def get_common_ancestors(id1, id2):
e1 = ssm.get_id(id1.replace(":", "_"))
e2 = ssm.get_id(id2.replace(":", "_"))
#print(id1, id2, e1, e2)
a = ssm.common_ancestors(e1, e2)
a = [ssm.get_name(x) for x in a]
return a
def get_common_ancestors(id1, id2):
"""
:param id1:
:param id2:
:return:
"""
if id1.startswith('CHEBI'):
ssm.semantic_base('bin/DiShIn/chebi.db')
if id1.startswith('HP'):
ssm.semantic_base('bin/DiShIn/hp.db')
if id1.startswith('GO'):
ssm.semantic_base('bin/DiShIn/go.db')
if id1.startswith('DOID'):
ssm.semantic_base('bin/DiShIn/doid.db')
e1 = ssm.get_id(id1.replace(':', '_'))
if id2.startswith('CHEBI'):
ssm.semantic_base('bin/DiShIn/chebi.db')
if id2.startswith('HP'):
ssm.semantic_base('bin/DiShIn/hp.db')
if id2.startswith('GO'):
ssm.semantic_base('bin/DiShIn/go.db')
if id2.startswith('DOID'):
ssm.semantic_base('bin/DiShIn/doid.db')
e2 = ssm.get_id(id2.replace(':', '_'))
a = ssm.common_ancestors(e1, e2)
a = [ssm.get_name(x) for x in a]
return a
def get_path_to_root(id1):
global chebi_cache
if id1 in chebi_cache:
#logging.info("using chebi cache")
return chebi_cache[id1]
else:
e1 = ssm.get_id(id1.replace(":", "_"))
a = ssm.common_ancestors(e1, e1)
a = [ssm.get_name(x) for x in a]
chebi_cache[id1] = a
return a
def get_common_ancestors(id1, id2):
global chebi_cache
if (id1, id2) in chebi_cache:
#logging.info("using chebi cache")
return chebi_cache[(id1, id2)]
else:
e1 = ssm.get_id(id1.replace(":", "_"))
e2 = ssm.get_id(id2.replace(":", "_"))
#print(id1, id2, e1, e2)
a = ssm.common_ancestors(e1, e2)
a = [ssm.get_name(x) for x in a]
chebi_cache[(id1, id2)] = a
return a
def get_path_to_root(entity_id):
"""
:param entity_id:
:return:
"""
if entity_id.startswith('CHEBI'):
ssm.semantic_base('bin/DiShIn/chebi.db')
if entity_id.startswith('HP'):
ssm.semantic_base('bin/DiShIn/hp.db')
if entity_id.startswith('GO'):
ssm.semantic_base('bin/DiShIn/go.db')
if entity_id.startswith('DOID'):
ssm.semantic_base('bin/DiShIn/doid.db')
e1 = ssm.get_id(entity_id.replace(':', '_'))
a = ssm.common_ancestors(e1, e1)
a = [ssm.get_name(x) for x in a]
return a
def get_path_to_root(id1):
e1 = ssm.get_id(id1.replace(":", "_"))
a = ssm.common_ancestors(e1, e1)
a = [ssm.get_name(x) for x in a]
return a
import os
import xml.etree.ElementTree as ET
from chebi_ssm import get_best_chebi_id
import sys
sys.path.append("./")
from DiShIn import ssm
ssm.semantic_base("DiShIn/chebi.db")
chebi_ids = list(ssm.connection.execute("SELECT id FROM entry"))
with open("chebi_pop", 'w') as f:
for cid in chebi_ids:
name = ssm.get_name(cid[0]).replace("_", ':')
if name.startswith("CHEBI"):
ic = ssm.information_content_extrinsic(cid[0])
#ic = ssm.information_content_intrinsic(cid[0])
if ic != 0:
ic = 1 / ic
f.write("url:{}\t{}\n".format(name.replace("CHEBI", "http"), ic))
