def _make_mesh_entity(entity_chunk):
"""
Make a KBEntity from each MeSH chunk
:param entity_chunk:
:return:
"""
entity = KBEntity()
for line in entity_chunk:
fields = line.split(" = ")
if len(fields) != 2:
continue
key, value = fields[0], fields[1]
if key == 'UI':
entity.research_entity_id = value
elif key == 'MH' or key == 'SH':
entity.canonical_name = value
entity.aliases.append(value)
elif key == 'ENTRY' or key == 'PRINT ENTRY':
entity.aliases.append(value.split("|")[0])
elif key == 'MS':
entity.definition = value
return entity
def import_dbpedia(kb_name, kb_filename, entities_count=0):
"""
Instantiate a KnowledgeBase object with entities and relations from dbpedia
:param kb_name:
:param kb_filename:
:param entities_count:
:return:
"""
# initialize the KB.
kb = KnowledgeBase()
kb.name = kb_name
# only the "turtle" format is allowed for this kb.
assert ('.ttl' in kb_filename)
kb_filename = file_util.cache_file(kb_filename)
# parse the turtle file
abstracts_graph = rdflib.Graph()
abstracts_graph.parse(kb_filename, format='turtle')
logging.warning('done parsing dbpedia .ttl files.')
counter = 0
for item_subject, item_property, item_object in abstracts_graph:
entity = KBEntity()
entity.research_entity_id = str(item_subject)
if not entity.research_entity_id.startswith(
'http://dbpedia.org/resource/'):
continue
entity.canonical_name = entity.research_entity_id[
len('http://dbpedia.org/resource/'):].replace('_', ' ')
entity.aliases.append(entity.canonical_name)
entity.definition = str(item_object)
# verify and add entity to the KB.
kb.add_entity(entity)
counter += 1
if counter >= entities_count > 0:
break
return kb
def import_obo_kb(kb_name, kb_filename):
"""
Create a KnowledgeBase object with entities and relations from an OBO file
:param kb_name:
:param kb_filename: OBO file where KB is located
:return:
"""
# initialize the KB
kb = KnowledgeBase()
kb.name = kb_name
for chunk in KBLoader._chunkify(file_util.read_lines(kb_filename),
KBLoader.OBO_ENTITY_START_TAG):
# instantiate an empty entity.
entity = KBEntity()
# list of KBRelations to add
relations = []
for line_index, line in enumerate(chunk):
if line.startswith('id: '):
# research_entity_id
entity.research_entity_id = line[len('id: '):]
elif line.startswith('name: '):
# canonical_name
entity.canonical_name = line[len('name: '):].replace(
'_', ' ')
entity.aliases.append(entity.canonical_name)
elif line.startswith('def: '):
# definition
start_offset, end_offset = line.index(
'"') + 1, line.rindex('"')
entity.definition = line[start_offset:end_offset]
elif line.startswith('synonym: '):
# other aliases
start_offset, end_offset = line.index(
'"') + 1, line.rindex('"')
entity.aliases.append(line[start_offset:end_offset])
elif line.startswith('is_a: '):
# is_a relationships
assert entity.research_entity_id
splits = line.strip().split(' ')
assert (len(splits) > 1)
target_research_entity_id = splits[1]
relation = KBRelation(relation_type='is_a',
entity_ids=[
entity.research_entity_id,
target_research_entity_id
],
symmetric=True)
relations.append(relation)
elif line.startswith('relationship: '):
# other relationships
assert entity.research_entity_id
splits = line.split(' ')
assert (len(splits) > 2)
relation_type = splits[1]
target_research_entity_id = splits[2]
# is the relation symmetric?
if relation_type in KBLoader.OBO_ASYM_RELATION_SET:
symmetric = False
elif relation_type in KBLoader.OBO_SYM_RELATION_SET:
symmetric = True
else:
# unknown relation type
logging.info('unknown relation type: ' + relation_type)
assert False
relation = KBRelation(relation_type=relation_type,
entity_ids=[
entity.research_entity_id,
target_research_entity_id
],
symmetric=symmetric)
relations.append(relation)
elif line.startswith('intersection_of: ') or \
line.startswith('is_obsolete: ') or \
line.startswith('comment: ') or \
line.startswith('disjoint_from: ') or \
line.startswith('alt_id: ') or \
line.startswith('xref: ') or \
line.startswith('property_value: has_rank') or \
line.startswith('subset: ') or \
line.startswith('xref_analog') or \
line.startswith('xylem') or \
line.startswith('related_synonym') or \
line.startswith('exact_synonym') or \
line.startswith('broad_synonym') or \
line.startswith('narrow_synonym') or \
line.startswith('namespace') or \
line.startswith('consider') or \
line.startswith('replaced_by') or \
line.startswith('union_of'):
# properties don't map naturally to the unified schema.
pass
else:
# unknown obo property.
logging.info('unknown OBO property: ' + line)
assert False
# add relations to entity and to kb
for rel in relations:
kb.add_relation(rel)
rel_index = len(kb.relations) - 1
entity.relation_ids.append(rel_index)
# add entity to kb
kb.add_entity(entity)
return kb