regenerate artifacts

infores_catalog.yaml

@@ -56,6 +56,7 @@ information_resources:
       - infores:automat-cam-kp
       - infores:automat-ctd
       - infores:automat-drug-central
+      - infores:automat-ehr-may-treat-kp
       - infores:automat-genome-alliance
       - infores:automat-gtex
       - infores:automat-gtopdb
@@ -565,6 +566,7 @@ information_resources:
       (EHR) Machine Learning Analysis (MLA)
       using the Providence health records
     consumed_by:
+      - infores:aragorn
       - infores:arax
     consumes:
       - infores:providence-st-joseph-ehr

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: 2024-10-21T08:40:39
+# Generation date: 2024-10-21T09:03:53
 # 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": "2024-10-21T08:40:39",
+      "generation_date": "2024-10-21T09:03:53",
       "source": "information_resource_registry.yaml"
    },
    "@context": {

project/jsonld/information_resource_registry.jsonld

@@ -649,7 +649,7 @@
   "source_file": "information_resource_registry.yaml",
   "source_file_date": "2024-09-18T16:41:40",
   "source_file_size": 11239,
-  "generation_date": "2024-10-21T08:40:39",
+  "generation_date": "2024-10-21T09:03:53",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/information_resource_registry.context.jsonld",

project/owl/information_resource.owl.ttl

@@ -64,70 +64,70 @@ biolink:information_resource_registry.yaml.owl.ttl a owl:Ontology ;
 infores:InformationResource a owl:Class ;
     rdfs:label "InformationResource" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom infores:AgentTypeEnum ;
-            owl:onProperty infores:agent_type ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:xref ],
+            owl:minCardinality 0 ;
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
             owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:status ],
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:description ],
+            owl:allValuesFrom infores:InformationResourceStatusEnum ;
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:id ],
+            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:name ],
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:agent_type ],
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:id ],
+            owl:allValuesFrom infores:KnowledgeLevelEnum ;
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:description ],
+            owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:allValuesFrom infores:KnowledgeLevelEnum ;
-            owl:onProperty infores:knowledge_level ],
+            owl:allValuesFrom infores:AgentTypeEnum ;
+            owl:onProperty infores:agent_type ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:status ],
+            owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
+            owl:allValuesFrom xsd:string ;
             owl:onProperty infores:description ],
         [ a owl:Restriction ;
-            owl:minCardinality 1 ;
+            owl:allValuesFrom xsd:string ;
             owl:onProperty infores:id ],
         [ a owl:Restriction ;
-            owl:allValuesFrom infores:InformationResourceStatusEnum ;
-            owl:onProperty infores:status ],
+            owl:minCardinality 0 ;
+            owl:onProperty infores:name ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:agent_type ],
+            owl:minCardinality 0 ;
+            owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:onProperty infores:xref ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
             owl:onProperty infores:name ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:synonym ],
+            owl:minCardinality 1 ;
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
+            owl:allValuesFrom xsd:string ;
             owl:onProperty infores:xref ],
         linkml:ClassDefinition ;
     skos:altLabel "knowledgebase" ;

project/shacl/information_resource_registry.shacl.ttl

@@ -20,17 +20,6 @@ infores:InformationResource a sh:NodeShape ;
     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: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 "A human-readable name for an attribute or entity." ;
             sh:maxCount 1 ;
             sh:nodeKind sh:Literal ;
@@ -44,24 +33,35 @@ infores:InformationResource a sh:NodeShape ;
             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:description "A free-text description of an entity or attribute." ;
+            sh:maxCount 1 ;
             sh:nodeKind sh:Literal ;
-            sh:order 3 ;
-            sh:path infores:xref ],
+            sh:order 5 ;
+            sh:path rdfs:comment ],
+        [ 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: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: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 status of the infores identifier, the default is \"released\"" ;
+            sh:in ( "released" "deprecated" "draft" "modified" ) ;
             sh:maxCount 1 ;
-            sh:order 7 ;
-            sh:path infores:agent_type ],
+            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:path infores:synonym ],
+        [ 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: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: 2024-10-21T08:40:46
+# Generation date: 2024-10-21T09:04:01
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml

src/information_resource_registry/translator_dataflow/data/consume_info.csv

@@ -57,6 +57,7 @@ infores:automat-ubergraph,infores:arax,1
 infores:automat-viral-proteome,infores:aragorn,1
 infores:automat-viral-proteome,infores:arax,1
 infores:automat-viral-proteome,infores:service-provider-trapi,1
+infores:automat-ehr-may-treat-kp,infores:aragorn,1
 infores:automat-ehr-may-treat-kp,infores:arax,1
 infores:bfo,infores:rtx-kg2,1
 infores:bigg-models,infores:molepro,1