Add additional namespaces in Reach processor

sorgerlab · Apr 4, 2023 · db24187 · db24187
1 parent b358526
commit db24187
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/indra/databases/identifiers.py b/indra/databases/identifiers.py
@@ -35,7 +35,8 @@
 non_registry = {
     'SDIS', 'SCHEM', 'SFAM', 'SCOMP', 'HMS-LINCS', 'NXPFA',
     'OMIM', 'LSPCI', 'UPLOC', 'BFO', 'CCLE', 'CLO', 'GENBANK', 'CALOHA',
-    'DRUGBANK.SALT', 'SMILES', 'NIHREPORTER.PROJECT', 'GOOGLE.PATENT', 'SPINE'
+    'DRUGBANK.SALT', 'SMILES', 'NIHREPORTER.PROJECT', 'GOOGLE.PATENT', 'SPINE',
+    'VO', 'EMAPA', 'INO', 'CIDO', 'OAE', 'OHPI', 'PHIPO'
 }
 
 # These are reverse mappings from identifiers.org namespaces to INDRA

diff --git a/indra/sources/reach/processor.py b/indra/sources/reach/processor.py
@@ -520,6 +520,10 @@ def _get_db_refs(entity_term, organism_priority=None):
                 db_refs['UBERON'] = xr['id']
             elif ns == 'cellosaurus':
                 db_refs['CVCL'] = xr['id']
+            elif ns in ['uo', 'ncit', 'edam.topic', 'ncbitaxon', 'vo', 'bto',
+                        'efo', 'swo', 'iobc', 'ohpi', 'obi', 'ino',
+                        'ido', 'pr']:
+                db_refs[ns.upper()] = xr['id']
             # These name spaces are ignored
             elif ns in ['uaz']:
                 pass