Merge branch 'issue191' of https://github.com/puja-trivedi/models into issue191

Author: puja-trivedi

jsonld-context-autogen/bke_taxonomy.context.jsonld

@@ -88,7 +88,7 @@
          "@prefix": true
       },
       "NBO-PROPERTY": "http://purl.obolibrary.org/obo/nbo#",
-      "NCBIGene": "https://www.ncbi.nlm.nih.gov/gene/",
+      "NCBIGene": "http://identifiers.org/ncbigene/",
       "NCBITaxon": "https://www.ncbi.nlm.nih.gov/taxonomy/",
       "NCIT": {
          "@id": "http://purl.obolibrary.org/obo/NCIT_",

jsonld-context-autogen/genome_annotation.context.jsonld

@@ -90,10 +90,7 @@
       "NBO-PROPERTY": "http://purl.obolibrary.org/obo/nbo#",
       "NCBIAssembly": "https://www.ncbi.nlm.nih.gov/assembly/",
       "NCBIGene": "http://identifiers.org/ncbigene/",
-      "NCBITaxon": {
-         "@id": "http://purl.obolibrary.org/obo/NCBITaxon_",
-         "@prefix": true
-      },
+      "NCBITaxon": "https://www.ncbi.nlm.nih.gov/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_",
@@ -297,10 +290,7 @@
       "in_taxon_label": {
          "@id": "biolink:in_taxon_label"
       },
-      "iri": {
-         "@type": "xsd:anyURI",
-         "@id": "biolink:iri"
-      },
+      "iri": "@type",
       "license": {
          "@id": "biolink:license"
       },
@@ -349,10 +339,7 @@
       "version": {
          "@id": "biolink:version"
       },
-      "xref": {
-         "@type": "xsd:anyURI",
-         "@id": "biolink:xref"
-      },
+      "xref": "@type",
       "Activity": {
          "@id": "biolink:Activity"
       },

models_py-autogen/genome_annotation.py

@@ -72,12 +72,12 @@ def __contains__(self, key:str) -> bool:
      'name': 'genome-annotation-schema',
      'prefixes': {'NCBIAssembly': {'prefix_prefix': 'NCBIAssembly',
                                    'prefix_reference': 'https://www.ncbi.nlm.nih.gov/assembly/'},
+                  'NCBITaxon': {'prefix_prefix': 'NCBITaxon',
+                                'prefix_reference': 'https://www.ncbi.nlm.nih.gov/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',