Merge pull request #192 from puja-trivedi/issue191

updating genome_annotation schema

Author: puja-trivedi

jsonld-context-autogen/bke_taxonomy.context.jsonld

@@ -89,10 +89,7 @@
       },
       "NBO-PROPERTY": "http://purl.obolibrary.org/obo/nbo#",
       "NCBIGene": "http://identifiers.org/ncbigene/",
-      "NCBITaxon": {
-         "@id": "http://purl.obolibrary.org/obo/NCBITaxon_",
-         "@prefix": true
-      },
+      "NCBITaxon": "http://identifiers.org/taxonomy/",
       "NCIT": {
          "@id": "http://purl.obolibrary.org/obo/NCIT_",
          "@prefix": true
@@ -221,7 +218,10 @@
          },
          "@id": "authority"
       },
-      "category": "@type",
+      "category": {
+         "@type": "xsd:anyURI",
+         "@id": "biolink:category"
+      },
       "cell_type_set_type": {
          "@id": "cell_type_set_type"
       },
@@ -764,4 +764,5 @@
          "@id": "VersionedNamedThing"
       }
    }
-}
+}
+

jsonld-context-autogen/genome_annotation.context.jsonld

@@ -88,12 +88,9 @@
          "@prefix": true
       },
       "NBO-PROPERTY": "http://purl.obolibrary.org/obo/nbo#",
-      "NCBIAssembly": "https://www.ncbi.nlm.nih.gov/assembly/",
+      "NCBIAssembly": "http://identifiers.org/assembly/",
       "NCBIGene": "http://identifiers.org/ncbigene/",
-      "NCBITaxon": {
-         "@id": "http://purl.obolibrary.org/obo/NCBITaxon_",
-         "@prefix": true
-      },
+      "NCBITaxon": "http://identifiers.org/taxonomy/",
       "NCIT": {
          "@id": "http://purl.obolibrary.org/obo/NCIT_",
          "@prefix": true
@@ -176,10 +173,6 @@
       "gff3": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#",
       "gpi": "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#",
       "linkml": "https://w3id.org/linkml/",
-      "ncbi": {
-         "@id": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=",
-         "@prefix": true
-      },
       "oboInOwl": "http://www.geneontology.org/formats/oboInOwl#",
       "orphanet": {
          "@id": "http://www.orpha.net/ORDO/Orphanet_",
@@ -214,7 +207,10 @@
          },
          "@id": "authority"
       },
-      "category": "@type",
+      "category": {
+         "@type": "xsd:anyURI",
+         "@id": "biolink:category"
+      },
       "checksum_algorithm": {
          "@context": {
             "text": "skos:notation",
@@ -453,4 +449,5 @@
          "@id": "VersionedNamedThing"
       }
    }
-}
+}
+

linkml-schema/genome_annotation.yaml

@@ -8,8 +8,9 @@ prefixes:
   linkml: https://w3id.org/linkml/
   bican: https://identifiers.org/brain-bican/vocab/
   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/
+  NCBIAssembly: http://identifiers.org/assembly/
+  NCBIGene: http://identifiers.org/ncbigene/ 
+  NCBITaxon: http://identifiers.org/taxonomy/
 
 imports:
   - linkml:types

models_py-autogen/genome_annotation.py

@@ -71,13 +71,15 @@ def __contains__(self, key:str) -> bool:
      'imports': ['linkml:types', 'bican_biolink', 'bican_core'],
      'name': 'genome-annotation-schema',
      'prefixes': {'NCBIAssembly': {'prefix_prefix': 'NCBIAssembly',
-                                   'prefix_reference': 'https://www.ncbi.nlm.nih.gov/assembly/'},
+                                   'prefix_reference': 'http://identifiers.org/assembly/'},
+                  'NCBIGene': {'prefix_prefix': 'NCBIGene',
+                               'prefix_reference': 'http://identifiers.org/ncbigene/'},
+                  'NCBITaxon': {'prefix_prefix': 'NCBITaxon',
+                                'prefix_reference': 'http://identifiers.org/taxonomy/'},
                   'bican': {'prefix_prefix': 'bican',
                             'prefix_reference': 'https://identifiers.org/brain-bican/vocab/'},
                   'linkml': {'prefix_prefix': 'linkml',
                              'prefix_reference': 'https://w3id.org/linkml/'},
-                  'ncbi': {'prefix_prefix': 'ncbi',
-                           'prefix_reference': 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id='},
                   'schema': {'prefix_prefix': 'schema',
                              'prefix_reference': 'http://schema.org/'}},
      'source_file': 'genome_annotation.yaml',