Merge pull request #17 from biolink/gglusman-patch-1

Gglusman patch 1 - fixing up test failures
biolink · Jul 15, 2024 · 22e2bca · 22e2bca
2 parents cbe8363 + b98c1b5
commit 22e2bca
Show file tree

Hide file tree

Showing 13 changed files with 181 additions and 68 deletions.
diff --git a/infores_catalog.yaml b/infores_catalog.yaml
@@ -639,16 +639,23 @@ information_resources:
     name: Multiomics Wellness KP API
     xref:
       - https://github.com/NCATSTranslator/Translator-All/wiki/Wellness-KP
-    knowledge level: correlation
-    agent type: not_provided
+    knowledge level: statistical_association
+    agent type: data_analysis_pipeline
     description: Documentation of the Multiomics Wellness KP query web services.
   - id: infores:biothings-multiomics-clinicaltrials
     status: released
     name: Multiomics ClinicalTrials KP API
     xref:
       - https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP
-    knowledge level: curated
-    agent type: not_provided
+    knowledge level: knowledge_assertion
+    agent type: manual_agent
+  - id: infores:biothings-multiomics-drugapprovals
+    status: released
+    name: Multiomics Drug Approvals KP API
+    xref:
+      - https://github.com/NCATSTranslator/Translator-All/wiki/Multiomics-Drug-Approvals-KP
+    knowledge level: knowledge_assertion
+    agent type: manual_agent
   - id: infores:biothings-pfocr
     status: modified
     name: BioThings PFOCR API

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: 2024-07-15T22:28:45
+# Generation date: 2024-07-15T15:48:21
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml
@@ -151,9 +151,15 @@ class KnowledgeLevelEnum(EnumDefinitionImpl):
     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.
     """
+    knowledge_assertion = PermissibleValue(
+        text="knowledge_assertion",
+        description="""knowledge asserted by a human expert, based on their interpretation of data or published study results""")
+    statistical_association = PermissibleValue(
+        text="statistical_association",
+        description="""statistical associations calculated between variables in a clinical or omics dataset, by an automated  analysis pipeline""")
     curated = PermissibleValue(
         text="curated",
-        description="""knowledge generated through manual curation  or interpretation of data or published study results""")
+        description="""knowledge generated through manual curation or interpretation of data or published study results""")
     predicted = PermissibleValue(
         text="predicted",
         description="""predictions generated computationally through inference over less direct forms of evidence (without human  intervention or review)""")
@@ -186,12 +192,18 @@ class AgentTypeEnum(EnumDefinitionImpl):
     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.
     """
+    manual_agent = PermissibleValue(
+        text="manual_agent",
+        description="a human agent, such as a curator or expert")
     not_provided = PermissibleValue(
         text="not_provided",
         description="agent type is not provided or known")
     computational_model = PermissibleValue(
         text="computational_model",
         description="a computational model, such as a machine learning model")
+    data_analysis_pipeline = PermissibleValue(
+        text="data_analysis_pipeline",
+        description="a data analysis pipeline, such as a bioinformatics pipeline")
 
     _defn = EnumDefinition(
         name="AgentTypeEnum",

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": "2024-07-15T22:28:44",
+      "generation_date": "2024-07-15T15:48:19",
       "source": "information_resource_registry.yaml"
    },
    "@context": {

