From f0f835daa7939f8deaa59a1c057c0f88d03a6a37 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gw=C3=AAnlyn=20Glusman?= <gglusman@isbscience.org>
Date: Thu, 27 Jun 2024 12:36:02 -0700
Subject: [PATCH 1/4] Update infores_catalog.yaml

Edited KL/AT for Multiomics Wellness KP
Edited KL/AT for Multiomics Clinical Trials KP
Added entry for Multiomics Drug Approvals KP
---
 infores_catalog.yaml | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/infores_catalog.yaml b/infores_catalog.yaml
index d60efce..7b69d34 100644
--- 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

From 06815c85ac93b295f2282054a5040395b1991a38 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Mon, 15 Jul 2024 15:46:30 -0700
Subject: [PATCH 2/4] fix up source of python validation and add enumeration
 values to fix tests

---
 project/information_resource_registry.py      | 16 +++-
 ...formation_resource_registry.context.jsonld |  2 +-
 .../information_resource_registry.jsonld      | 24 ++++-
 .../information_resource_registry.schema.json |  6 +-
 project/owl/information_resource.owl.ttl      | 90 ++++++++++++-------
 .../information_resource_registry.shacl.ttl   | 46 +++++-----
 .../shex/information_resource_registry.shex   | 10 ++-
 .../information_resource_registry.py          | 16 +++-
 .../datamodel/pydanticmodel.py                | 10 ++-
 .../datamodel/pydanticmodel_v2.py             | 10 ++-
 .../schema/information_resource_registry.yaml | 15 +++-
 .../scripts/verify_infores.py                 |  9 +-
 12 files changed, 180 insertions(+), 74 deletions(-)

diff --git a/project/information_resource_registry.py b/project/information_resource_registry.py
index e088720..830e8e9 100644
--- 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: 2024-06-09T17:47:26
+# Generation date: 2024-07-15T15:42:36
 # 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
index 0807985..dd90238 100644
--- 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": "2024-06-09T17:47:25",
+      "generation_date": "2024-07-15T15:42:34",
       "source": "information_resource_registry.yaml"
    },
    "@context": {
diff --git a/project/jsonld/information_resource_registry.jsonld b/project/jsonld/information_resource_registry.jsonld
index f29cace..e291805 100644
--- 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",
@@ -410,6 +418,10 @@
       "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"
@@ -417,6 +429,10 @@
         {
           "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": "2024-06-09T17:46:43",
-  "source_file_size": 7882,
-  "generation_date": "2024-06-09T17:47:25",
+  "source_file_date": "2024-07-15T15:42:31",
+  "source_file_size": 8462,
+  "generation_date": "2024-07-15T15:42:35",
   "@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
index 3f28533..7eb0a4f 100644
--- 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
index 7226b8e..af88dfa 100644
--- a/project/owl/information_resource.owl.ttl
+++ b/project/owl/information_resource.owl.ttl
@@ -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,
@@ -39,71 +49,71 @@ biolink:information_resource_registry.yaml.owl.ttl a owl:Ontology ;
 infores:InformationResource a owl:Class ;
     rdfs:label "InformationResource" ;
     rdfs:subClassOf [ a owl:Restriction ;
-            owl:allValuesFrom infores:InformationResourceStatusEnum ;
-            owl:onProperty infores:status ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:id ],
-        [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:id ],
-        [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty infores:knowledge_level ],
-        [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:minCardinality 1 ;
             owl:onProperty infores:id ],
-        [ 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:allValuesFrom xsd:string ;
-            owl:onProperty infores:synonym ],
+            owl:onProperty infores:id ],
+        [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
             owl:onProperty infores:description ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom infores:InformationResourceStatusEnum ;
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
+            owl:maxCardinality 1 ;
             owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
             owl:onProperty infores:name ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:xref ],
+            owl:allValuesFrom infores:AgentTypeEnum ;
+            owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:description ],
+            owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
+            owl:minCardinality 0 ;
             owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:allValuesFrom infores:AgentTypeEnum ;
-            owl:onProperty infores:agent_type ],
+            owl:minCardinality 0 ;
+            owl:onProperty infores:xref ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
+            owl:minCardinality 0 ;
             owl:onProperty infores:name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom xsd:string ;
+            owl:onProperty infores:description ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom xsd:string ;
+            owl:onProperty infores:xref ],
+        [ a owl:Restriction ;
+            owl:minCardinality 0 ;
+            owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty infores:status ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom infores:KnowledgeLevelEnum ;
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:status ],
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:xref ],
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:knowledge_level ],
         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> .
 
