Merge pull request #174 from puja-trivedi/issue168_contenturl_to_bicancore

puja-trivedi · web-flow · commit b0c409b9aafa · 2025-07-01T12:59:15.000-07:00
resolving issue168: moving 'content_url' definition to bican_core
diff --git a/erdiagram-autogen/library_generation.md b/erdiagram-autogen/library_generation.md
@@ -2,7 +2,7 @@
 erDiagram
 DigitalAsset {
     stringList digest  
-    string content_url  
+    stringList content_url  
     string data_type  
     string id  
     iri_type iri  
diff --git a/json-schema-autogen/library_generation.json b/json-schema-autogen/library_generation.json
@@ -1530,8 +1530,11 @@
                     ]
                 },
                 "content_url": {
+                    "items": {
+                        "type": "string"
+                    },
                     "type": [
-                        "string",
+                        "array",
                         "null"
                     ]
                 },
diff --git a/jsonld-context-autogen/anatomical_structure.context.jsonld b/jsonld-context-autogen/anatomical_structure.context.jsonld
@@ -209,6 +209,9 @@
       "value": {
          "@id": "value"
       },
+      "content_url": {
+         "@id": "schema:url"
+      },
       "creation_date": {
          "@type": "xsd:date",
          "@id": "biolink:creation_date"
diff --git a/jsonld-context-autogen/genome_annotation.context.jsonld b/jsonld-context-autogen/genome_annotation.context.jsonld
@@ -324,6 +324,10 @@
          "@type": "@id",
          "@id": "biolink:related_to_at_instance_level"
       },
+      "revision_of": {
+         "@type": "@id",
+         "@id": "revision_of"
+      },
       "rights": {
          "@id": "biolink:rights"
       },
@@ -444,6 +448,9 @@
       },
       "ThingWithTaxon": {
          "@id": "biolink:ThingWithTaxon"
+      },
+      "VersionedNamedThing": {
+         "@id": "VersionedNamedThing"
       }
    }
 }
diff --git a/jsonld-context-autogen/library_generation.context.jsonld b/jsonld-context-autogen/library_generation.context.jsonld
@@ -257,7 +257,7 @@
          "@id": "value"
       },
       "content_url": {
-         "@id": "content_url"
+         "@id": "schema:url"
       },
       "creation_date": {
          "@type": "xsd:date",
@@ -463,6 +463,10 @@
          "@type": "@id",
          "@id": "biolink:related_to_at_instance_level"
       },
+      "revision_of": {
+         "@type": "@id",
+         "@id": "revision_of"
+      },
       "rights": {
          "@id": "biolink:rights"
       },
@@ -657,6 +661,9 @@
       },
       "TissueSample": {
          "@id": "TissueSample"
+      },
+      "VersionedNamedThing": {
+         "@id": "VersionedNamedThing"
       }
    }
 }
diff --git a/linkml-schema/bican_core.yaml b/linkml-schema/bican_core.yaml
@@ -53,6 +53,10 @@ slots:
   checksum algorithm:
     description: The type of cryptographic hash function used to calculate the checksum value.
     range: DigestType
+  
+  content_url:
+    slot_uri: schema:url
+    multivalued: true
 
 enums:
   DigestType:
diff --git a/linkml-schema/bke_taxonomy.yaml b/linkml-schema/bke_taxonomy.yaml
@@ -6,6 +6,7 @@ id: https:/w3id.org/brain-bican/bke-taxonomy
 imports:
 - bican_biolink
 - bican_prov
+- bican_core
 - genome_annotation
 - anatomical_structure
 - linkml:types
@@ -467,6 +468,7 @@ classes:
         local_names:
           local_name_value: url
           local_name_source: allen
+        from_schema: bican_core
       xref:
         local_names:
           local_name_value: unique_id
@@ -574,6 +576,7 @@ classes:
         local_names:
           local_name_value: url
           local_name_source: allen
+        from_schema: bican_core
       xref:
         local_names:
           local_name_value: unique_id
diff --git a/linkml-schema/genome_annotation.yaml b/linkml-schema/genome_annotation.yaml
@@ -85,10 +85,6 @@ slots:
       - range: BioType
       - range: string
 
-  content_url:
-    slot_uri: schema:url
-    multivalued: true
-
   authority:
     description: The organization responsible for publishing the data. 
