Regenerate artifacts from infores_catalog.yaml

biolink · Oct 28, 2024 · 85f4593 · 85f4593
1 parent 43b3b42
commit 85f4593
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Showing 10 changed files with 81 additions and 52 deletions.
diff --git a/infores_catalog.yaml b/infores_catalog.yaml
@@ -528,6 +528,7 @@ information_resources:
     consumed_by:
       - infores:aragorn
       - infores:arax
+      - infores:cohd
   - id: infores:automat-ubergraph-nonredundant
     status: deprecated
     name: Automat Ubergraph Nonredundant
@@ -1437,6 +1438,8 @@ information_resources:
       the 1980s.
     knowledge_level: knowledge_assertion
     agent_type: not_provided
+    consumed_by:
+      - infores:cohd
   - id: infores:cohd
     status: released
     name: Columbia Open Health Data (COHD)
@@ -1492,7 +1495,12 @@ information_resources:
     consumed_by:
       - infores:aragorn
       - infores:arax
+      - infores:openpredict
       - infores:service-provider-trapi
+    consumes:
+      - infores:automat-ubergraph
+      - infores:columbia-cdw-ehr-data
+      - infores:omop-ohdsi
   - id: infores:cohd-covid
     status: released
     name: Columbia Open Health Data (COHD) for COVID-19 Research
@@ -1851,6 +1859,7 @@ information_resources:
       with comprehensive drug target (i.e. sequence, structure, and pathway) information
     consumed_by:
       - infores:molepro
+      - infores:openpredict
       - infores:rtx-kg2
   - id: infores:drugcentral
     status: released
@@ -2641,6 +2650,8 @@ information_resources:
     consumed_by:
       - infores:aragorn
       - infores:arax
+    consumes:
+      - infores:nanopublications
   - id: infores:life-science-resource-registry
     status: released
     name: Life Science Resource Registry
@@ -3035,6 +3046,8 @@ information_resources:
       - Nanopublications
     knowledge_level: knowledge_assertion
     agent_type: not_provided
+    consumed_by:
+      - infores:knowledge-collaboratory
   - id: infores:nbo
     status: released
     name: Neuro Behavior Ontology
@@ -3217,6 +3230,7 @@ information_resources:
     knowledge_level: knowledge_assertion
     agent_type: not_provided
     consumed_by:
+      - infores:openpredict
       - infores:rtx-kg2
   - id: infores:omnicorp
     status: released
@@ -3263,6 +3277,10 @@ information_resources:
     consumed_by:
       - infores:aragorn
       - infores:arax
+    consumes:
+      - infores:cohd
+      - infores:drugbank
+      - infores:omim
   - id: infores:ordo
     status: released
     name: Orphanet Rare Disease Ontology
@@ -4754,3 +4772,6 @@ information_resources:
     knowledge_level: not_provided
     agent_type: not_provided
     status: released
+  - id: infores:omop-ohdsi
+    consumed_by:
+      - infores:cohd
diff --git 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: 2024-10-28T05:22:20
+# Generation date: 2024-10-28T16:31:44
 # 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
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-10-28T05:22:20",
+      "generation_date": "2024-10-28T16:31:44",
       "source": "information_resource_registry.yaml"
    },
    "@context": {

diff --git 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": "2024-10-28T05:21:24",
+  "source_file_date": "2024-10-28T16:30:46",
   "source_file_size": 11239,
-  "generation_date": "2024-10-28T05:22:20",
+  "generation_date": "2024-10-28T16:31:44",
   "@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
@@ -65,34 +65,34 @@ infores:InformationResource a owl:Class ;
     rdfs:label "InformationResource" ;
     rdfs:subClassOf [ 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:status ],
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
             owl:onProperty infores:name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom infores:KnowledgeLevelEnum ;
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
+            owl:maxCardinality 1 ;
             owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:name ],
+            owl:onProperty infores:status ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom xsd:string ;
+            owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:agent_type ],
+            owl:allValuesFrom xsd:string ;
+            owl:onProperty infores:xref ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:allValuesFrom infores:InformationResourceStatusEnum ;
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
             owl:onProperty infores:id ],
@@ -101,34 +101,34 @@ infores:InformationResource a owl:Class ;
             owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:description ],
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:id ],
+            owl:onProperty infores:agent_type ],
         [ 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:minCardinality 0 ;
             owl:onProperty infores:xref ],
         [ a owl:Restriction ;
             owl:allValuesFrom infores:AgentTypeEnum ;
             owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:description ],
+            owl:minCardinality 0 ;
+            owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:allValuesFrom infores:KnowledgeLevelEnum ;
+            owl:minCardinality 0 ;
             owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
             owl:onProperty infores:synonym ],
-        [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:minCardinality 1 ;
             owl:onProperty infores:id ],
-        [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:xref ],
         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
@@ -19,45 +19,45 @@ 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:property [ 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ;
+            sh:description "A free-text description of an entity or attribute." ;
             sh:maxCount 1 ;
-            sh:minCount 1 ;
             sh:nodeKind sh:Literal ;
-            sh:order 2 ;
-            sh:path infores:id ],
-        [ sh:datatype xsd:string ;
-            sh:description "A human-readable name for an attribute or entity." ;
+            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:nodeKind sh:Literal ;
-            sh:order 1 ;
-            sh:path rdfs:label ],
+            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:nodeKind sh:Literal ;
             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:minCount 1 ;
+            sh:nodeKind sh:Literal ;
+            sh:order 2 ;
+            sh:path infores:id ],
         [ 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 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 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 ;