 
diff --git a/project/shacl/information_resource_registry.shacl.ttl b/project/shacl/information_resource_registry.shacl.ttl
index f742d54..b108499 100644
--- a/project/shacl/information_resource_registry.shacl.ttl
+++ b/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 status of the infores identifier, the default is \"released\"" ;
+    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:order 3 ;
+            sh:path infores:xref ],
+        [ 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:order 1 ;
-            sh:path rdfs:label ],
-        [ 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 ( "not_provided" "computational_model" ) ;
+            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:order 7 ;
-            sh:path infores:agent_type ],
+            sh:minCount 1 ;
+            sh:order 2 ;
+            sh:path infores:id ],
         [ sh:datatype xsd:string ;
             sh:description "Alternate human-readable names for a thing" ;
             sh:order 4 ;
             sh:path infores:synonym ],
         [ 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:order 2 ;
-            sh:path infores:id ],
+            sh:order 5 ;
+            sh:path rdfs:comment ],
         [ 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:order 3 ;
-            sh:path infores:xref ],
+            sh:description "A human-readable name for an attribute or entity." ;
+            sh:maxCount 1 ;
+            sh:order 1 ;
+            sh:path rdfs:label ],
+        [ 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" "computational_model" "data_analysis_pipeline" ) ;
+            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 ( "curated" "predicted" "text_mined" "correlation" "observed" "other" "mixed" ) ;
+            sh:in ( "knowledge_assertion" "statistical_association" "curated" "predicted" "text_mined" "correlation" "observed" "other" "mixed" ) ;
             sh:maxCount 1 ;
             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:order 5 ;
-            sh:path rdfs:comment ] ;
+            sh:path infores:knowledge_level ] ;
     sh:targetClass infores:InformationResource .
 
diff --git a/project/shex/information_resource_registry.shex b/project/shex/information_resource_registry.shex
index 732c467..6f12317 100644
--- a/project/shex/information_resource_registry.shex
+++ b/project/shex/information_resource_registry.shex
@@ -53,15 +53,19 @@ linkml:Sparqlpath xsd:string
           <xref> @linkml:String * ;
           <synonym> @linkml:String * ;
           rdfs:comment @linkml:String ? ;
-          <knowledge_level> [ <https://w3id.org/biolink/infores/KnowledgeLevelEnum#curated>
+          <knowledge_level> [ <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> ] ? ;
-          <agent_type> [ <https://w3id.org/biolink/infores/AgentTypeEnum#not_provided>
-             <https://w3id.org/biolink/infores/AgentTypeEnum#computational_model> ] ?
+          <agent_type> [ <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> ] ?
        ) ;
        rdf:type [ <InformationResource> ] ?
     )
diff --git a/src/information_resource_registry/datamodel/information_resource_registry.py b/src/information_resource_registry/datamodel/information_resource_registry.py
index e20641c..488b154 100644
--- 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: 2024-06-09T17:47:33
+# Generation date: 2024-07-15T15:42:45
 # 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/src/information_resource_registry/datamodel/pydanticmodel.py b/src/information_resource_registry/datamodel/pydanticmodel.py
index 2310b8e..cdce3a4 100644
--- a/src/information_resource_registry/datamodel/pydanticmodel.py
+++ b/src/information_resource_registry/datamodel/pydanticmodel.py
@@ -50,7 +50,11 @@ class KnowledgeLevelEnum(str, Enum):
     """
     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.
     """
-    # knowledge generated through manual curation  or interpretation of data or published study results
+    # knowledge asserted by a human expert, based on their interpretation of data or published study results
+    knowledge_assertion = "knowledge_assertion"
+    # statistical associations calculated between variables in a clinical or omics dataset, by an automated  analysis pipeline
+    statistical_association = "statistical_association"
+    # knowledge generated through manual curation or interpretation of data or published study results
     curated = "curated"
     # predictions generated computationally through inference over less direct forms of evidence (without human  intervention or review)
     predicted = "predicted"
@@ -71,10 +75,14 @@ class AgentTypeEnum(str, Enum):
     """
     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.
     """
+    # a human agent, such as a curator or expert
+    manual_agent = "manual_agent"
     # agent type is not provided or known
     not_provided = "not_provided"
     # a computational model, such as a machine learning model
     computational_model = "computational_model"
+    # a data analysis pipeline, such as a bioinformatics pipeline
+    data_analysis_pipeline = "data_analysis_pipeline"
     