     range: AuthorityType
diff --git a/linkml-schema/library_generation.yaml b/linkml-schema/library_generation.yaml
@@ -1822,9 +1822,6 @@ enums:
       years:
         description: years
         meaning: NIMP:PD-AVAVEV39
-slots:
-  content_url:
-    from_schema: https://identifiers.org/brain-bican/library-generation-schema
 classes:
   Donor:
     description: A person or organism that is the source of a biological sample for
@@ -2962,7 +2959,8 @@ classes:
         range: LibraryPool
       digest:
         from_schema: bican_core
-      content_url: {}
+      content_url:
+        from_schema: bican_core
     attributes:
       data_type:
         description: The type of data in the file.
diff --git a/linkml-schema/source_bke_taxonomy/gsheet_output/Schema.tsv b/linkml-schema/source_bke_taxonomy/gsheet_output/Schema.tsv
@@ -1,4 +1,4 @@
 Schema	uri	Description	Schema Prefix	Imports	Title
 > schema	id	description	default_prefix	imports	title
 >				internal_separator: "|"	
-BKETaxonomy	https:/w3id.org/brain-bican/bke-taxonomy	The BKE Taxonomy Schema represents the structure of classifications of cell types and their hierarchical relationships in the mammalian brain.	bican	bican_biolink|bican_prov|genome_annotation|anatomical_structure	BKE Taxonomy Schema
+BKETaxonomy	https:/w3id.org/brain-bican/bke-taxonomy	The BKE Taxonomy Schema represents the structure of classifications of cell types and their hierarchical relationships in the mammalian brain.	bican	bican_biolink|bican_prov|bican_core|genome_annotation|anatomical_structure	BKE Taxonomy Schema
diff --git a/linkml-schema/source_bke_taxonomy/gsheet_output/Slots.tsv b/linkml-schema/source_bke_taxonomy/gsheet_output/Slots.tsv
@@ -1,52 +1,52 @@
-LinkML Class Name	LinkML Slot or Attribute Name	example	Definition	Nullable	Permissible Values	Data Type	Integer MIN Value	BKE Local Name	Local Name Source
-> class	slot	examples             	description	ignore	ignore	range	minimum_value	local_names	local_names
->								inner_key: local_name_value	inner_key: local_name_source
-Abbreviation	id		( database GUID)	FALSE		string			
-Abbreviation	term	IT	An abbreviation term.	FALSE		string			
-Abbreviation	meaning	intratelencephalic-projecting glutamatergic cortical neuron	The meaning of an abbreviation term.	FALSE		string			
-Abbreviation	entity_type	cell type	The entity type which the abbreviation term denotes.	FALSE	cell type, gene, structure	string			
-Abbreviation	xref							unique_id	allen
-CellTypeSet	id		( database GUID)	FALSE		string			
-CellTypeSet	accession_id	CCN20230722_CLAS	A provider assigned accession identifier for the cell type set.	FALSE		string			
-CellTypeSet	name	class	Name of the cell type set taxonomy.	FALSE		string			
-CellTypeSet	description	The top level of cell type definition in the mouse whole brain taxonomy. It is primarily determined by broad brain region and neurotransmitter type. All cells within a subclass belong to the same class. Class provides a broader categorization of cell types.	Description of the cell type set.	FALSE		string			
-CellTypeSet	cell_type_set_type	taxonomic_level	A tag denoting the type or purpose of the cell type set.	FALSE	taxonomic level, neighborhood	string		type	allen
-CellTypeSet	order	1	The priority or display order of the cell type set among all other sets of the same type.	TRUE		integer	0	order_idx	allen
-CellTypeSet	xref							unique_id	allen
-CellTypeTaxon	id		( database GUID)	FALSE		string			
-CellTypeTaxon	accession_id	CS20230722_CLAS_11	A provider assigned accession identifier for the cell type taxon.	FALSE		string			
-CellTypeTaxon	name	11 CNU-HYa GABA	Name of the cell type taxon.	FALSE		string			
-CellTypeTaxon	order	11	The priority or display order of the cell type taxon among all other taxons in the taxonomy.	TRUE		integer	0	order_idx	allen
-CellTypeTaxon	description		Description of the cell type taxon (optional).	TRUE		string			
-CellTypeTaxon	number_of_cells		The aggregated number of cells that defines the cell type taxon.	FALSE		integer	0		
