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Automat ohdc #49

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merged 2 commits into from
Nov 5, 2024
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Merged

Automat ohdc #49

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fd5542f
Regenerate artifacts from infores_catalog.yaml
actions-user Nov 5, 2024
b5b6616
Add openhealthdata-carolina automat infores
maximusunc Nov 1, 2024
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13 changes: 13 additions & 0 deletions infores_catalog.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion project/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: 2024-11-04T07:22:04
# Generation date: 2024-11-05T16:56:20
# Schema: Information-Resource-Registry-Schema
#
# id: https://w3id.org/biolink/information_resource_registry.yaml
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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": "2024-11-04T07:22:04",
"generation_date": "2024-11-05T16:56:20",
"source": "information_resource_registry.yaml"
},
"@context": {
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4 changes: 2 additions & 2 deletions project/jsonld/information_resource_registry.jsonld
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Expand Up @@ -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",
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76 changes: 38 additions & 38 deletions project/owl/information_resource.owl.ttl
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Expand Up @@ -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" ;
Expand Down Expand Up @@ -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 ],
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54 changes: 27 additions & 27 deletions project/shacl/information_resource_registry.shacl.ttl
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Expand Up @@ -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 ;
Expand All @@ -51,28 +40,39 @@ 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 ;
sh:minCount 1 ;
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 .

2 changes: 1 addition & 1 deletion src/information_resource_registry/datamodel/information_resource_registry.py
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Original file line number Diff line number Diff line change
@@ -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
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