     
 
diff --git a/src/information_resource_registry/datamodel/pydanticmodel_v2.py b/src/information_resource_registry/datamodel/pydanticmodel_v2.py
index 5f62cf4..f128c06 100644
--- a/src/information_resource_registry/datamodel/pydanticmodel_v2.py
+++ b/src/information_resource_registry/datamodel/pydanticmodel_v2.py
@@ -47,7 +47,11 @@ class KnowledgeLevelEnum(str, Enum):
     """
     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.
     """
-    # knowledge generated through manual curation  or interpretation of data or published study results
+    # knowledge asserted by a human expert, based on their interpretation of data or published study results
+    knowledge_assertion = "knowledge_assertion"
+    # statistical associations calculated between variables in a clinical or omics dataset, by an automated  analysis pipeline
+    statistical_association = "statistical_association"
+    # knowledge generated through manual curation or interpretation of data or published study results
     curated = "curated"
     # predictions generated computationally through inference over less direct forms of evidence (without human  intervention or review)
     predicted = "predicted"
@@ -68,10 +72,14 @@ class AgentTypeEnum(str, Enum):
     """
     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.
     """
+    # a human agent, such as a curator or expert
+    manual_agent = "manual_agent"
     # agent type is not provided or known
     not_provided = "not_provided"
     # a computational model, such as a machine learning model
     computational_model = "computational_model"
+    # a data analysis pipeline, such as a bioinformatics pipeline
+    data_analysis_pipeline = "data_analysis_pipeline"
     
     
 
diff --git a/src/information_resource_registry/schema/information_resource_registry.yaml b/src/information_resource_registry/schema/information_resource_registry.yaml
index 892ee36..307f8c5 100644
--- a/src/information_resource_registry/schema/information_resource_registry.yaml
+++ b/src/information_resource_registry/schema/information_resource_registry.yaml
@@ -165,9 +165,16 @@ enums:
         knowledge level would be "curated", and the evidence would be described
         in more detail in the evidence graph.
     permissible_values:
+      knowledge_assertion:
+        description: >-
+          knowledge asserted by a human expert, based on their interpretation of data or published study results
+      statistical_association:
+        description: >-
+          statistical associations calculated between variables in a clinical or omics dataset, by an automated 
+          analysis pipeline
       curated:
         description: >-
-          knowledge generated through manual curation  or interpretation of data or published study results
+          knowledge generated through manual curation or interpretation of data or published study results
       predicted:
         description: >-
           predictions generated computationally through inference over less direct forms of evidence (without human 
@@ -202,9 +209,15 @@ enums:
         agent type would be "publication", and the evidence would be described
         in more detail in the evidence graph.
     permissible_values:
+      manual_agent:
+        description: >-
+          a human agent, such as a curator or expert
       not_provided:
         description: >-
           agent type is not provided or known
       computational_model:
         description: >-
           a computational model, such as a machine learning model
+      data_analysis_pipeline:
+        description: >-
+          a data analysis pipeline, such as a bioinformatics pipeline
diff --git a/src/information_resource_registry/scripts/verify_infores.py b/src/information_resource_registry/scripts/verify_infores.py
index a1bc67f..e515534 100755
--- a/src/information_resource_registry/scripts/verify_infores.py
+++ b/src/information_resource_registry/scripts/verify_infores.py
@@ -65,13 +65,18 @@ def validate(self):
                                                           "correlation",
                                                           "observed",
                                                           "other",
-                                                          "mixed"]:
+                                                          "mixed",
+                                                          "statistical_association",
+                                                          "knowledge_assertion"]:
                     print(infores)
                     print("Invalid infores knowledge level:" + infores.get("knowledge level")
                           + " for " + infores.get("name"))
                     raise ValueError("invalid knowledge level for " + infores.get("name") + " for " + infores.get("id"))
 
-                if infores.get("agent type") not in ["not_provided", "computational_model"]:
+                if infores.get("agent type") not in ["not_provided",
+                                                     "computational_model",
+                                                     "data_analysis_pipeline",
+                                                     "manual_agent"]:
                     print(infores)
                     print("Invalid infores agent type:" + infores.get("agent type") + " for " + infores.get("name"))
                     raise ValueError("invalid agent type for " + infores.get("name") + " for " + infores.get("id"))

From f704831d3e21b31d5b798fcabfb91246f90be29d Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Mon, 15 Jul 2024 15:52:19 -0700
Subject: [PATCH 3/4] fixing tests

