def clean_ner_result(result_file):
ord_mention_list = list()
med_mention_list = list()
fin = open(result_file, 'rb')
for line in fin:
line = line.strip()
if len(line) == 0:
continue
vals = line.strip().split('\t')
span = (int(vals[0]), int(vals[1]))
mention = Mention()
mention.span = span
if len(vals) == 4:
mention.mtype = vals[3]
ord_mention_list.append(mention)
else:
mention.mtype = vals[3]
if vals[4].startswith('MESH'):
mention.mesh_id = vals[4][5:]
elif vals[4].startswith('CHEBI'):
mention.chebi_id = int(vals[4][6:])
med_mention_list.append(mention)
fin.close()
merged_mention_list = list()
Mention.merge_mention_list(med_mention_list, merged_mention_list)
Mention.merge_mention_list(ord_mention_list, merged_mention_list)
return merged_mention_list
def clean_ner_result(result_file):
ord_mention_list = list()
med_mention_list = list()
fin = open(result_file, 'rb')
for line in fin:
line = line.strip()
if len(line) == 0:
continue
vals = line.strip().split('\t')
# TODO
if vals[3] == 'Disease' or vals[3] == 'Chemical':
span = (int(vals[0]), int(vals[1]) - 1)
else:
span = (int(vals[0]), int(vals[1]))
mention = Mention()
mention.span = span
mention.mtype = vals[3]
if len(vals) == 4:
ord_mention_list.append(mention)
else:
if vals[4].startswith('MESH'):
mention.mesh_id = vals[4][5:]
elif vals[4].startswith('CHEBI'):
mention.chebi_id = int(vals[4][6:])
med_mention_list.append(mention)
fin.close()
merged_mention_list = list()
Mention.merge_mention_list(med_mention_list, merged_mention_list)
Mention.merge_mention_list(ord_mention_list, merged_mention_list)
return merged_mention_list
def __find_mesh_mentions(self, text):
mesh_spans, mesh_ids = self.mesh_match.find_all_terms(text)
mention_list = list()
for mesh_span, mesh_id in izip(mesh_spans, mesh_ids):
mention = Mention()
mention.span = mesh_span
mention.mtype = 'MISC'
mention.mesh_id = mesh_id
mention_list.append(mention)
return mention_list
