Merge pull request #208 from puja-trivedi/20251020_bketaxonomy

20251020 bketaxonomy

Author: puja-trivedi

json-schema-autogen/bke_taxonomy.json

@@ -6237,12 +6237,12 @@
         "Region": {
             "description": "",
             "enum": [
-                "STR",
-                "GPe",
-                "GPi",
-                "SN",
-                "Adj",
-                "STH"
+                "str",
+                "gpe",
+                "gpi",
+                "sn",
+                "adj",
+                "sth"
             ],
             "title": "Region",
             "type": "string"
@@ -6555,6 +6555,8 @@
                 },
                 "sth": {
                     "description": "Proportion of composition found in Subthalamic Nucleus",
+                    "maximum": "1.0",
+                    "minimum": "0.0",
                     "type": [
                         "number",
                         "null"

linkml-schema/bke_taxonomy.yaml

@@ -35,18 +35,24 @@ enums:
   Region:
     from_schema: https://w3id.org/brain-bican/bke-taxonomy
     permissible_values:
-      STR:
+      str:
         description: Striatum
-      GPe:
+        title: STR
+      gpe:
         description: External Globus Pallidus
-      GPi:
+        title: GPe
+      gpi:
         description: Internal Globus Pallidus
-      SN:
+        title: GPi
+      sn:
         description: Substantia Nigra
-      Adj:
+        title: SN
+      adj:
         description: Adjacent Regions
-      STH:
+        title: Adj
+      sth:
         description: Subthalamic Nucleus
+        title: STH
 slots:
   part_of_taxonomy:
     from_schema: https://w3id.org/brain-bican/bke-taxonomy
@@ -804,3 +810,5 @@ classes:
         description: Proportion of composition found in Subthalamic Nucleus
         from_schema: https://w3id.org/brain-bican/bke-taxonomy
         range: float
+        minimum_value: '0.0'
+        maximum_value: '1.0'

linkml-schema/source_bke_taxonomy/gsheet_output/Slots.tsv

@@ -58,4 +58,4 @@ SpatialProportions		gpe	float	Proportion of composition found in External Globus
 SpatialProportions		gpi	float	Proportion of composition found in Internal Globus Pallidus					0	1		
 SpatialProportions		sn	float	Proportion of composition found in Substantia Nigra					0	1		
 SpatialProportions		adj	float	Proportion of composition found in Adjacent Regions					0	1		
-SpatialProportions		sth	float	Proportion of composition found in Subthalamic Nucleus								
+SpatialProportions		sth	float	Proportion of composition found in Subthalamic Nucleus					0	1		

linkml-schema/source_bke_taxonomy/gsheet_output/ValueSets.tsv

@@ -1,13 +1,13 @@
-variable_name	value	description
-> enum	permissible_value	description
-AbbreviationEntityType	cell_type	Abbreviation denotes a Cell Type entity.
-AbbreviationEntityType	gene	Abbreviation denotes a Gene entity.
-AbbreviationEntityType	anatomical	Abbreviation denotes a Anatomical Structure entity.
-CellTypeSetType	taxonomic_level	Denotes CellTypeSet is at Taxonomic level.
-CellTypeSetType	neighborhood	Denotes CellTypeSet is at Neighborhood level.
-Region	STR	Striatum
-Region	GPe	External Globus Pallidus
-Region	GPi	Internal Globus Pallidus
-Region	SN	Substantia Nigra
-Region	Adj	Adjacent Regions
-Region	STH	Subthalamic Nucleus
+variable_name	value	title	meaning	description
+> enum	permissible_value	title	meaning	description
+AbbreviationEntityType	cell_type			Abbreviation denotes a Cell Type entity.
+AbbreviationEntityType	gene			Abbreviation denotes a Gene entity.
+AbbreviationEntityType	anatomical			Abbreviation denotes a Anatomical Structure entity.
+CellTypeSetType	taxonomic_level			Denotes CellTypeSet is at Taxonomic level.
+CellTypeSetType	neighborhood			Denotes CellTypeSet is at Neighborhood level.
+Region	str	STR		Striatum
+Region	gpe	GPe		External Globus Pallidus
+Region	gpi	GPi		Internal Globus Pallidus
+Region	sn	SN		Substantia Nigra
+Region	adj	Adj		Adjacent Regions
+Region	sth	STH		Subthalamic Nucleus

models_py-autogen/bke_taxonomy.py

@@ -134,17 +134,17 @@ class CellTypeSetType(str, Enum):
 
 class Region(str, Enum):
     # Striatum
-    STR = "STR"
+    STR = "str"
     # External Globus Pallidus
-    GPe = "GPe"
+    GPe = "gpe"
     # Internal Globus Pallidus
-    GPi = "GPi"
+    GPi = "gpi"
     # Substantia Nigra
-    SN = "SN"
+    SN = "sn"
     # Adjacent Regions
-    Adj = "Adj"
+    Adj = "adj"
     # Subthalamic Nucleus
-    STH = "STH"
+    STH = "sth"
 
 
 
@@ -18885,7 +18885,7 @@ class SpatialProportions(ProvEntity, RelativeFrequencyAnalysisResult):
     gpi: Optional[float] = Field(default=None, description="""Proportion of composition found in Internal Globus Pallidus""", ge=0, le=1, json_schema_extra = { "linkml_meta": {'alias': 'gpi', 'domain_of': ['SpatialProportions']} })
     sn: Optional[float] = Field(default=None, description="""Proportion of composition found in Substantia Nigra""", ge=0, le=1, json_schema_extra = { "linkml_meta": {'alias': 'sn', 'domain_of': ['SpatialProportions']} })
     adj: Optional[float] = Field(default=None, description="""Proportion of composition found in Adjacent Regions""", ge=0, le=1, json_schema_extra = { "linkml_meta": {'alias': 'adj', 'domain_of': ['SpatialProportions']} })
-    sth: Optional[float] = Field(default=None, description="""Proportion of composition found in Subthalamic Nucleus""", json_schema_extra = { "linkml_meta": {'alias': 'sth', 'domain_of': ['SpatialProportions']} })
+    sth: Optional[float] = Field(default=None, description="""Proportion of composition found in Subthalamic Nucleus""", ge=0, le=1, json_schema_extra = { "linkml_meta": {'alias': 'sth', 'domain_of': ['SpatialProportions']} })
     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',
          'domain_of': ['ProvEntity',
                        'CellTypeTaxonomy',