---
 project/information_resource_registry.py      |  2 +-
 ...formation_resource_registry.context.jsonld |  2 +-
 .../information_resource_registry.jsonld      |  4 +-
 project/owl/information_resource.owl.ttl      | 54 +++++++++----------
 .../information_resource_registry.shacl.ttl   | 46 ++++++++--------
 .../information_resource_registry.py          |  2 +-
 6 files changed, 55 insertions(+), 55 deletions(-)

diff --git a/project/information_resource_registry.py b/project/information_resource_registry.py
index 8e41264..6f0e295 100644
--- 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: 2024-07-15T15:46:55
+# Generation date: 2024-07-15T15:48:21
 # 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
index 15c3565..33668f6 100644
--- 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": "2024-07-15T15:46:54",
+      "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
index 48240d5..0f79fe1 100644
--- a/project/jsonld/information_resource_registry.jsonld
+++ b/project/jsonld/information_resource_registry.jsonld
@@ -628,9 +628,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "information_resource_registry.yaml",
-  "source_file_date": "2024-07-15T15:42:31",
+  "source_file_date": "2024-07-15T15:47:44",
   "source_file_size": 8462,
-  "generation_date": "2024-07-15T15:46:54",
+  "generation_date": "2024-07-15T15:48:19",
   "@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
index 67f8190..1d27371 100644
--- 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" ;
@@ -49,41 +49,41 @@ 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:xref ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:synonym ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom infores:InformationResourceStatusEnum ;
-            owl:onProperty infores:status ],
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty infores:name ],
+        [ a owl:Restriction ;
+            owl:allValuesFrom infores:AgentTypeEnum ;
+            owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:id ],
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:synonym ],
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:description ],
+            owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:description ],
+            owl:onProperty infores:status ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:onProperty infores:xref ],
         [ a owl:Restriction ;
-            owl:allValuesFrom infores:AgentTypeEnum ;
-            owl:onProperty infores:agent_type ],
+            owl:minCardinality 0 ;
+            owl:onProperty infores:knowledge_level ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
             owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:agent_type ],
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom infores:KnowledgeLevelEnum ;
             owl:onProperty infores:knowledge_level ],
@@ -92,28 +92,28 @@ infores:InformationResource a owl:Class ;
             owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:id ],
+            owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:xref ],
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:description ],
         [ 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:maxCardinality 1 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:minCardinality 1 ;
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:name ],
+            owl:minCardinality 0 ;
+            owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
-            owl:onProperty infores:status ],
+            owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty infores:agent_type ],
-        [ a owl:Restriction ;
-            owl:minCardinality 1 ;
-            owl:onProperty infores:id ],
         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
index 2f542bd..2b91933 100644
--- a/project/shacl/information_resource_registry.shacl.ttl
+++ b/project/shacl/information_resource_registry.shacl.ttl
@@ -20,43 +20,43 @@ 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 unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ;
+            sh:description "A human-readable name for an attribute or entity." ;
             sh:maxCount 1 ;
-            sh:minCount 1 ;
-            sh:order 2 ;
-            sh:path infores:id ],
+            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: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:order 5 ;
             sh:path rdfs:comment ],
-        [ 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: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" "computational_model" "data_analysis_pipeline" ) ;
             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 "Alternate human-readable names for a thing" ;
-            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 ;
-            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" "curated" "predicted" "text_mined" "correlation" "observed" "other" "mixed" ) ;
             sh:maxCount 1 ;
             sh:order 6 ;
-            sh:path infores:knowledge_level ] ;
+            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:maxCount 1 ;
+            sh:minCount 1 ;
+            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:order 3 ;
+            sh:path infores:xref ],
+        [ sh:datatype xsd:string ;
+            sh:description "Alternate human-readable names for a thing" ;
+            sh:order 4 ;
+            sh:path infores:synonym ] ;
     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
index 4db5016..282f7bc 100644
--- 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: 2024-07-15T15:47:06
+# Generation date: 2024-07-15T15:48:30
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml

From b98c1b5e1788523c14e5652c7b771ada4126db15 Mon Sep 17 00:00:00 2001
From: Sierra Taylor Moxon <sierra.taylor@gmail.com>
Date: Mon, 15 Jul 2024 15:52:43 -0700
Subject: [PATCH 4/4] regenerating python project files

---
 .../datamodel/information_resource_registry.py                  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/information_resource_registry/datamodel/information_resource_registry.py b/src/information_resource_registry/datamodel/information_resource_registry.py
index 282f7bc..7085188 100644
--- 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: 2024-07-15T15:48:30
+# Generation date: 2024-07-15T15:52:30
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml