Regenerate artifacts from information_resource_registry.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: 2024-03-08T12:38:21
+# Generation date: 2024-03-08T21:05:11
 # 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": "2024-03-08T12:38:19",
+      "generation_date": "2024-03-08T21:05:10",
       "source": "information_resource_registry.yaml"
    },
    "@context": {

project/jsonld/information_resource_registry.jsonld

@@ -612,9 +612,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "information_resource_registry.yaml",
-  "source_file_date": "2024-03-08T12:18:13",
-  "source_file_size": 7890,
-  "generation_date": "2024-03-08T12:38:19",
+  "source_file_date": "2024-03-08T21:04:28",
+  "source_file_size": 7882,
+  "generation_date": "2024-03-08T21:05:10",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/information_resource_registry.context.jsonld",

project/jsonschema/information_resource_registry.schema.json

@@ -100,7 +100,7 @@
         }
     },
     "$id": "https://w3id.org/biolink/information_resource_registry.yaml",
-    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$schema": "https://json-schema.org/draft/2019-09/schema",
     "additionalProperties": true,
     "description": "A collection of information resources",
     "metamodel_version": "1.7.0",

project/owl/information_resource.owl.ttl

@@ -39,71 +39,71 @@ biolink:information_resource_registry.yaml.owl.ttl a owl:Ontology ;
 infores:InformationResource a owl:Class ;
     rdfs:label "InformationResource" ;
     rdfs:subClassOf [ a owl:Restriction ;
+            owl:maxCardinality 1 ;
+            owl:onProperty infores:status ],
+        [ 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:minCardinality 0 ;
-            owl:onProperty infores:synonym ],
+            owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:minCardinality 0 ;
             owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:description ],
-        [ a owl:Restriction ;
-            owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:name ],
+            owl:minCardinality 0 ;
+            owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:knowledge_level ],
-        [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:knowledge_level ],
+            owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:xref ],
+            owl:onProperty infores:synonym ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:id ],
-        [ 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 infores:InformationResourceStatusEnum ;
             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:minCardinality 0 ;
+            owl:onProperty infores:xref ],
         [ a owl:Restriction ;
             owl:allValuesFrom infores:AgentTypeEnum ;
             owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:minCardinality 1 ;
+            owl:allValuesFrom xsd:string ;
             owl:onProperty infores:id ],
         [ a owl:Restriction ;
             owl:allValuesFrom xsd:string ;
-            owl:onProperty infores:synonym ],
-        [ a owl:Restriction ;
-            owl:maxCardinality 1 ;
-            owl:onProperty infores:status ],
+            owl:onProperty infores:description ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
-            owl:onProperty infores:id ],
+            owl:onProperty infores:agent_type ],
         [ a owl:Restriction ;
-            owl:allValuesFrom infores:InformationResourceStatusEnum ;
+            owl:minCardinality 0 ;
             owl:onProperty infores:status ],
         [ a owl:Restriction ;
-            owl:minCardinality 0 ;
-            owl:onProperty infores:description ],
+            owl:allValuesFrom xsd:string ;
+            owl:onProperty infores:name ],
         [ a owl:Restriction ;
             owl:maxCardinality 1 ;
             owl:onProperty infores:name ],
+        [ a owl:Restriction ;
+            owl:minCardinality 1 ;
+            owl:onProperty infores:id ],
+        [ a owl:Restriction ;
+            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." ;

project/shacl/information_resource_registry.shacl.ttl

@@ -19,36 +19,21 @@ 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: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 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:maxCount 1 ;
             sh:order 6 ;
             sh:path infores:knowledge_level ],
-        [ 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 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: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: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:order 3 ;
-            sh:path infores:xref ],
         [ sh:datatype xsd:string ;
             sh:description "A human-readable name for an attribute or entity." ;
             sh:maxCount 1 ;
@@ -57,6 +42,21 @@ infores:InformationResource a sh:NodeShape ;
         [ sh:datatype xsd:string ;
             sh:description "Alternate human-readable names for a thing" ;
             sh:order 4 ;
-            sh:path infores:synonym ] ;
+            sh:path infores:synonym ],
+        [ 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:maxCount 1 ;
+            sh:order 7 ;
+            sh:path infores:agent_type ],
+        [ 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: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:targetClass infores:InformationResource .
 