diff --git a/project/jsonld/information_resource_registry.jsonld b/project/jsonld/information_resource_registry.jsonld
@@ -374,9 +374,17 @@
       "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.",
       "from_schema": "https://w3id.org/biolink/information_resource_registry.yaml",
       "permissible_values": [
+        {
+          "text": "knowledge_assertion",
+          "description": "knowledge asserted by a human expert, based on their interpretation of data or published study results"
+        },
+        {
+          "text": "statistical_association",
+          "description": "statistical associations calculated between variables in a clinical or omics dataset, by an automated  analysis pipeline"
+        },
         {
           "text": "curated",
-          "description": "knowledge generated through manual curation  or interpretation of data or published study results"
+          "description": "knowledge generated through manual curation or interpretation of data or published study results"
         },
         {
           "text": "predicted",
@@ -410,13 +418,21 @@
       "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.",
       "from_schema": "https://w3id.org/biolink/information_resource_registry.yaml",
       "permissible_values": [
+        {
+          "text": "manual_agent",
+          "description": "a human agent, such as a curator or expert"
+        },
         {
           "text": "not_provided",
           "description": "agent type is not provided or known"
         },
         {
           "text": "computational_model",
           "description": "a computational model, such as a machine learning model"
+        },
+        {
+          "text": "data_analysis_pipeline",
+          "description": "a data analysis pipeline, such as a bioinformatics pipeline"
         }
       ]
     }
@@ -612,9 +628,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "information_resource_registry.yaml",
-  "source_file_date": "2024-07-15T22:28:00",
-  "source_file_size": 7882,
-  "generation_date": "2024-07-15T22:28:45",
+  "source_file_date": "2024-07-15T15:47:44",
+  "source_file_size": 8462,
+  "generation_date": "2024-07-15T15:48:19",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/information_resource_registry.context.jsonld",

diff --git a/project/jsonschema/information_resource_registry.schema.json b/project/jsonschema/information_resource_registry.schema.json
@@ -3,8 +3,10 @@
         "AgentTypeEnum": {
             "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.",
             "enum": [
+                "manual_agent",
                 "not_provided",
-                "computational_model"
+                "computational_model",
+                "data_analysis_pipeline"
             ],
             "title": "AgentTypeEnum",
             "type": "string"
@@ -87,6 +89,8 @@
         "KnowledgeLevelEnum": {
             "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.",
             "enum": [
+                "knowledge_assertion",
+                "statistical_association",
                 "curated",
                 "predicted",
                 "text_mined",

diff --git a/project/owl/information_resource.owl.ttl b/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" ;
@@ -31,6 +31,16 @@ biolink:information_resource_registry.yaml.owl.ttl a owl:Ontology ;
     rdfs:subClassOf infores:AgentTypeEnum,
         linkml:PermissibleValue .
 
+<https://w3id.org/biolink/infores/AgentTypeEnum#data_analysis_pipeline> a owl:Class ;
+    rdfs:label "data_analysis_pipeline" ;
+    rdfs:subClassOf infores:AgentTypeEnum,
+        linkml:PermissibleValue .
+
+<https://w3id.org/biolink/infores/AgentTypeEnum#manual_agent> a owl:Class ;
+    rdfs:label "manual_agent" ;
+    rdfs:subClassOf infores:AgentTypeEnum,
+        linkml:PermissibleValue .
+
 <https://w3id.org/biolink/infores/AgentTypeEnum#not_provided> a owl:Class ;
     rdfs:label "not_provided" ;
     rdfs:subClassOf infores:AgentTypeEnum,
@@ -42,68 +52,68 @@ infores:InformationResource a owl:Class ;
             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:id ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:description ],
+            owl:onProperty infores:name ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
+            owl:allValuesFrom infores:AgentTypeEnum ;
             owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:synonym ],
-        [ a owl:Restriction ;
-            owl:minCardinality 0 ;
+            owl:maxCardinality 1 ;
             owl:onProperty infores:knowledge_level ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:synonym ],
-        [ a owl:Restriction ;
-            owl:minCardinality 1 ;
-            owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
             owl:onProperty infores:status ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:id ],
+            owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty infores:status ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty infores:xref ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
             owl:onProperty infores:description ],
         [ a owl:Restriction ;
-            owl:allValuesFrom infores:InformationResourceStatusEnum ;
-            owl:onProperty infores:status ],
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom infores:KnowledgeLevelEnum ;
             owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            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 ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
             owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
             owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:allValuesFrom infores:AgentTypeEnum ;
-            owl:onProperty infores:agent_type ],
+            owl:allValuesFrom infores:InformationResourceStatusEnum ;
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:minCardinality 1 ;
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:xref ],
+            owl:onProperty infores:synonym ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty infores:description ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            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." ;
@@ -139,6 +149,11 @@ infores:InformationResource a owl:Class ;
     rdfs:subClassOf infores:KnowledgeLevelEnum,
         linkml:PermissibleValue .
 
