def process_all(self):
self._extract_features()
self.get_modifications()
self.get_regulate_activities()
self.get_activity_modification()
self.get_regulate_amounts()
self.get_conversions()
self.get_gap_gef()
self.eliminate_exact_duplicates()
print_validation_report(self.statements)
match.term.entry_name)
if chebi_match and mesh_match:
mappings.add((chebi_match, mesh_match))
chebi_cnts = Counter([m[0] for m in mappings])
mesh_cnts = Counter([m[1] for m in mappings])
with open('chebi_mesh_pred.tsv', 'w') as fh:
for chebi, mesh in mappings:
if chebi_cnts[chebi] == 1 and mesh_cnts[mesh] == 1:
fh.write(
f'chebi\t{chebi[1]}\t{chebi[2]}\tskos:exactMatch\tmesh'
f'\t{mesh[1]}\t{mesh[2]}\tlexical\t0.9\t'
f'https://github.com/indralab/panacea_indra/blob/master/'
f'panacea_indra/make_ctd_tests.py\n')
if __name__ == '__main__':
with open(CTD_CHEMICAL_DISEASE, 'rb') as fh:
stmts = pickle.load(fh)
pain_stmts = filter_objects(stmts, pain_and_children)
print_validation_report(pain_stmts)
for stmt in pain_stmts:
for agent in stmt.real_agent_list():
standardize_agent_name(agent, standardize_refs=True)
with open('chemical_pain_ctd_stmts.pkl', 'wb') as fh:
pickle.dump(pain_stmts, fh)
pain_stmt_tests = [StatementCheckingTest(stmt) for stmt in pain_stmts]
with open('chemical_pain_ctd_tests.pkl', 'wb') as fh:
pickle.dump(pain_stmt_tests, fh)
hash_map[rel_id] = sc.to_json()['matches_hash']
return hash_map
if __name__ == '__main__':
# There are 3 types of relations:
# 'With Drug', 'Vaccine type', 'Entry Receptor'
rels = read_relations()
evs = read_evidences()
with_drug_rels = {
k: v
for k, v in rels.items() if v['relationType'] == 'With Drug'
}
with_drug_stmts = [
get_with_drug_statement(rels[rel_id], evs[rel_id])
for rel_id in with_drug_rels
]
print_validation_report(with_drug_stmts)
test_stmts = [StatementCheckingTest(stmt) for stmt in with_drug_stmts]
rel_to_hash_map = get_rel_hash_map(with_drug_rels, test_stmts)
with open(
os.path.join(here, os.pardir,
'covid19_mitre_tests_rel_to_hash.json'), 'w') as fh:
json.dump(rel_to_hash_map, fh, indent=1)
test_fname = os.path.join(here, os.pardir, 'stmts',
'covid19_mitre_tests.pkl')
with open(test_fname, 'wb') as fh:
pickle.dump(test_stmts, fh)