project/shex/information_resource_registry.shex

@@ -44,14 +44,24 @@ linkml:Jsonpath xsd:string
 linkml:Sparqlpath xsd:string
 
 <InformationResource> CLOSED {
-    (  $<InformationResource_tes> (  <status> @<InformationResourceStatusEnum> ? ;
+    (  $<InformationResource_tes> (  <status> [ <https://w3id.org/biolink/infores/InformationResourceStatusEnum#released>
+             <https://w3id.org/biolink/infores/InformationResourceStatusEnum#deprecated>
+             <https://w3id.org/biolink/infores/InformationResourceStatusEnum#draft>
+             <https://w3id.org/biolink/infores/InformationResourceStatusEnum#modified> ] ? ;
           rdfs:label @linkml:String ? ;
           <id> @linkml:String ;
           <xref> @linkml:String * ;
           <synonym> @linkml:String * ;
           rdfs:comment @linkml:String ? ;
-          <knowledge_level> @<KnowledgeLevelEnum> ? ;
-          <agent_type> @<AgentTypeEnum> ?
+          <knowledge_level> [ <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> ] ?
        ) ;
        rdf:type [ <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: 2024-03-08T12:38:32
+# Generation date: 2024-03-08T21:05:18
 # Schema: Information-Resource-Registry-Schema
 #
 # id: https://w3id.org/biolink/information_resource_registry.yaml

src/information_resource_registry/datamodel/pydanticmodel.py

@@ -1,8 +1,11 @@
 from __future__ import annotations
 from datetime import datetime, date
 from enum import Enum
+
+from decimal import Decimal
 from typing import List, Dict, Optional, Any, Union
-from pydantic import BaseModel as BaseModel, ConfigDict, Field
+from pydantic import BaseModel as BaseModel, Field, validator
+import re
 import sys
 if sys.version_info >= (3, 8):
     from typing import Literal
@@ -23,8 +26,10 @@ class ConfiguredBaseModel(WeakRefShimBaseModel,
                 extra = 'forbid',
                 arbitrary_types_allowed = True,
                 use_enum_values = True):
+
     pass
 
+
 
 class InformationResourceStatusEnum(str, Enum):
     """
@@ -79,6 +84,7 @@ class InformationResourceContainer(ConfiguredBaseModel):
     """
     information_resources: Optional[List[InformationResource]] = Field(default_factory=list, description="""a collection of information resources""")
 
+
 
 class InformationResource(ConfiguredBaseModel):
     """
@@ -93,6 +99,7 @@ class InformationResource(ConfiguredBaseModel):
     knowledge_level: Optional[KnowledgeLevelEnum] = Field(None, 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.""")
     agent_type: Optional[AgentTypeEnum] = Field(None, 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.""")
 
+
 
 
 # Update forward refs

src/information_resource_registry/datamodel/pydanticmodel_v2.py

@@ -1,8 +1,11 @@
 from __future__ import annotations
 from datetime import datetime, date
 from enum import Enum
+
+from decimal import Decimal
 from typing import List, Dict, Optional, Any, Union
-from pydantic import BaseModel as BaseModel, ConfigDict, Field
+from pydantic import BaseModel as BaseModel, ConfigDict,  Field, field_validator
+import re
 import sys
 if sys.version_info >= (3, 8):
     from typing import Literal
@@ -21,6 +24,9 @@ class ConfiguredBaseModel(BaseModel):
         arbitrary_types_allowed=True,
         use_enum_values = True)
 
+    pass
+
+
 
 class InformationResourceStatusEnum(str, Enum):
     """
@@ -75,6 +81,7 @@ class InformationResourceContainer(ConfiguredBaseModel):
     """
     information_resources: Optional[List[InformationResource]] = Field(default_factory=list, description="""a collection of information resources""")
 
+
 
 class InformationResource(ConfiguredBaseModel):
     """
@@ -89,6 +96,7 @@ class InformationResource(ConfiguredBaseModel):
     knowledge_level: Optional[KnowledgeLevelEnum] = Field(None, 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.""")
     agent_type: Optional[AgentTypeEnum] = Field(None, 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.""")
 
+
 
 
 # Model rebuild