-CellTypeTaxon	xref							unique_id	allen
-CellTypeTaxonomy	id		( database GUID)	FALSE		string			
-CellTypeTaxonomy	created_at		The creation date of the cell type taxonomy.	FALSE		datetime			
-CellTypeTaxonomy	accession_id	CCN20230722	A provider assigned accession identifier for the taxonomy.	FALSE		string			
-CellTypeTaxonomy	name	AIT21.0	Name of the cell type taxonomy.	FALSE		string			
-CellTypeTaxonomy	description		Description of the cell type taxonomy.	FALSE		string			
-CellTypeTaxonomy	xref							unique_id	allen
-Cluster	id		( database GUID)	FALSE		string			
-Cluster	accession_id	CS20230722_1019	A provider assigned accession identifier for the cluster which is unique amongs all clusters in cluster set.	FALSE		string			
-Cluster	name	1019	Name of the cluster.	FALSE		string			
-Cluster	number_of_observations	448	The number of observations in the cluster.	TRUE		integer	0		
-Cluster	xref							unique_id	allen
-ClusterSet	id		( database GUID)	FALSE		string			
-ClusterSet	created_at		The creation date of the cluster set.	FALSE		datetime			
-ClusterSet	accession_id		A provider assigned accession identifier for the cluster set.	FALSE		string			
-ClusterSet	name		Name of the cluster set.	TRUE		string			
-ClusterSet	description		Description of the cluster set.	TRUE		string			
-ClusterSet	xref							unique_id	allen
-ColorPalette	id		( database GUID)	FALSE		string			
-ColorPalette	name		Name of the color palette.	FALSE		string			
-ColorPalette	description		Description of the color palette.	FALSE		string			
-ColorPalette	xref							unique_id	allen
-DisplayColor	id		( database GUID)	FALSE		string			
-DisplayColor	color_hex_triplet	#450099	A hex string representing the display color for an associated entity.	FALSE		string			
-DisplayColor	xref							unique_id	allen
-MatrixFile	content_url							url	allen
-MatrixFile	xref							unique_id	allen
-ObservationMatrix	content_url							url	allen
-ObservationMatrix	xref							unique_id	allen
-ObservationRow	label								
-ObservationRow	xref							unique_id	allen
+LinkML Class Name	LinkML Slot or Attribute Name	from_schema	example	Definition	Nullable	Permissible Values	Data Type	Integer MIN Value	BKE Local Name	Local Name Source
+> class	slot	from_schema	examples             	description	ignore	ignore	range	minimum_value	local_names	local_names
+>									inner_key: local_name_value	inner_key: local_name_source
+Abbreviation	id			( database GUID)	FALSE		string			
+Abbreviation	term		IT	An abbreviation term.	FALSE		string			
+Abbreviation	meaning		intratelencephalic-projecting glutamatergic cortical neuron	The meaning of an abbreviation term.	FALSE		string			
+Abbreviation	entity_type		cell type	The entity type which the abbreviation term denotes.	FALSE	cell type, gene, structure	string			
+Abbreviation	xref								unique_id	allen
+CellTypeSet	id			( database GUID)	FALSE		string			
+CellTypeSet	accession_id		CCN20230722_CLAS	A provider assigned accession identifier for the cell type set.	FALSE		string			
+CellTypeSet	name		class	Name of the cell type set taxonomy.	FALSE		string			
+CellTypeSet	description		The top level of cell type definition in the mouse whole brain taxonomy. It is primarily determined by broad brain region and neurotransmitter type. All cells within a subclass belong to the same class. Class provides a broader categorization of cell types.	Description of the cell type set.	FALSE		string			
+CellTypeSet	cell_type_set_type		taxonomic_level	A tag denoting the type or purpose of the cell type set.	FALSE	taxonomic level, neighborhood	string		type	allen
+CellTypeSet	order		1	The priority or display order of the cell type set among all other sets of the same type.	TRUE		integer	0	order_idx	allen
+CellTypeSet	xref								unique_id	allen
+CellTypeTaxon	id			( database GUID)	FALSE		string			
+CellTypeTaxon	accession_id		CS20230722_CLAS_11	A provider assigned accession identifier for the cell type taxon.	FALSE		string			
+CellTypeTaxon	name		11 CNU-HYa GABA	Name of the cell type taxon.	FALSE		string			
