Regenerate artifacts from infores_catalog.yaml

biolink · Oct 21, 2024 · 6f2e68d · 6f2e68d
1 parent 50f2440
commit 6f2e68d
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Showing 10 changed files with 62 additions and 59 deletions.
diff --git a/infores_catalog.yaml b/infores_catalog.yaml
@@ -973,6 +973,7 @@ information_resources:
     consumed_by:
       - infores:aragorn
       - infores:arax
+      - infores:rtx-kg2
       - infores:service-provider-trapi
     consumes:
       - infores:aact
@@ -3657,6 +3658,7 @@ information_resources:
       - infores:mi
       - infores:mirbase
       - infores:mondo
+      - infores:multiomics-clinicaltrials
       - infores:nbo
       - infores:ncbi-gene
       - infores:ncbi-taxon

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: 2024-10-14T05:21:32
+# Generation date: 2024-10-21T05:21:58
 # 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": "2024-10-14T05:21:32",
+      "generation_date": "2024-10-21T05:21:58",
       "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": "2024-10-14T05:20:38",
+  "source_file_date": "2024-10-21T05:21:02",
   "source_file_size": 11239,
-  "generation_date": "2024-10-14T05:21:32",
+  "generation_date": "2024-10-21T05:21:58",
   "@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
@@ -64,71 +64,71 @@ biolink:information_resource_registry.yaml.owl.ttl a owl:Ontology ;
 infores:InformationResource a owl:Class ;
     rdfs:label "InformationResource" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:minCardinality 0 ;
+            owl:allValuesFrom xsd:string ;
             owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:agent_type ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom infores:InformationResourceStatusEnum ;
-            owl:onProperty infores:status ],
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
-            owl:allValuesFrom infores:KnowledgeLevelEnum ;
+            owl:maxCardinality 1 ;
             owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
+            owl:allValuesFrom infores:InformationResourceStatusEnum ;
             owl:onProperty infores:status ],
-        [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty infores:xref ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:status ],
+            owl:onProperty infores:description ],
+        [ a owl:Restriction ;
+            owl:minCardinality 1 ;
+            owl:onProperty infores:id ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:synonym ],
+            owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
+            owl:onProperty infores:synonym ],
+        [ 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:allValuesFrom xsd:string ;
+            owl:maxCardinality 1 ;
             owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:description ],
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:allValuesFrom infores:AgentTypeEnum ;
             owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:xref ],
+            owl:onProperty infores:name ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
+            owl:minCardinality 0 ;
             owl:onProperty infores:description ],
         [ a owl:Restriction ;
-            owl:minCardinality 1 ;
+            owl:allValuesFrom xsd:string ;
             owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:name ],
-        [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:name ],
-        [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:name ],
+            owl:onProperty infores:xref ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:description ],
-        [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:id ],
+            owl:onProperty infores:agent_type ],
         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
@@ -19,49 +19,49 @@ 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:property [ 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 free-text description of an entity or attribute." ;
             sh:maxCount 1 ;
-            sh:order 7 ;
-            sh:path infores:agent_type ],
+            sh:nodeKind sh:Literal ;
+            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 "Alternate human-readable names for a thing" ;
             sh:nodeKind sh:Literal ;
             sh:order 4 ;
             sh:path infores:synonym ],
-        [ 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 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: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 "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 status of the infores identifier, the default is \"released\"" ;
-            sh:in ( "released" "deprecated" "draft" "modified" ) ;
+        [ 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 0 ;
-            sh:path infores:status ] ;
+            sh:order 6 ;
+            sh:path infores:knowledge_level ],
+        [ 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: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
@@ -1,5 +1,5 @@
 # Auto generated from information_resource_registry.yaml by pythongen.py version: 0.0.1
-# Generation date: 2024-10-14T05:21:37
+# Generation date: 2024-10-21T05:22:02
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml

diff --git a/src/information_resource_registry/relation_map/data/consume_info.csv b/src/information_resource_registry/relation_map/data/consume_info.csv
@@ -83,6 +83,7 @@ infores:providence-st-joseph-ehr,infores:automat-ehr-may-treat-kp,1
 infores:biothings-multiomics-wellness,infores:service-provider-trapi,1
 infores:multiomics-clinicaltrials,infores:aragorn,1
 infores:multiomics-clinicaltrials,infores:arax,1
+infores:multiomics-clinicaltrials,infores:rtx-kg2,1
 infores:multiomics-clinicaltrials,infores:service-provider-trapi,1
 infores:biothings-multiomics-clinicaltrials,infores:rtx-kg2,1
 infores:multiomics-drugapprovals,infores:aragorn,1

diff --git a/src/information_resource_registry/relation_map/data/rtx-kg2.json b/src/information_resource_registry/relation_map/data/rtx-kg2.json
@@ -1,6 +1,6 @@
 {
   "infores:rtx-kg2": [
-    "infores:biothings-multiomics-clinicaltrials",
+    "infores:multiomics-clinicaltrials",
     "infores:dgidb",
     "infores:disease-ontology",
     "infores:disgenet",

diff --git a/src/information_resource_registry/relation_map/data/sankey_diagram.png b/src/information_resource_registry/relation_map/data/sankey_diagram.png