Merge pull request #390 from bgyori/biopax_grounding

BioPAX grounding improvements

indra/databases/chebi_client.py

@@ -7,28 +7,6 @@
     from functools32 import lru_cache
 from indra.util import read_unicode_csv
 
-def read_chebi_to_pubchem():
-    chebi_to_pubchem_file = join(dirname(abspath(__file__)),
-                                 '../resources/chebi_to_pubchem.tsv')
-    csv_reader = read_unicode_csv(chebi_to_pubchem_file, delimiter='\t')
-    chebi_pubchem = {}
-    pubchem_chebi = {}
-    for row in csv_reader:
-        chebi_pubchem[row[0]] = row[1]
-        pubchem_chebi[row[1]] = row[0]
-    return chebi_pubchem, pubchem_chebi
-
-def read_chebi_to_chembl():
-    chebi_to_chembl_file = join(dirname(abspath(__file__)),
-                                '../resources/chebi_to_chembl.tsv')
-    csv_reader = read_unicode_csv(chebi_to_chembl_file, delimiter='\t')
-    chebi_chembl = {}
-    for row in csv_reader:
-        chebi_chembl[row[0]] = row[1]
-    return chebi_chembl
-
-chebi_pubchem, pubchem_chebi = read_chebi_to_pubchem()
-chebi_chembl = read_chebi_to_chembl()
 
 def get_pubchem_id(chebi_id):
     """Return the PubChem ID corresponding to a given ChEBI ID.
@@ -47,6 +25,7 @@ def get_pubchem_id(chebi_id):
     pubchem_id = chebi_pubchem.get(chebi_id)
     return pubchem_id
 
+
 def get_chebi_id_from_pubchem(pubchem_id):
     """Return the ChEBI ID corresponding to a given Pubchem ID.
 
@@ -64,5 +43,80 @@ def get_chebi_id_from_pubchem(pubchem_id):
     chebi_id = pubchem_chebi.get(pubchem_id)
     return chebi_id
 
+
 def get_chembl_id(chebi_id):
+    """Return a ChEMBL ID from a given ChEBI ID.
+
+    Parameters
+    ----------
+    chebi_id : str
+        ChEBI ID to be converted.
+
+    Returns
+    -------
+    chembl_id : str
+        ChEMBL ID corresponding to the given ChEBI ID. If the lookup fails,
+        None is returned.
+    """
     return chebi_chembl.get(chebi_id)
+
+
+def get_chebi_id_from_cas(cas_id):
+    """Return a ChEBI ID corresponding to the given CAS ID.
+
+    Parameters
+    ----------
+    cas_id : str
+        The CAS ID to be converted.
+
+    Parameters
+    ----------
+    chebi_id : str
+        The ChEBI ID corresponding to the given CAS ID. If the lookup
+        fails, None is returned.
+    """
+    return cas_chebi.get(cas_id)
+
+
+def _read_chebi_to_pubchem():
+    chebi_to_pubchem_file = join(dirname(abspath(__file__)),
+                                 '../resources/chebi_to_pubchem.tsv')
+    csv_reader = read_unicode_csv(chebi_to_pubchem_file, delimiter='\t')
+    chebi_pubchem = {}
+    pubchem_chebi = {}
+    for row in csv_reader:
+        chebi_pubchem[row[0]] = row[1]
+        pubchem_chebi[row[1]] = row[0]
+    return chebi_pubchem, pubchem_chebi
+
+
+def _read_chebi_to_chembl():
+    chebi_to_chembl_file = join(dirname(abspath(__file__)),
+                                '../resources/chebi_to_chembl.tsv')
+    csv_reader = read_unicode_csv(chebi_to_chembl_file, delimiter='\t')
+    chebi_chembl = {}
+    for row in csv_reader:
+        chebi_chembl[row[0]] = row[1]
+    return chebi_chembl
+
+
+def _read_cas_to_chebi():
+    cas_to_chebi_file = join(dirname(abspath(__file__)),
+                             '../resources/cas_to_chebi.tsv')
+    csv_reader = read_unicode_csv(cas_to_chebi_file, delimiter='\t')
+    cas_chebi = {}
+    next(csv_reader)
+    for row in csv_reader:
+        cas_chebi[row[0]] = row[1]
+    # These are missing from the resource but appear often, so we map
+    # them manually
+    extra_entries = {'24696-26-2': '17761',
+                     '23261-20-3': '18035',
+                     '165689-82-7': '16618'}
+    cas_chebi.update(extra_entries)
+    return cas_chebi
+
+
+chebi_pubchem, pubchem_chebi = _read_chebi_to_pubchem()
+chebi_chembl = _read_chebi_to_chembl()
+cas_chebi = _read_cas_to_chebi()

indra/resources/README.txt

@@ -75,6 +75,10 @@ grounding_agents.json
 - manually curated list of grounding mappings to INDRA Agents with states 
 (phosphorylation, mutation, etc.)
 
+cas_to_chebi.tsv
+- Manually curated based on common occurrences in Pathway Commons data. Could
+be replaced by a more comprehensive map.
+
 Files that don't need periodical updates
 ========================================
 amino_acids.tsv