Merge branch 'fix_bke_taxonomy_model_20250924' of https://github.com/puja-trivedi/models into fix_bke_taxonomy_model_20250924

Author: puja-trivedi

erdiagram-autogen/bke_taxonomy.md

@@ -52,7 +52,7 @@ Abbreviation {
     uriorcurieList xref  
     string term  
     string meaning  
-    string entity_type  
+    abbreviation_entity_type entity_type  
     iri_type iri  
     uriorcurieList category  
     stringList type  
@@ -183,7 +183,7 @@ CellTypeSet {
     string description  
     integer order  
     uriorcurieList xref  
-    string cell_type_set_type  
+    cell_type_set_type cell_type_set_type  
     iri_type iri  
     uriorcurieList category  
     stringList type  

json-schema-autogen/bke_taxonomy.json

@@ -74,11 +74,8 @@
                     ]
                 },
                 "entity_type": {
-                    "description": "The entity type which the abbreviation term denotes.",
-                    "type": [
-                        "string",
-                        "null"
-                    ]
+                    "$ref": "#/$defs/AbbreviationEntityType",
+                    "description": "The entity type which the abbreviation term denotes."
                 },
                 "full_name": {
                     "description": "a long-form human readable name for a thing",
@@ -197,6 +194,16 @@
             "title": "Abbreviation",
             "type": "object"
         },
+        "AbbreviationEntityType": {
+            "description": "",
+            "enum": [
+                "cell type",
+                "gene",
+                "structure"
+            ],
+            "title": "AbbreviationEntityType",
+            "type": "string"
+        },
         "Activity": {
             "additionalProperties": false,
             "description": "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.",
@@ -941,11 +948,8 @@
                     ]
                 },
                 "cell_type_set_type": {
-                    "description": "A tag denoting the type or purpose of the cell type set.",
-                    "type": [
-                        "string",
-                        "null"
-                    ]
+                    "$ref": "#/$defs/CellTypeSetType",
+                    "description": "A tag denoting the type or purpose of the cell type set."
                 },
                 "contains_taxon": {
                     "description": "One of potentially many cell types taxons which together defines the cell type set.",
@@ -1106,6 +1110,15 @@
             "title": "CellTypeSet",
             "type": "object"
         },
+        "CellTypeSetType": {
+            "description": "",
+            "enum": [
+                "taxonomic level",
+                "neighborhood"
+            ],
+            "title": "CellTypeSetType",
+            "type": "string"
+        },
         "CellTypeTaxon": {
             "additionalProperties": false,
             "description": "A cell type taxon is a node in a taxonomy. Taxons represents a unit of cell type classification and is defined by a set of clusters. Taxons may be organized into a heirarchy and levels. Taxons at higher levels represents broader cell type classes and partitioned into more specific types at lower levels. Additionally, taxons may be organized into neighborhoods or related groups.",

jsonld-context-autogen/bke_taxonomy.context.jsonld

@@ -199,6 +199,11 @@
          "@id": "denotes_parcellation_term"
       },
       "entity_type": {
+         "@context": {
+            "text": "skos:notation",
+            "description": "skos:prefLabel",
+            "meaning": "@id"
+         },
          "@id": "entity_type"
       },
       "meaning": {
@@ -244,6 +249,11 @@
          "@id": "biolink:category"
       },
       "cell_type_set_type": {
+         "@context": {
+            "text": "skos:notation",
+            "description": "skos:prefLabel",
+            "meaning": "@id"
+         },
          "@id": "cell_type_set_type"
       },
       "contains_taxon": {

models_py-autogen/bke_taxonomy.py

@@ -116,6 +116,22 @@ class DISTANCEUNIT(str, Enum):
     meter = "m"
 
 
+class AbbreviationEntityType(str, Enum):
+    # Abbreviation denotes a Cell Type entity.
+    cell_type = "cell type"
+    # Abbreviation denotes a Gene entity.
+    gene = "gene"
+    # Abbreviation denotes a Structure entity.
+    structure = "structure"
+
+
+class CellTypeSetType(str, Enum):
+    # Denotes CellTypeSet is at Taxonomic level.
+    taxonomic_level = "taxonomic level"
+    # Denotes CellTypeSet is at Neighborhood level.
+    neighborhood = "neighborhood"
+
+
 
 class OntologyClass(ConfiguredBaseModel):
     """
@@ -11159,7 +11175,7 @@ class CellTypeSet(ProvEntity, NamedThing):
          'narrow_mappings': ['gff3:Dbxref', 'gpi:DB_Xrefs'],
          'slot_uri': 'biolink:xref'} })
     contains_taxon: Optional[List[str]] = Field(default=None, description="""One of potentially many cell types taxons which together defines the cell type set.""", json_schema_extra = { "linkml_meta": {'alias': 'contains_taxon', 'domain_of': ['CellTypeSet']} })
-    cell_type_set_type: Optional[str] = Field(default=None, description="""A tag denoting the type or purpose of the cell type set.""", json_schema_extra = { "linkml_meta": {'alias': 'cell_type_set_type',
+    cell_type_set_type: Optional[CellTypeSetType] = Field(default=None, description="""A tag denoting the type or purpose of the cell type set.""", json_schema_extra = { "linkml_meta": {'alias': 'cell_type_set_type',
          'domain_of': ['CellTypeSet'],
          'examples': [{'value': 'taxonomic_level'}],
          'local_names': {'allen': {'local_name_source': 'allen',
@@ -14637,7 +14653,7 @@ class Abbreviation(ProvEntity, NamedThing):
          'domain_of': ['Abbreviation'],
          'examples': [{'value': 'intratelencephalic-projecting glutamatergic cortical '
                                 'neuron'}]} })
-    entity_type: Optional[str] = Field(default=None, description="""The entity type which the abbreviation term denotes.""", json_schema_extra = { "linkml_meta": {'alias': 'entity_type',
+    entity_type: Optional[AbbreviationEntityType] = Field(default=None, description="""The entity type which the abbreviation term denotes.""", json_schema_extra = { "linkml_meta": {'alias': 'entity_type',
          'domain_of': ['Abbreviation'],
          'examples': [{'value': 'cell type'}]} })
     was_derived_from: Optional[str] = Field(default=None, description="""A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity.""", json_schema_extra = { "linkml_meta": {'alias': 'was_derived_from',