def extract_relations_from_bioc_object(bioc_object, task, id_prefix,
denotations):
relations = []
known_types = dict(
(t['code'], t) for t in get_task_types(task, relation=True))
for b_relation in bioc_object.relations:
nodes = list(b_relation.nodes)
subj_id = denotations.get(nodes[0].refid, None)
obj_id = denotations.get(nodes[1].refid, None)
if subj_id is not None and obj_id is not None:
relation_type = None
b_relation_infons = b_relation.infons.values()
for value in b_relation_infons:
relation_type = known_types.get(value, None)
if relation_type is not None:
break
relation = {
'id': id_prefix + b_relation.id,
'subj': subj_id,
'obj': obj_id,
'pred': relation_type
}
if relation_type is None:
label_guesses = filter(
lambda x: x[0] in ['label', 'type'] or
(x[1] != 'None' and x[1] is not None and x[1] !=
'undefined'), b_relation.infons.iteritems())
if len(label_guesses) > 0:
relation['pred'] = {'label': label_guesses[0][1]}
relations.append(relation)
return relations
def extract_relations_from_bioc_object(bioc_object, task, id_prefix, denotations):
relations = []
known_types = dict((t['code'], t) for t in get_task_types(task, relation=True))
for b_relation in bioc_object.relations:
nodes = list(b_relation.nodes)
subj_id = denotations.get(nodes[0].refid, None)
obj_id = denotations.get(nodes[1].refid, None)
if subj_id is not None and obj_id is not None:
relation_type = None
b_relation_infons = b_relation.infons.values()
for value in b_relation_infons:
relation_type = known_types.get(value, None)
if relation_type is not None:
break
relation = {'id': id_prefix + b_relation.id,
'subj': subj_id,
'obj': obj_id,
'pred': relation_type
}
if relation_type is None:
label_guesses = filter(
lambda x: x[0] in ['label', 'type'] or (x[1] != 'None' and x[1] is not None and x[1] != 'undefined'),
b_relation.infons.iteritems())
if len(label_guesses) > 0:
relation['pred'] = {'label': label_guesses[0][1]}
relations.append(relation)
return relations
def extract_denotations_from_bioc_object(bioc_object, task, id_prefix):
denotations = []
known_types = dict(
(t['code'], t) for t in get_task_types(task, relation=False))
for annotation in bioc_object.annotations:
denotation = {'id': id_prefix + annotation.id, 'span': {}}
denotation['span']['begin'] = annotation.locations[0].offset
denotation['span']['end'] = annotation.locations[
0].offset + annotation.locations[0].length
annotation_info = annotation.infons.values()
for value in annotation_info:
umls_type = known_types.get(value, None)
if umls_type is not None:
denotation['obj'] = umls_type
break
if denotation.get('obj') is None:
label_guesses = filter(
lambda x: x[0] in ['label', 'type'] or
(x[1] != 'None' and x[1] is not None and x[1] != 'undefined'),
annotation.infons.iteritems())
if len(label_guesses) > 0:
denotation['obj'] = {'label': label_guesses[0][1]}
denotations.append(denotation)
return denotations
def extract_denotations_from_bioc_object(bioc_object, task, id_prefix):
denotations = []
known_types = dict((t['code'], t) for t in get_task_types(task, relation=False))
for annotation in bioc_object.annotations:
denotation = {'id': id_prefix + annotation.id, 'span': {}}
denotation['span']['begin'] = annotation.locations[0].offset
denotation['span']['end'] = annotation.locations[0].offset + annotation.locations[0].length
annotation_info = annotation.infons.values()
for value in annotation_info:
umls_type = known_types.get(value, None)
if umls_type is not None:
denotation['obj'] = umls_type
break
if denotation.get('obj') is None:
label_guesses = filter(
lambda x: x[0] in ['label', 'type'] or (x[1] != 'None' and x[1] is not None and x[1] != 'undefined'),
annotation.infons.iteritems())
if len(label_guesses) > 0:
denotation['obj'] = {'label': label_guesses[0][1]}
denotations.append(denotation)
return denotations