diff --git 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: 2024-10-28T05:22:24
+# Generation date: 2024-10-28T16:31:49
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml

diff --git a/src/information_resource_registry/translator_dataflow/data/aragorn_to_kps.json b/src/information_resource_registry/translator_dataflow/data/aragorn_to_kps.json
@@ -26,6 +26,7 @@
     "infores:connections-hypothesis",
     "infores:gelinea",
     "infores:genetics-data-provider",
+    "infores:knowledge-collaboratory",
     "infores:molepro",
     "infores:multiomics-clinicaltrials",
     "infores:multiomics-drugapprovals",

diff --git a/src/information_resource_registry/translator_dataflow/data/consume_info.csv b/src/information_resource_registry/translator_dataflow/data/consume_info.csv
@@ -54,6 +54,7 @@ infores:automat-string-db,infores:aragorn,1
 infores:automat-string-db,infores:arax,1
 infores:automat-ubergraph,infores:aragorn,1
 infores:automat-ubergraph,infores:arax,1
+infores:automat-ubergraph,infores:cohd,1
 infores:automat-viral-proteome,infores:aragorn,1
 infores:automat-viral-proteome,infores:arax,1
 infores:automat-viral-proteome,infores:service-provider-trapi,1
@@ -122,8 +123,10 @@ infores:cl,infores:rtx-kg2,1
 infores:clingen,infores:mygene-info,1
 infores:clinvar,infores:myvariant-info,1
 infores:cmap,infores:molepro,1
+infores:columbia-cdw-ehr-data,infores:cohd,1
 infores:cohd,infores:aragorn,1
 infores:cohd,infores:arax,1
+infores:cohd,infores:openpredict,1
 infores:cohd,infores:service-provider-trapi,1
 infores:connections-hypothesis,infores:aragorn,1
 infores:connections-hypothesis,infores:arax,1
@@ -150,6 +153,7 @@ infores:disgenet,infores:mydisease-info,1
 infores:disgenet,infores:rtx-kg2,1
 infores:drug-repurposing-hub,infores:molepro,1
 infores:drugbank,infores:molepro,1
+infores:drugbank,infores:openpredict,1
 infores:drugbank,infores:rtx-kg2,1
 infores:drugcentral,infores:molepro,1
 infores:drugcentral,infores:mychem-info,1
@@ -226,6 +230,7 @@ infores:mychem-info,infores:service-provider-trapi,1
 infores:mydisease-info,infores:service-provider-trapi,1
 infores:mygene-info,infores:service-provider-trapi,1
 infores:myvariant-info,infores:service-provider-trapi,1
+infores:nanopublications,infores:knowledge-collaboratory,1
 infores:nbo,infores:rtx-kg2,1
 infores:ncbi-gene,infores:mygene-info,1
 infores:ncbi-gene,infores:rtx-kg2,1
@@ -235,6 +240,7 @@ infores:ncit,infores:rtx-kg2,1
 infores:nddf-umls,infores:rtx-kg2,1
 infores:ndfrt,infores:rtx-kg2,1
 infores:ols,infores:service-provider-trapi,1
+infores:omim,infores:openpredict,1
 infores:omim,infores:rtx-kg2,1
 infores:openpredict,infores:aragorn,1
 infores:openpredict,infores:arax,1
@@ -317,3 +323,4 @@ infores:automat-robokop,infores:arax,1
 infores:automat-robokop,infores:service-provider-trapi,1
 infores:chv-umls,infores:rtx-kg2,1
 infores:dsstoxdb,infores:molepro,1
+infores:omop-ohdsi,infores:cohd,1
diff --git a/src/information_resource_registry/translator_dataflow/data/data_flow_diagram.png b/src/information_resource_registry/translator_dataflow/data/data_flow_diagram.png