Added the VMH database to the dictionaries #27 #36

Additionally, sorted all dictionary entries alphabetically.
draeger-lab · Nov 17, 2022 · 0cade80 · 0cade80
1 parent b5023df
commit 0cade80
Showing 1 changed file with 22 additions and 16 deletions.
diff --git a/refinegems/cvterms.py b/refinegems/cvterms.py
@@ -5,43 +5,49 @@
 """
 from libsbml import CVTerm, BIOLOGICAL_QUALIFIER, BQB_IS
 
-metabol_db_dict = {'BIGG': 'bigg.metabolite:',
+metabol_db_dict = {
+                   'BIGG': 'bigg.metabolite:',
+                   'BIOCYC': 'metacyc.compound:',
+                   'BioCyc': 'metacyc.compound:',
                    'BRENDA': 'brenda:',
                    'CHEBI': 'CHEBI:',
                    'ChEBI': 'CHEBI:',
+                   'HMDB': 'hmdb:HMDB',
+                   'Human Metabolome Database': 'hmdb:HMDB',
                    'INCHI': 'inchi:',
                    'InChI': 'inchi:',
                    'KEGG': 'kegg.compound:',
                    #'KEGG Compound': 'kegg.compound:',
                    'METACYC': 'metacyc.compound:',
                    'MXNREF': 'metanetx.chemical:',
                    'MetaNetX': 'metanetx.chemical:',
-                   'SEED': 'seed.compound:',
-                   #'UPA': 'unipathway.compound:', #closed due to financial issues
-                   #'UniPathway Compound': 'unipathway.compound:',
-                   'HMDB': 'hmdb:HMDB',
-                   'Human Metabolome Database': 'hmdb:HMDB',
+                   'PUBCHEM': 'pubchem.compound:',
                    'REACTOME': 'reactome:',
                    'Reactome': 'reactome:',
-                   'BIOCYC': 'metacyc.compound:',
-                   'BioCyc': 'metacyc.compound:',
-                   'PUBCHEM': 'pubchem.compound:',}
+                   'SEED': 'seed.compound:',
+                   #'UPA': 'unipathway.compound:', #closed due to financial issues
+                   #'UniPathway Compound': 'unipathway.compound:'
+                   'VMH': 'vmhmetabolite:'
+                  }
 
-reaction_db_dict = {'BIGG': 'bigg.reaction:',
+reaction_db_dict = {
+                    'BIGG': 'bigg.reaction:',
+                    'BioCyc': 'metacyc.reaction:',
                     'BRENDA': 'brenda:',
+                    'EC': 'ec-code:',
+                    'HMDB': 'hmdb:HMDB',
                     'KEGG': 'kegg.reaction:',
                     'METACYC': 'metacyc.reaction:',
-                    'BioCyc': 'metacyc.reaction:',
                     'MXNREF': 'metanetx.reaction:',
                     'MetaNetX': 'metanetx.reaction:',
-                    'SEED': 'seed.reaction:',
-                    #'UPA': 'unipathway.reaction:',
-                    #'UniPathway Reaction': 'unipathway.reaction:',
-                    'HMDB': 'hmdb:HMDB',
                     'REACTOME': 'reactome:',
                     'Reactome': 'reactome:',
                     'RHEA': 'rhea:',
-                    'EC': 'ec-code:'}
+                    'SEED': 'seed.reaction:',
+                    #'UPA': 'unipathway.reaction:',
+                    #'UniPathway Reaction': 'unipathway.reaction:'
+                    'VMH': 'vmhreaction:'
+                   }
 
 gene_db_dict = {'NCBI': 'ncbiprotein:'}