def get_concept_categories(): # noqa: E501
"""get_concept_categories
Get a list of concept categories and number of their concept instances documented by the knowledge source. These types should be mapped onto the Translator-endorsed Biolink Model concept type classes with local types, explicitly added as mappings to the Biolink Model YAML file. # noqa: E501
:rtype: List[BeaconConceptCategory]
"""
data = utils.load_bioentities()
categories = []
for key in data['bioentity'].keys():
if key in blm.schema().classes:
category_id = f'blm:{key}'
category = key
uri = blm.class_uri(key)
else:
category_id = f'blm:{blm.DEFAULT_CATEGORY}'
category = blm.DEFAULT_CATEGORY
uri = blm.class_uri(blm.DEFAULT_CATEGORY)
categories.append(
BeaconConceptCategory(
category=category,
local_category=key,
description=None,
frequency=None,
))
return categories
def get_predicates(): # noqa: E501
"""get_predicates
Get a list of predicates used in statements issued by the knowledge source # noqa: E501
:rtype: List[BeaconPredicate]
"""
data = utils.load_kmap()
predicates = []
s = set()
for a in data['associations']:
s.add(safe_get(a, 'predicate'))
for p in s:
if p.replace('_', ' ') in blm.schema().slots:
edge_label = p.replace(' ', '_')
predicate_id = f'blm:{edge_label}'
relation = edge_label
uri = blm.slot_uri(edge_label)
else:
predicate_id = f'blm:{blm.DEFAULT_EDGE_LABEL}'
edge_label = blm.DEFAULT_EDGE_LABEL
relation = p
uri = blm.slot_uri(blm.DEFAULT_EDGE_LABEL)
try:
description = blm.schema().slots[edge_label.replace(
'_', ' ')].description
except:
description = None
predicates.append(
BeaconPredicate(description=description,
edge_label=edge_label,
relation=relation,
frequency=None))
return predicates
def build_statement(object_id, object_name, object_category, subject_id,
subject_name, subject_category, predicate_id,
predicate_name):
if predicate_id is None:
predicate_id = predicate_name
if predicate_name.replace('_', ' ') not in blm.schema().slots:
predicate_name = blm.DEFAULT_EDGE_LABEL
beacon_subject = BeaconStatementSubject(id=utils.fix_curie(subject_id),
name=subject_name,
categories=[subject_category])
beacon_object = BeaconStatementObject(id=utils.fix_curie(object_id),
name=object_name,
categories=[object_category])
beacon_predicate = BeaconStatementPredicate(edge_label=predicate_name,
relation=predicate_id,
negated=False)
statement_id = '{}:{}:{}'.format(subject_id, predicate_name, object_id)
return BeaconStatement(id=statement_id,
subject=beacon_subject,
predicate=beacon_predicate,
object=beacon_object)
def lookup_category(prefix:str) -> str:
"""
Returns the category that this prefix belongs to
"""
global _category_map
if _category_map == None:
response = requests.get(bioentities_endpoint)
if response.ok:
_category_map = {}
data = response.json()
for category, prefixes in data['bioentity'].items():
for prefix in prefixes:
_category_map[prefix.lower()] = category
else:
abort(500, 'Could not connect to: {}'.format(bioentities_endpoint))
category = _category_map.get(prefix.lower())
if category in blm.schema().classes:
return category
else:
return blm.DEFAULT_CATEGORY
def get_knowledge_map(): # noqa: E501
"""get_knowledge_map
Get a high level knowledge map of the all the beacons by subject semantic type, predicate and semantic object type # noqa: E501
:rtype: List[BeaconKnowledgeMapStatement]
"""
data = utils.load_kmap()
d = defaultdict(lambda: defaultdict(set))
statements = []
for a in data['associations']:
subject_category = safe_get(a, 'subject', 'semantic_type')
subject_prefix = safe_get(a, 'subject', 'prefix')
predicate = safe_get(a, 'predicate')
object_category = safe_get(a, 'object', 'semantic_type')
object_prefix = safe_get(a, 'object', 'prefix')
endpoint = safe_get(a, 'endpoint')
k = f'{subject_category}{predicate}{object_category}'
d[k]['subject_prefix'].add(subject_prefix)
d[k]['object_prefix'].add(object_prefix)
d[k]['subject_category'] = subject_category
d[k]['object_category'] = object_category
d[k]['predicate'] = predicate
d[k]['endpoint'] = endpoint
for p in d.values():
object_category = p['object_category']
subject_category = p['subject_category']
if object_category not in blm.schema().classes:
object_category = blm.DEFAULT_CATEGORY
if subject_category not in blm.schema().classes:
subject_category = blm.DEFAULT_CATEGORY
if p['predicate'].replace('_', ' ') in blm.schema().slots:
edge_label = p['predicate'].replace(' ', '_')
relation = edge_label
else:
edge_label = blm.DEFAULT_EDGE_LABEL
relation = p['predicate']
o = BeaconKnowledgeMapObject(category=object_category,
prefixes=list(p['object_prefix']))
s = BeaconKnowledgeMapSubject(category=subject_category,
prefixes=list(p['subject_prefix']))
r = BeaconKnowledgeMapPredicate(edge_label=edge_label,
relation=relation,
negated=False)
statements.append(
BeaconKnowledgeMapStatement(subject=s, object=o, predicate=r))
return statements