Regenerate artifacts from infores_catalog.yaml

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: 2024-10-10T04:58:57
+# Generation date: 2024-10-10T05:07:24
 # 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": "2024-10-10T04:58:57",
+      "generation_date": "2024-10-10T05:07:24",
       "source": "information_resource_registry.yaml"
    },
    "@context": {

project/jsonld/information_resource_registry.jsonld

@@ -647,9 +647,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "information_resource_registry.yaml",
-  "source_file_date": "2024-10-10T04:57:56",
+  "source_file_date": "2024-10-10T05:06:25",
   "source_file_size": 11239,
-  "generation_date": "2024-10-10T04:58:57",
+  "generation_date": "2024-10-10T05:07:24",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/information_resource_registry.context.jsonld",

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

@@ -19,44 +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 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 "Alternate human-readable names for a thing" ;
+    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 4 ;
-            sh:path infores:synonym ],
+            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 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:maxCount 1 ;
-            sh:order 0 ;
-            sh:path infores:status ],
-        [ 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: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 7 ;
-            sh:path infores:agent_type ],
-        [ 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: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: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:datatype xsd:string ;
             sh:description "A human-readable name for an attribute or entity." ;
             sh:maxCount 1 ;

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: 2024-10-10T04:59:01
+# Generation date: 2024-10-10T05:07:28
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml

src/information_resource_registry/relation_map/data/consume_info.csv

@@ -244,6 +244,8 @@ infores:pr,infores:rtx-kg2,1
 infores:probe-miner,infores:molepro,1
 infores:psy-umls,infores:rtx-kg2,1
 infores:pubchem,infores:molepro,1
+infores:pubmed-central,infores:multiomics-multiomics,1
+infores:pubmed-central,infores:multiomics-microbiome,1
 infores:reactome,infores:molepro,1
 infores:reactome,infores:mygene-info,1
 infores:reactome,infores:rtx-kg2,1