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fixing up check-infores script
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@sierra-moxon
sierra-moxon committed Mar 8, 2024
1 parent 90629b2 commit ae0dd16
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Showing 8 changed files with 52 additions and 52 deletions.
2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -131,7 +131,7 @@ tests:
$(RUN) yamllint -c .yamllint-config infores_catalog.yaml
$(RUN) python scripts/verify_infores.py

test: test-schema test-python test-examples lint spell
test: test-schema test-python test-examples lint spell tests validate_infores

test-schema: gen-project

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2 changes: 1 addition & 1 deletion project/jsonld/information_resource_registry.context.jsonld
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@@ -1,7 +1,7 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
"generation_date": "2024-03-08T11:03:16",
"generation_date": "2024-03-08T11:19:57",
"source": "information_resource_registry.yaml"
},
"@context": {
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2 changes: 1 addition & 1 deletion project/jsonld/information_resource_registry.jsonld
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Expand Up @@ -614,7 +614,7 @@
"source_file": "information_resource_registry.yaml",
"source_file_date": "2024-03-08T10:47:50",
"source_file_size": 7890,
"generation_date": "2024-03-08T11:03:16",
"generation_date": "2024-03-08T11:19:57",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/information_resource_registry.context.jsonld",
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56 changes: 28 additions & 28 deletions project/owl/information_resource.owl.ttl
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Expand Up @@ -40,70 +40,70 @@ infores:InformationResource a owl:Class ;
rdfs:label "InformationResource" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty infores:id ],
owl:onProperty infores:description ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty infores:status ],
owl:onProperty infores:knowledge_level ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty infores:description ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty infores:agent_type ],
owl:onProperty infores:status ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty infores:knowledge_level ],
owl:onProperty infores:status ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty infores:id ],
owl:onProperty infores:name ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty infores:xref ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:minCardinality 0 ;
owl:onProperty infores:name ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty infores:description ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty infores:agent_type ],
[ a owl:Restriction ;
owl:allValuesFrom infores:InformationResourceStatusEnum ;
owl:onProperty infores:status ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty infores:xref ],
owl:onProperty infores:agent_type ],
[ a owl:Restriction ;
owl:allValuesFrom infores:KnowledgeLevelEnum ;
owl:onProperty infores:knowledge_level ],
owl:maxCardinality 1 ;
owl:onProperty infores:name ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty infores:synonym ],
[ a owl:Restriction ;
owl:allValuesFrom infores:AgentTypeEnum ;
owl:onProperty infores:agent_type ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty infores:synonym ],
owl:onProperty infores:xref ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty infores:synonym ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty infores:status ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty infores:knowledge_level ],
[ a owl:Restriction ;
owl:allValuesFrom infores:AgentTypeEnum ;
owl:onProperty infores:agent_type ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty infores:name ],
owl:onProperty infores:id ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty infores:id ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:allValuesFrom xsd:string ;
owl:onProperty infores:description ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty infores:name ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty infores:name ],
owl:onProperty infores:id ],
[ a owl:Restriction ;
owl:allValuesFrom infores:KnowledgeLevelEnum ;
owl:onProperty infores:knowledge_level ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty infores:knowledge_level ],
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." ;
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40 changes: 20 additions & 20 deletions project/shacl/information_resource_registry.shacl.ttl
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Expand Up @@ -19,44 +19,44 @@ 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: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 ( "not_provided" "computational_model" ) ;
sh:maxCount 1 ;
sh:order 7 ;
sh:path infores:agent_type ],
[ sh:datatype xsd:string ;
sh:description "A free-text description of an entity or attribute." ;
sh:maxCount 1 ;
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 "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:order 3 ;
sh:path infores:xref ],
[ sh:datatype xsd:string ;
sh:description "Alternate human-readable names for a thing" ;
sh:order 4 ;
sh:path infores:synonym ],
[ sh:datatype xsd:string ;
sh:description "A free-text description of an entity or attribute." ;
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:order 3 ;
sh:path infores:xref ],
[ 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:order 5 ;
sh:path rdfs:comment ],
sh:minCount 1 ;
sh:order 2 ;
sh:path infores:id ],
[ sh:datatype xsd:string ;
sh:description "A human-readable name for an attribute or entity." ;
sh:maxCount 1 ;
sh:order 1 ;
sh:path rdfs:label ],
[ 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 ( "not_provided" "computational_model" ) ;
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:in ( "curated" "predicted" "text_mined" "correlation" "observed" "other" "mixed" ) ;
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:order 2 ;
sh:path infores:id ] ;
sh:path infores:knowledge_level ] ;
sh:targetClass infores:InformationResource .

2 changes: 1 addition & 1 deletion src/information_resource_registry/datamodel/information_resource_registry.py
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@@ -1,5 +1,5 @@
# Auto generated from information_resource_registry.yaml by pythongen.py version: 0.0.1
# Generation date: 2024-03-08T11:03:28
# Generation date: 2024-03-08T11:20:09
# Schema: Information-Resource-Registry-Schema
#
# id: https://w3id.org/biolink/information_resource_registry.yaml
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0 src/scripts/extract_unhelpful_urls.py → ...egistry/scripts/extract_unhelpful_urls.py
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0 src/scripts/verify_infores.py → ...source_registry/scripts/verify_infores.py
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