From fd5542f563d948e2c75a89861489669262145ba6 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 5 Nov 2024 16:56:48 +0000 Subject: [PATCH 1/2] Regenerate artifacts from infores_catalog.yaml --- project/information_resource_registry.py | 2 +- ...formation_resource_registry.context.jsonld | 2 +- .../information_resource_registry.jsonld | 4 +- project/owl/information_resource.owl.ttl | 76 +++++++++---------- .../information_resource_registry.shacl.ttl | 54 ++++++------- .../information_resource_registry.py | 2 +- 6 files changed, 70 insertions(+), 70 deletions(-) diff --git a/project/information_resource_registry.py b/project/information_resource_registry.py index 04cab27..3edb8a8 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: 2024-11-04T07:22:04 +# Generation date: 2024-11-05T16:56:20 # 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 486fba3..585f6cb 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": "2024-11-04T07:22:04", + "generation_date": "2024-11-05T16:56:20", "source": "information_resource_registry.yaml" }, "@context": { diff --git a/project/jsonld/information_resource_registry.jsonld b/project/jsonld/information_resource_registry.jsonld index 2b88296..70520c9 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": "2024-11-04T07:21:24", + "source_file_date": "2024-11-05T16:55:41", "source_file_size": 11116, - "generation_date": "2024-11-04T07:22:04", + "generation_date": "2024-11-05T16:56:20", "@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 138115a..3838dee 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" ; @@ -158,80 +158,80 @@ 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:xref ], + owl:minCardinality 0 ; + owl:onProperty infores:agent_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty infores:agent_type ], + owl:onProperty infores:description ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty infores:status ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; - owl:onProperty infores:consumes ], + owl:onProperty infores:consumed_by ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:synonym ], + owl:maxCardinality 1 ; + owl:onProperty infores:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty infores:knowledge_level ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:name ], + owl:allValuesFrom infores:InformationResourceStatusEnum ; + owl:onProperty infores:status ], [ a owl:Restriction ; owl:allValuesFrom infores:AgentTypeEnum ; owl:onProperty infores:agent_type ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty infores:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:agent_type ], + owl:onProperty infores:synonym ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty infores:status ], + owl:allValuesFrom xsd:string ; + owl:onProperty infores:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:xref ], + owl:onProperty infores:name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty infores:status ], + owl:allValuesFrom xsd:string ; + owl:onProperty infores:id ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty infores:consumes ], [ a owl:Restriction ; - owl:allValuesFrom infores:InformationResourceStatusEnum ; - owl:onProperty infores:status ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty infores:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty infores:description ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty infores:knowledge_level ], + owl:allValuesFrom xsd:string ; + owl:onProperty infores:synonym ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty infores:xref ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty infores:name ], [ a owl:Restriction ; - owl:allValuesFrom infores:KnowledgeLevelEnum ; - owl:onProperty infores:knowledge_level ], + owl:maxCardinality 1 ; + owl:onProperty infores:status ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty infores:description ], + owl:onProperty infores:agent_type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty infores:consumed_by ], + owl:allValuesFrom infores:KnowledgeLevelEnum ; + owl:onProperty infores:knowledge_level ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty infores:description ], + owl:onProperty infores:xref ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty infores:synonym ], + owl:onProperty infores:description ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty infores:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty infores:id ], + owl:minCardinality 0 ; + owl:onProperty infores:consumes ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty infores:knowledge_level ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty infores:consumed_by ], diff --git a/project/shacl/information_resource_registry.shacl.ttl b/project/shacl/information_resource_registry.shacl.ttl index 761c337..a3c8e88 100644 --- a/project/shacl/information_resource_registry.shacl.ttl +++ b/project/shacl/information_resource_registry.shacl.ttl @@ -19,22 +19,11 @@ 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 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: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: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 "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -51,16 +40,12 @@ infores:InformationResource a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path rdfs:comment ], - [ sh:datatype xsd:anyURI ; - sh:description "A collection of information resources that consume this information resource" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path infores:consumed_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A collection of information resources that are consumed by this information resource" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path infores:consumes ], + [ sh:description "the status of the infores identifier, the default is \"released\"" ; + sh:in ( "released" "deprecated" "draft" "modified" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path infores:status ], [ 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 ; @@ -68,11 +53,26 @@ 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:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path infores:status ] ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A collection of information resources that are consumed by this information resource" ; + 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:anyURI ; + sh:description "A collection of information resources that consume this information resource" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path infores:consumed_by ] ; 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 fbce8b9..00c27d7 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: 2024-11-04T07:22:09 +# Generation date: 2024-11-05T16:56:24 # Schema: Information-Resource-Registry-Schema # # id: https://w3id.org/biolink/information_resource_registry.yaml From b5b66168f87111c70f6bb4a21f0c334051f97c68 Mon Sep 17 00:00:00 2001 From: Max Wang Date: Fri, 1 Nov 2024 14:45:32 -0400 Subject: [PATCH 2/2] Add openhealthdata-carolina automat infores --- infores_catalog.yaml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/infores_catalog.yaml b/infores_catalog.yaml index 3290a29..86a51a0 100644 --- a/infores_catalog.yaml +++ b/infores_catalog.yaml @@ -452,6 +452,19 @@ information_resources: knowledge_level: knowledge_assertion agent_type: not_provided description: A graph for ontological hierarchy extracted from Uberongraph. + - id: infores:automat-openhealthdata-carolina + status: released + name: Automat Openhealth Data at Carolina + xref: + - https://github.com/NCATSTranslator/Translator-All/wiki/Automat + knowledge_level: statistical_association + agent_type: not_provided + description: >- + A graph based on infores:openhealthdata-carolina, providing access to counts + and frequencies of conditions, procedures, drug exposures, and patient demographics, + and the co-occurrence frequencies between them. + consumed_by: + - infores:aragorn - id: infores:automat-panther status: released name: Automat PANTHER