+<https://w3id.org/biolink/infores/KnowledgeLevelEnum#knowledge_assertion> a owl:Class ;
+    rdfs:label "knowledge_assertion" ;
+    rdfs:subClassOf infores:KnowledgeLevelEnum,
+        linkml:PermissibleValue .
+
 <https://w3id.org/biolink/infores/KnowledgeLevelEnum#mixed> a owl:Class ;
     rdfs:label "mixed" ;
     rdfs:subClassOf infores:KnowledgeLevelEnum,
@@ -159,6 +174,11 @@ infores:InformationResource a owl:Class ;
     rdfs:subClassOf infores:KnowledgeLevelEnum,
         linkml:PermissibleValue .
 
+<https://w3id.org/biolink/infores/KnowledgeLevelEnum#statistical_association> a owl:Class ;
+    rdfs:label "statistical_association" ;
+    rdfs:subClassOf infores:KnowledgeLevelEnum,
+        linkml:PermissibleValue .
+
 <https://w3id.org/biolink/infores/KnowledgeLevelEnum#text_mined> a owl:Class ;
     rdfs:label "text_mined" ;
     rdfs:subClassOf infores:KnowledgeLevelEnum,
@@ -228,8 +248,10 @@ infores:status a owl:ObjectProperty ;
 
 infores:AgentTypeEnum a owl:Class ;
     rdfs:subClassOf linkml:EnumDefinition ;
-    owl:unionOf ( <https://w3id.org/biolink/infores/AgentTypeEnum#not_provided> <https://w3id.org/biolink/infores/AgentTypeEnum#computational_model> ) ;
+    owl:unionOf ( <https://w3id.org/biolink/infores/AgentTypeEnum#manual_agent> <https://w3id.org/biolink/infores/AgentTypeEnum#not_provided> <https://w3id.org/biolink/infores/AgentTypeEnum#computational_model> <https://w3id.org/biolink/infores/AgentTypeEnum#data_analysis_pipeline> ) ;
     linkml:permissible_values <https://w3id.org/biolink/infores/AgentTypeEnum#computational_model>,
+        <https://w3id.org/biolink/infores/AgentTypeEnum#data_analysis_pipeline>,
+        <https://w3id.org/biolink/infores/AgentTypeEnum#manual_agent>,
         <https://w3id.org/biolink/infores/AgentTypeEnum#not_provided> .
 
 infores:InformationResourceStatusEnum a owl:Class ;
@@ -242,13 +264,15 @@ infores:InformationResourceStatusEnum a owl:Class ;
 
 infores:KnowledgeLevelEnum a owl:Class ;
     rdfs:subClassOf linkml:EnumDefinition ;
-    owl:unionOf ( <https://w3id.org/biolink/infores/KnowledgeLevelEnum#curated> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#predicted> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#text_mined> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#correlation> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#observed> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#other> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#mixed> ) ;
+    owl:unionOf ( <https://w3id.org/biolink/infores/KnowledgeLevelEnum#knowledge_assertion> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#statistical_association> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#curated> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#predicted> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#text_mined> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#correlation> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#observed> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#other> <https://w3id.org/biolink/infores/KnowledgeLevelEnum#mixed> ) ;
     linkml:permissible_values <https://w3id.org/biolink/infores/KnowledgeLevelEnum#correlation>,
         <https://w3id.org/biolink/infores/KnowledgeLevelEnum#curated>,
+        <https://w3id.org/biolink/infores/KnowledgeLevelEnum#knowledge_assertion>,
         <https://w3id.org/biolink/infores/KnowledgeLevelEnum#mixed>,
         <https://w3id.org/biolink/infores/KnowledgeLevelEnum#observed>,
         <https://w3id.org/biolink/infores/KnowledgeLevelEnum#other>,
         <https://w3id.org/biolink/infores/KnowledgeLevelEnum#predicted>,
+        <https://w3id.org/biolink/infores/KnowledgeLevelEnum#statistical_association>,
         <https://w3id.org/biolink/infores/KnowledgeLevelEnum#text_mined> .