generate another formats for bke_taxonomy model(s)

Author: [email protected]

json-schema-autogen/bke_taxonomy.json

@@ -2409,7 +2409,7 @@
         },
         "GeneAnnotation": {
             "additionalProperties": false,
-            "description": "An annotation describing the location, boundaries, and functions of  individual genes within a genome annotation.",
+            "description": "Represents a single gene. Includes metadata about the gene, such as its molecular type and the genome annotation it was referenced from.",
             "properties": {
                 "category": {
                     "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}. NOTE: The category slot was modified to have a curie range and a pattern for bican categories.",
@@ -2531,7 +2531,7 @@
                             "type": "string"
                         }
                     ],
-                    "description": "The genome annotation that this gene annotation was referenced from.",
+                    "description": "The genome annotation that this gene was referenced from.",
                     "type": "string"
                 },
                 "source_id": {
@@ -2724,7 +2724,7 @@
         },
         "GenomeAnnotation": {
             "additionalProperties": false,
-            "description": "Location and nomenclature of genes and all of the coding regions in a genome assembly  and the classification of genes and transcripts into types.",
+            "description": "Represents a genome annotation. Includes metadata about the genome, such as its version and reference assembly.",
             "properties": {
                 "authority": {
                     "$ref": "#/$defs/AuthorityType",
@@ -2911,7 +2911,7 @@
         },
         "GenomeAssembly": {
             "additionalProperties": false,
-            "description": "Genome assembly to contain version and label information",
+            "description": "Represents a genome assembly. A genome assembly is a computational representation of a genome sequence.",
             "properties": {
                 "category": {
                     "description": "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}. NOTE: The category slot was modified to have a curie range and a pattern for bican categories.",

models_py-autogen/bke_taxonomy.py

@@ -5717,7 +5717,7 @@ def pattern_category(cls, v):
 
 class GeneAnnotation(Gene):
     """
-    An annotation describing the location, boundaries, and functions of  individual genes within a genome annotation.
+    Represents a single gene. Includes metadata about the gene, such as its molecular type and the genome annotation it was referenced from.
     """
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://identifiers.org/brain-bican/genome-annotation-schema'})
 
@@ -5727,7 +5727,7 @@ class GeneAnnotation(Gene):
     source_id: Optional[str] = Field(default=None, description="""The authority specific identifier.""", json_schema_extra = { "linkml_meta": {'alias': 'source_id',
          'domain_of': ['GeneAnnotation'],
          'slot_uri': 'schema:identifier'} })
-    referenced_in: Union[GenomeAnnotation, str] = Field(default=..., description="""The genome annotation that this gene annotation was referenced from.""", json_schema_extra = { "linkml_meta": {'alias': 'referenced_in',
+    referenced_in: Union[GenomeAnnotation, str] = Field(default=..., description="""The genome annotation that this gene was referenced from.""", json_schema_extra = { "linkml_meta": {'alias': 'referenced_in',
          'any_of': [{'range': 'GenomeAnnotation'}, {'range': 'string'}],
          'domain_of': ['GeneAnnotation']} })
     id: str = Field(default=..., description="""A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI""", json_schema_extra = { "linkml_meta": {'alias': 'id',
@@ -6129,7 +6129,7 @@ def pattern_category(cls, v):
 
 class GenomeAnnotation(Genome):
     """
-    Location and nomenclature of genes and all of the coding regions in a genome assembly  and the classification of genes and transcripts into types.
+    Represents a genome annotation. Includes metadata about the genome, such as its version and reference assembly.
     """
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://identifiers.org/brain-bican/genome-annotation-schema'})
 
@@ -6542,7 +6542,7 @@ def pattern_category(cls, v):
 
 class GenomeAssembly(ThingWithTaxon, NamedThing):
     """
-    Genome assembly to contain version and label information
+    Represents a genome assembly. A genome assembly is a computational representation of a genome sequence.
     """
     linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'https://identifiers.org/brain-bican/genome-annotation-schema',
          'mixins': ['thing with taxon']})