformationResource" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty infores:status ], + owl:allValuesFrom xsd:string ; + owl:onProperty infores:synonym ], [ a owl:Restriction ; - owl:allValuesFrom infores:InformationResourceStatusEnum ; - owl:onProperty infores:status ], + owl:allValuesFrom infores:AgentTypeEnum ; + owl:onProperty infores:agent_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty infores:status ], + owl:allValuesFrom xsd:string ; + owl:onProperty infores:xref ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty infores:knowledge_level ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:agent_type ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty infores:id ], + owl:onProperty infores:knowledge_level ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty infores:description ], + owl:allValuesFrom xsd:string ; + owl:onProperty infores:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:xref ], + owl:onProperty infores:description ], [ a owl:Restriction ; - owl:allValuesFrom infores:AgentTypeEnum ; + owl:maxCardinality 1 ; owl:onProperty infores:agent_type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty infores:name ], + owl:minCardinality 1 ; + owl:onProperty infores:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:synonym ], + owl:onProperty infores:status ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:synonym ], + owl:minCardinality 0 ; + owl:onProperty infores:agent_type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:name ], + owl:allValuesFrom infores:InformationResourceStatusEnum ; + owl:onProperty infores:status ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty infores:xref ], + owl:onProperty infores:description ], + [ a owl:Restriction ; + owl:allValuesFrom infores:KnowledgeLevelEnum ; + owl:onProperty infores:knowledge_level ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty infores:name ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:id ], - [ a owl:Restriction ; - owl:allValuesFrom infores:KnowledgeLevelEnum ; - owl:onProperty infores:knowledge_level ], + owl:minCardinality 0 ; + owl:onProperty infores:xref ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty infores:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:description ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty infores:knowledge_level ], + owl:onProperty infores:synonym ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; + owl:onProperty infores:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty infores:status ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty infores:description ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty infores:agent_type ], + owl:onProperty infores:name ], 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 4a0b0f0..e85859a 100644 --- a/project/shacl/information_resource_registry.shacl.ttl +++ b/project/shacl/information_resource_registry.shacl.ttl @@ -19,16 +19,16 @@ 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 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 "Alternate human-readable names for a thing" ; + sh:property [ 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 4 ; - sh:path infores:synonym ], + sh:order 3 ; + sh:path infores:xref ], + [ 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36,27 +36,27 @@ infores:InformationResource a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path infores:id ], - [ sh:description "the status of the infores identifier, the default is \"released\"" ; - sh:in ( "released" "deprecated" "draft" "modified" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path infores:status ], - [ 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: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 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:order 6 ; + sh:path infores:knowledge_level ], [ 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:description "the status of the infores identifier, the default is \"released\"" ; + sh:in ( "released" "deprecated" "draft" "modified" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path infores:status ], + [ 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:maxCount 1 ; diff --git a/src/information_resource_registry/datamodel/information_resource_registry.py b/src/information_resource_registry/datamodel/information_resource_registry.py index c9baad7..e7410c7 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: 2024-10-10T04:59:01 +# Generation date: 2024-10-10T05:07:28 # Schema: Information-Resource-Registry-Schema # # id: https://w3id.org/biolink/information_resource_registry.yaml diff --git a/src/information_resource_registry/relation_map/data/consume_info.csv b/src/information_resource_registry/relation_map/data/consume_info.csv index 821ea6d..bafd0d7 100644 --- a/src/information_resource_registry/relation_map/data/consume_info.csv +++ b/src/information_resource_registry/relation_map/data/consume_info.csv @@ -244,6 +244,8 @@ infores:pr,infores:rtx-kg2,1 infores:probe-miner,infores:molepro,1 infores:psy-umls,infores:rtx-kg2,1 infores:pubchem,infores:molepro,1 +infores:pubmed-central,infores:multiomics-multiomics,1 +infores:pubmed-central,infores:multiomics-microbiome,1 infores:reactome,infores:molepro,1 infores:reactome,infores:mygene-info,1 infores:reactome,infores:rtx-kg2,1 diff --git a/src/information_resource_registry/relation_map/data/sankey_diagram.png b/src/information_resource_registry/relation_map/data/sankey_diagram.png index bb60b07..f77b1ed 100644 Binary files a/src/information_resource_registry/relation_map/data/sankey_diagram.png and b/src/information_resource_registry/relation_map/data/sankey_diagram.png differ