Merge pull request #73 from puja-trivedi/20240930_create_bican_core_m…

…odels

Create bican core models

.github/workflows/generate_yaml_model.yaml

@@ -36,7 +36,7 @@ jobs:
       - name: Generate yaml model
         run: |
           cd linkml-schema
-          bkbit schema2model -o library_generation.yaml --template source_library_generation/classes_base.yaml --gsheet --gsheet-download-dir source_library_generation/gsheet_output  source_library_generation/gsheet.yaml  --no-inlined
+          bkbit schema2model -o library_generation.yaml --gsheet --gsheet-download-dir source_library_generation/gsheet_output  source_library_generation/gsheet.yaml  --no-inlined
           cd ..
 
       - name: Adding other model representations to git

linkml-schema/bican_biolink.yaml

@@ -1,6 +1,8 @@
-name: Biolink-Model
-description: Entity and association taxonomy and datamodel for life-sciences data
-id: https://w3id.org/biolink/biolink-model
+id: https://w3id.org/biolink/bican-biolink-schema
+name: bican-biolink-schema
+title: BICAN Biolink Schema
+description: |-
+  The BICAN Biolink schema contains a subset of classes from the Biolink Model that are frequently used in BICAN schemas. The Biolink model represents life-sciences data and defines entities and association taxonomy classes.
 version: 4.2.0-rc.2
 imports:
 - linkml:types

linkml-schema/bican_core.yaml

@@ -0,0 +1,55 @@
+id: https://identifiers.org/brain-bican/bican-core-schema
+name: bican-core-schema
+title: BICAN Core Schema
+description: |-
+  The BICAN Core schema is designed to represent classes, slots, and enums that are frequently used in BICAN schemas.
+  
+prefixes:
+  linkml: https://w3id.org/linkml/
+  bican: https://identifiers.org/brain-bican/vocab/
+  spdx: http://spdx.org/rdf/terms#
+
+
+imports:
+  - linkml:types
+  - bican_biolink
+
+default_range: string
+default_prefix: bican
+
+classes:
+  checksum:
+    is_a: entity
+    description: >-
+      Checksum values associated with digital entities.
+    slots:
+      - checksum algorithm
+    attributes:
+      value: 
+        description: The checksum value obtained from a specific cryotographic hash function.
+
+slots:
+  digest:
+    description: Stores checksum information. 
+    multivalued: true
+    inlined_as_list: true
+    any_of:
+      - range: checksum
+      - range: string
+
+  checksum algorithm:
+    description: The type of cryptographic hash function used to calculate the checksum value.
+    range: DigestType
+
+enums:
+  DigestType:
+    permissible_values:
+      spdx:checksumAlgorithm_sha1:
+        title: SHA1
+        meaning: spdx:checksumAlgorithm_sha1
+      spdx:checksumAlgorithm_md5:
+        title: MD5
+        meaning: spdx:checksumAlgorithm_md5
+      spdx:checksumAlgorithm_sha256:
+        title: SHA256
+        meaning: spdx:checksumAlgorithm_sha256

linkml-schema/source_library_generation/classes_base.yaml → linkml-schema/bican_prov.yaml

@@ -1,3 +1,21 @@
+id: https://identifiers.org/brain-bican/genome-prov-schema
+name: bican-prov-schema
+title: BICAN Prov Schema
+description: |-
+  The BICAN Prov schema contains a subset of classes from the Prov Data Model (PROV-DM) that are frequently used in BICAN schemas.
+
+prefixes:
+  linkml: https://w3id.org/linkml/
+  bican: https://identifiers.org/brain-bican/vocab/
+  schema: http://schema.org/
+  prov: http://www.w3.org/ns/prov#
+
+imports:
+  - linkml:types
+
+default_range: string
+default_prefix: bican
+
 classes:
   ProvActivity:
     mixin: true

linkml-schema/genome_annotation.yaml

@@ -7,15 +7,14 @@ description: |-
 prefixes:
   linkml: https://w3id.org/linkml/
   bican: https://identifiers.org/brain-bican/vocab/
-  spdx: http://spdx.org/rdf/terms#
   schema: http://schema.org/
   ncbi: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=
   NCBIAssembly: https://www.ncbi.nlm.nih.gov/assembly/
-  prov: http://www.w3.org/ns/prov#
 
 imports:
   - linkml:types
   - bican_biolink
+  - bican_core
 default_range: string
 default_prefix: bican
 
@@ -70,16 +69,6 @@ classes:
       - version
       - strain
 
-  checksum:
-    is_a: entity
-    description: >-
-      Checksum values associated with digital entities.
-    slots:
-      - checksum algorithm
-    attributes:
-      value: 
-        description: The checksum value obtained from a specific cryotographic hash function.
-
   annotation collection:
     tree_root: true
     attributes:
@@ -103,14 +92,6 @@ slots:
       - range: BioType
       - range: string
 
-  digest:
-    description: Stores checksum information. 
-    multivalued: true
-    inlined_as_list: true
-    any_of:
-      - range: checksum
-      - range: string
-
   content_url:
     slot_uri: schema:url
     multivalued: true
@@ -119,10 +100,6 @@ slots:
     description: The organization responsible for publishing the data. 
     range: AuthorityType
 
-  checksum algorithm:
-    description: The type of cryptographic hash function used to calculate the checksum value.
-    range: DigestType
-
   source id:
     description: The authority specific identifier. 
     slot_uri: schema:identifier
@@ -132,18 +109,6 @@ slots:
 
 
 enums:
-  DigestType:
-    permissible_values:
-      spdx:checksumAlgorithm_sha1:
-        title: SHA1
-        meaning: spdx:checksumAlgorithm_sha1
-      spdx:checksumAlgorithm_md5:
-        title: MD5
-        meaning: spdx:checksumAlgorithm_md5
-      spdx:checksumAlgorithm_sha256:
-        title: SHA256
-        meaning: spdx:checksumAlgorithm_sha256
-
   BioType:
     permissible_values:
       protein_coding:

linkml-schema/source_library_generation/gsheet.yaml

@@ -12,5 +12,7 @@ sheets:
     gid: "1299830797"
   - name: "Prefixes"
     gid: "621222810"
+  - name: "Schema"
+    gid: "1383357145"
   - name: "ValueSets"
     gid: "475538568"

pyproject.toml

@@ -4,12 +4,12 @@ requires = ["setuptools >= 61.0", "setuptools-scm"]
 build-backend = 'setuptools.build_meta'
 
 [project]
-name = "atlaskb-models"
+name = "models"
 version = "0.0.1"
 authors = [
-  { name="atlaskb developers"},
+  { name="brain-bican-models developers"},
 ]
-description = "A library for atlaskb data models"
+description = "A library for brain-bican data models"
 readme = "README.md"
 requires-python = ">=3.7"
 classifiers = [
@@ -31,4 +31,4 @@ docs = [
 ]
 
 [project.urls]
-"Homepage" = "https://github.com/atlaskb/models"
+"Homepage" = "https://brain-bican.github.io/models/"