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):
"""
Returns compact associations for a given input set
"""
args = parser.parse_args()
M = GolrFields()
results = search_associations(
subjects=args.get('subject'),
select_fields=[M.SUBJECT, M.RELATION, M.OBJECT],
use_compact_associations=True,
rows=MAX_ROWS,
facet_fields=[],
user_agent=USER_AGENT,
**args)
return results
def get(self):
"""
Returns homology associations for a given input set of genes
"""
args = parser.parse_args()
M = GolrFields()
rel = 'RO:0002434' # TODO; allow other types
results = search_associations(
subjects=args.get('subject'),
select_fields=[M.SUBJECT, M.RELATION, M.OBJECT],
use_compact_associations=True,
relation=rel,
rows=MAX_ROWS,
facet_fields=[],
**args)
return results
def get(self):
"""
Summary statistics for objects associated
"""
args = parser.parse_args()
M = GolrFields()
results = search_associations(
subjects=args.get('subject'),
rows=0,
facet_fields=[M.OBJECT_CLOSURE, M.IS_DEFINED_BY],
facet_limit=-1,
**args)
print("RESULTS=" + str(results))
obj_count_dict = results['facet_counts'][M.OBJECT_CLOSURE]
del results['facet_counts'][M.OBJECT_CLOSURE]
return {'results': obj_count_dict, 'facets': results['facet_counts']}
def get(self):
"""
Returns compact associations for a given input set
"""
args = parser.parse_args()
M = GolrFields()
#results = search_associations(subjects=args.get('subject'),
# rows=0,
# pivot_subject_object=True,
# facet_fields=[],
# facet_limit=-1,
# **args)
results = search_associations(
subjects=args.get('subject'),
select_fields=[M.SUBJECT, M.RELATION, M.OBJECT],
use_compact_associations=True,
rows=MAX_ROWS,
facet_fields=[],
**args)
return results
import logging
from flask import request
from flask_restplus import Resource
from biolink.datamodel.serializers import association, association_results
from biolink.api.restplus import api
from ontobio.golr.golr_associations import get_association, search_associations, GolrFields
from biolink import USER_AGENT
log = logging.getLogger(__name__)
M = GolrFields()
parser = api.parser()
parser.add_argument(
'subject_taxon',
help='SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default')
parser.add_argument(
'evidence',
help="""Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)
or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.
""")
class RelationUsageResource(Resource):
@api.expect(parser)
@api.marshal_list_with(association_results)
def get(self):
"""
All relations used plus count of associations
"""