def loadOmimFromMgi(self):
# Load all OMIM terms from MGD.
# Where: accid -> OMIM id and term -> OMIM name
query = '''
SELECT t._term_key, t.term, a.accid
FROM VOC_Term t, ACC_Accession a
WHERE t._vocab_key = 44
AND a._object_key = t._term_key
AND a._mgitype_key = 13
AND a._logicaldb_key = 15
AND a.preferred = 1
'''
for r in db.sqliter(query):
omim_id = "OMIM:" + r['accid']
omim_name_parts = r['term'].split(";")
omim_name = omim_name_parts[0].strip()
omim_lines = [('id', omim_id), ('name', omim_name)]
if len(omim_name_parts) > 1:
omim_lines.append( self.formatSynonym(omim_name_parts[1]) )
stanza = ('Term', omim_lines)
self.stanzas.append( stanza )
self.tk2stanza[r['_term_key']] = stanza
# Load secondary ids
query = '''
SELECT a._object_key as _term_key, a.accid
FROM ACC_Accession a
WHERE a._mgitype_key = 13
AND a._logicaldb_key = 15
AND a.preferred = 0
ORDER BY a._object_key
'''
for r in db.sqliter(query):
tk = r['_term_key']
id = "OMIM:" + r['accid']
stanza = self.tk2stanza.get(tk, None)
if stanza:
stanza[1].append( ('alt_id', id) )
# Load synonyms
query = '''
SELECT t._term_key, ms.synonym, ms._synonymtype_key
FROM MGI_Synonym ms, VOC_Term t
WHERE t._vocab_key = 44
AND t._term_key = ms._object_key
ORDER BY t._term_key
'''
for r in db.sqliter(query):
tk = r['_term_key']
stk = r['_synonymtype_key']
st = "exact" if stk==1017 else "broad"
s = self.formatSynonym(r['synonym'], st)
stanza = self.tk2stanza.get(tk, None)
if stanza:
stanza[1].append( s )
def sqliter(self, q):
self.log(str(q))
return db.sqliter(q)