+CellTypeTaxon	order		11	The priority or display order of the cell type taxon among all other taxons in the taxonomy.	TRUE		integer	0	order_idx	allen
+CellTypeTaxon	description			Description of the cell type taxon (optional).	TRUE		string			
+CellTypeTaxon	number_of_cells			The aggregated number of cells that defines the cell type taxon.	FALSE		integer	0		
+CellTypeTaxon	xref								unique_id	allen
+CellTypeTaxonomy	id			( database GUID)	FALSE		string			
+CellTypeTaxonomy	created_at			The creation date of the cell type taxonomy.	FALSE		datetime			
+CellTypeTaxonomy	accession_id		CCN20230722	A provider assigned accession identifier for the taxonomy.	FALSE		string			
+CellTypeTaxonomy	name		AIT21.0	Name of the cell type taxonomy.	FALSE		string			
+CellTypeTaxonomy	description			Description of the cell type taxonomy.	FALSE		string			
+CellTypeTaxonomy	xref								unique_id	allen
+Cluster	id			( database GUID)	FALSE		string			
+Cluster	accession_id		CS20230722_1019	A provider assigned accession identifier for the cluster which is unique amongs all clusters in cluster set.	FALSE		string			
+Cluster	name		1019	Name of the cluster.	FALSE		string			
+Cluster	number_of_observations		448	The number of observations in the cluster.	TRUE		integer	0		
+Cluster	xref								unique_id	allen
+ClusterSet	id			( database GUID)	FALSE		string			
+ClusterSet	created_at			The creation date of the cluster set.	FALSE		datetime			
+ClusterSet	accession_id			A provider assigned accession identifier for the cluster set.	FALSE		string			
+ClusterSet	name			Name of the cluster set.	TRUE		string			
+ClusterSet	description			Description of the cluster set.	TRUE		string			
+ClusterSet	xref								unique_id	allen
+ColorPalette	id			( database GUID)	FALSE		string			
+ColorPalette	name			Name of the color palette.	FALSE		string			
+ColorPalette	description			Description of the color palette.	FALSE		string			
+ColorPalette	xref								unique_id	allen
+DisplayColor	id			( database GUID)	FALSE		string			
+DisplayColor	color_hex_triplet		#450099	A hex string representing the display color for an associated entity.	FALSE		string			
+DisplayColor	xref								unique_id	allen
+MatrixFile	content_url	bican_core							url	allen
+MatrixFile	xref								unique_id	allen
+ObservationMatrix	content_url	bican_core							url	allen
+ObservationMatrix	xref								unique_id	allen
+ObservationRow	label									
+ObservationRow	xref								unique_id	allen
diff --git a/linkml-schema/source_library_generation/gsheet.yaml b/linkml-schema/source_library_generation/gsheet.yaml
@@ -4,15 +4,15 @@ sheets:
     gid: "1511023596"
   - name: "Relations"
     gid: "503493337"
-  - name: "LocalNames"
-    gid: "1773206664"
   - name: "Slots"
+    gid: "1773206664"
+  - name: "Attributes"
     gid: "990672642"
+  - name: "ValueSets"
+    gid: "475538568"
   - name: "Subsets"
     gid: "1299830797"
   - name: "Prefixes"
     gid: "621222810"
   - name: "Schema"
     gid: "1383357145"
-  - name: "ValueSets"
-    gid: "475538568"
diff --git a/linkml-schema/source_library_generation/gsheet_output/Attributes.tsv b/linkml-schema/source_library_generation/gsheet_output/Attributes.tsv
diff --git a/linkml-schema/source_library_generation/gsheet_output/LocalNames.tsv b/linkml-schema/source_library_generation/gsheet_output/LocalNames.tsv
diff --git a/linkml-schema/source_library_generation/gsheet_output/Slots.tsv b/linkml-schema/source_library_generation/gsheet_output/Slots.tsv
diff --git a/models_py-autogen/bke_taxonomy.py b/models_py-autogen/bke_taxonomy.py
diff --git a/models_py-autogen/genome_annotation.py b/models_py-autogen/genome_annotation.py
diff --git a/models_py-autogen/library_generation.py b/models_py-autogen/library_generation.py

Original file line number	Diff line number	Diff line change
`@@ -1530,8 +1530,11 @@`
`1530`	`1530`	`]`
`1531`	`1531`	`},`
`1532`	`1532`	`"content_url": {`
	`1533`	`+ "items": {`
	`1534`	`+ "type": "string"`
	`1535`	`+ },`
`1533`	`1536`	`"type": [`
`1534`		`- "string",`
	`1537`	`+ "array",`
`1535`	`1538`	`"null"`
`1536`	`1539`	`]`
`1537`	`1540`	`},`