def find_compound_by_unii(self, unii):
"""
Find compound by a unii
"""
# slect * is not a good practice rather than * distinct listing is better.
id = "UNII:" + unii
query = """
select
UNII.UNII,
UNII.PT,
UNII.RN,
UNII.NCIT,
UNII.PUBCHEM,
UNII.INCHIKEY,
UNII.SMILES,
RXNCONSO.CODE
from RXNCONSO
join UNII on RXNCONSO.CODE = UNII.UNII
where (UNII.UNII = ?)
"""
cur = connection.execute(
query,
(unii,
)) # in order to make the varible as a tuple of one explicitely.
compound = Element(id=id,
biolink_class='ChemicalSubstance',
identifiers={'unii': unii},
attributes=self.find_compound_attributes(unii),
connections=[],
source=self.info.name)
# TODO issue SQL query and collect results
# for each hit (i.e., of the same drug name, an unlikely but possible occurrence)
for row in cur.fetchall():
if (row['UNII'] == unii):
compound.names_synonyms = [
Names(name=row['PT'], synonyms=[], source=UNIISOURCE)
] # add names & synonyms from the database
compound.identifiers = {
'unii': id,
'cas': 'CAS:' + row['RN'],
'ncit': 'NCIT:' + row['NCIT'],
'inchikey': row['INCHIKEY'],
'smiles': row['SMILES'],
'pubchem': 'CID:' + str(row['pubchem'])
}
return [compound]
def get_or_create_indication(self, row, indications, indication_list):
mesh_id = MESH+row['mesh_id']
efo_id = row['efo_id']
if mesh_id is not None and mesh_id in indications:
return indications[mesh_id]
if efo_id is not None and efo_id in indications:
return indications[efo_id]
id = mesh_id if mesh_id is not None else efo_id
names = Names(name = row['mesh_heading'],synonyms=[],source=SOURCE)
indication = Element(id=id, biolink_class=DISEASE,connections=[])
indication.identifiers={'efo':[]}
indication.names_synonyms=[names]
indication.source = self.info.name
if mesh_id is not None:
indications[mesh_id] = indication
indication.identifiers['mesh'] = mesh_id
if efo_id is not None:
indications[efo_id] = indication
indication_list.append(indication)
return indication
