def preload_ontologies():
ontologies = settings.get_biolink_config().get('ontologies')
for ontology in ontologies:
handle = ontology['handle']
if ontology['pre_load']:
log.info("Loading {}".format(ontology['id']))
get_ontology(handle)
def get(self):
"""
Summary statistics for objects associated
"""
args = parser.parse_args()
M = GolrFields()
ont = None
ocat = args.get('object_category')
ontid = args.get('ontology')
if ontid is None:
if ocat == 'function':
ontid = 'go'
if ocat == 'phenotype':
# TODO: other phenotype ontologies
ontid = 'hp'
print("Loading: {}".format(ontid))
ont = get_ontology(ontid)
taxid = args.get('taxon')
max_p_value = float(args.max_p_value)
subjects = args.get('subject')
background = args.get('background')
afactory = AssociationSetFactory()
aset = afactory.create(ontology=ont,
subject_category='gene',
object_category=ocat,
taxon=taxid)
enr = aset.enrichment_test(subjects=subjects,
threshold=max_p_value,
labels=True)
return {'results': enr}
def get(self, ontology, node):
"""
Extract a subgraph from an ontology
"""
args = parser.parse_args()
qnodes = [node]
if args.cnode is not None:
qnodes += args.cnode
factory = OntologyFactory()
ont = get_ontology(ontology)
#subont = ont.subontology([id], relations=args.relations)
relations = args.relation
print("Traversing: {} using {}".format(qnodes,relations))
nodes = ont.traverse_nodes(qnodes,
up=True,
down=False,
relations=relations)
subont = ont.subontology(nodes, relations=relations)
ojr = OboJsonGraphRenderer(include_meta=args.include_meta)
json_obj = ojr.to_json(subont)
# TODO: remove this next release of ontobio
if not args.include_meta:
for g in json_obj['graphs']:
for n in g['nodes']:
n['meta']={}
return json_obj
def get(self, ontology):
"""
TEST
"""
ont = get_ontology(ontology)
return {'z': 'foo',
'nodes': len(ont.nodes())}
def post(self, ontology, node):
"""
Extract a subgraph from an ontology
"""
args = parser.parse_args()
qnodes = [node]
if args.cnode is not None:
qnodes += args.cnode
ont = get_ontology(ontology)
relations = args.relation
log.info("Traversing: {} using {}".format(qnodes, relations))
nodes = ont.traverse_nodes(qnodes,
up=args.include_ancestors,
down=args.include_descendants,
relations=relations)
subont = ont.subontology(nodes, relations=relations)
ojr = OboJsonGraphRenderer()
json_obj = ojr.to_json(subont, include_meta=args.include_meta)
return json_obj
def get(self, ontology, node):
"""
Extract a subgraph from an ontology
"""
args = parser.parse_args()
qnodes = [node]
if args.cnode is not None:
qnodes += args.cnode
factory = OntologyFactory()
ont = get_ontology(ontology)
relations = args.relation
print("Traversing: {} using {}".format(qnodes,relations))
nodes = ont.traverse_nodes(qnodes,
up=args.include_ancestors,
down=args.include_descendants,
relations=relations)
subont = ont.subontology(nodes, relations=relations)
# TODO: meta is included regardless of whether include_meta is True or False
ojr = OboJsonGraphRenderer(include_meta=args.include_meta)
json_obj = ojr.to_json(subont)
return json_obj
def get(self, id):
"""
Extract a subgraph from an ontology term
"""
args = subgraph_params.parse_args()
qnodes = [id]
if args.cnode is not None:
qnodes += args.cnode
# COMMENT: based on the CURIE of the id, we should be able to find out the ontology automatically
ont = get_ontology("go")
relations = args.relation
print("Traversing: {} using {}".format(qnodes, relations))
nodes = ont.traverse_nodes(qnodes,
up=args.include_ancestors,
down=args.include_descendants,
relations=relations)
subont = ont.subontology(nodes, relations=relations)
# TODO: meta is included regardless of whether include_meta is True or False
ojr = OboJsonGraphRenderer(include_meta=args.include_meta)
json_obj = ojr.to_json(subont, include_meta=args.include_meta)
return json_obj
