Regenerate artifacts from infores_catalog.yaml

infores_catalog.yaml

@@ -3228,20 +3228,19 @@ information_resources:
     agent_type: not_provided
     consumed_by:
       - infores:automat-openhealthdata-carolina
-    consumes:
     description: >-
       Open Health Data @ Carolina provides access to counts
       and frequencies (i.e., EHR prevalence) of conditions, procedures, drug exposures,
       and patient demographics, and the co-occurrence frequencies between them. Count
       and frequency data were derived from UNC Health's OMOP database on a five-year cohort
-      (~6M patients over years 2018 through 2022) of all UNC Health patients, 
-      including their inpatient and outpatient visit data. Counts represent the number of 
-      patients associated with a given concept, e.g., diagnosed with a condition, 
-      exposed to a drug, or who had a procedure. Frequencies are the number of unique patients
-      associated with the concept divided by the total number of patients in the dataset, 
-      i.e., prevalence in the electronic health records. To protect patient privacy, 
-      all concepts and pairs of concepts where the count was <= 10 were excluded, 
-      and counts were randomized by the Poisson distribution.
+      (~6M patients over years 2018 through 2022) of all UNC Health patients,  including their
+      inpatient and outpatient visit data. Counts represent the number of  patients associated
+      with a given concept, e.g., diagnosed with a condition,  exposed to a drug, or who had
+      a procedure. Frequencies are the number of unique patients
+      associated with the concept divided by the total number of patients in the dataset,  i.e.,
+      prevalence in the electronic health records. To protect patient privacy,  all concepts
+      and pairs of concepts where the count was <= 10 were excluded,  and counts were randomized
+      by the Poisson distribution.
   - id: infores:ols
     status: released
     name: Ontology Lookup Service API

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: 2024-10-30T21:33:10
+# Generation date: 2024-10-31T21:04:42
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml

project/jsonld/information_resource_registry.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-10-30T21:33:09",
+      "generation_date": "2024-10-31T21:04:42",
       "source": "information_resource_registry.yaml"
    },
    "@context": {

project/jsonld/information_resource_registry.jsonld

@@ -702,9 +702,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "information_resource_registry.yaml",
-  "source_file_date": "2024-10-30T21:32:33",
+  "source_file_date": "2024-10-31T21:04:04",
   "source_file_size": 11116,
-  "generation_date": "2024-10-30T21:33:09",
+  "generation_date": "2024-10-31T21:04:42",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/information_resource_registry.context.jsonld",

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 infores:KnowledgeLevelEnum ;
-            owl:onProperty infores:knowledge_level ],
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:name ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:id ],
+            owl:allValuesFrom xsd:anyURI ;
+            owl:onProperty infores:consumed_by ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
+            owl:onProperty infores:agent_type ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty infores:consumes ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty infores:agent_type ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom xsd:string ;
             owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom infores:InformationResourceStatusEnum ;
             owl:onProperty infores:status ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:allValuesFrom xsd:string ;
+            owl:onProperty infores:xref ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:name ],
+            owl:allValuesFrom xsd:string ;
+            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:consumed_by ],
+            owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:xref ],
+            owl:onProperty infores:knowledge_level ],
+        [ a owl:Restriction ;
+            owl:minCardinality 1 ;
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
             owl:onProperty infores:name ],
-        [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:description ],
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:anyURI ;
             owl:onProperty infores:consumes ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
+            owl:minCardinality 1 ;
             owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:agent_type ],
-        [ a owl:Restriction ;
-            owl:minCardinality 1 ;
-            owl:onProperty infores:id ],
-        [ a owl:Restriction ;
-            owl:minCardinality 1 ;
-            owl:onProperty infores:status ],
+            owl:onProperty infores:xref ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:description ],
+            owl:allValuesFrom infores:AgentTypeEnum ;
+            owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:anyURI ;
+            owl:minCardinality 0 ;
             owl:onProperty infores:consumed_by ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
             owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:consumes ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:xref ],
+            owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:agent_type ],
-        [ a owl:Restriction ;
-            owl:minCardinality 0 ;
             owl:onProperty infores:description ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:name ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom infores:AgentTypeEnum ;
-            owl:onProperty infores:agent_type ],
+            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." ;

project/shacl/information_resource_registry.shacl.ttl

@@ -19,60 +19,60 @@ 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:datatype xsd:string ;
+    sh:property [ 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: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: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 free-text description of an entity or attribute." ;
+            sh:maxCount 1 ;
+            sh:nodeKind sh:Literal ;
+            sh:order 5 ;
+            sh:path rdfs:comment ],
         [ 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 ;
+            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: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: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: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 human-readable name for an attribute or entity." ;
-            sh:maxCount 1 ;
-            sh:nodeKind sh:Literal ;
-            sh:order 1 ;
-            sh:path rdfs:label ],
         [ 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 free-text description of an entity or attribute." ;
-            sh:maxCount 1 ;
-            sh:nodeKind sh:Literal ;
-            sh:order 5 ;
-            sh:path rdfs:comment ] ;
+            sh:path infores:knowledge_level ] ;
     sh:targetClass infores:InformationResource .
 

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: 2024-10-30T21:33:14
+# Generation date: 2024-10-31T21:04:47
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml

src/information_resource_registry/translator_dataflow/data/consume_info.csv

@@ -241,6 +241,7 @@ infores:ncbi-taxonomy,infores:rtx-kg2,1
 infores:ncit,infores:rtx-kg2,1
 infores:nddf-umls,infores:rtx-kg2,1
 infores:ndfrt,infores:rtx-kg2,1
+infores:openhealthdata-carolina,infores:automat-openhealthdata-carolina,1
 infores:ols,infores:service-provider-trapi,1
 infores:omim,infores:openpredict,1
 infores:omim,infores:rtx-kg2,1