def get_object_genotype(id, **args):
obj = scigraph.bioobject(id, 'Genotype')
obj.phenotype_associations = search_associations(subject=id, object_category='phenotype', **args)['associations']
obj.disease_associations = search_associations(subject=id, object_category='disease', **args)['associations']
obj.gene_associations = search_associations(subject=id, object_category='gene', **args)['associations']
return(obj)
def get(self, id):
"""
Returns associations to GO terms for a gene
"""
args = core_parser_with_rel.parse_args()
if args['relationship_type'] == ACTS_UPSTREAM_OF_OR_WITHIN:
return search_associations(subject_category='gene',
object_category='function',
fq={'regulates_closure': id},
invert_subject_object=True,
**args)
elif args['relationship_type'] == INVOLVED_IN_REGULATION_OF:
# Temporary fix until https://github.com/geneontology/amigo/pull/469
# and https://github.com/owlcollab/owltools/issues/241 are resolved
return search_associations(subject_category='gene',
object_category='function',
fq={
'regulates_closure': id,
'-isa_partof_closure': id
},
invert_subject_object=True,
**args)
elif args['relationship_type'] == INVOLVED_IN:
return search_associations(subject_category='gene',
object_category='function',
subject=id,
invert_subject_object=True,
**core_parser.parse_args())
def get_object_gene(id, **args):
obj = scigraph.bioobject(id, 'Gene')
obj.phenotype_associations = search_associations(subject=id, object_category='phenotype', **args)['associations']
obj.homology_associations = search_associations(subject=id, rel=homol_rel, object_category='gene', **args)['associations']
obj.disease_associations = search_associations(subject=id, object_category='disease', **args)['associations']
obj.genotype_associations = search_associations(subject=id, invert_subject_object=True, object_category='genotype', **args)['associations']
return(obj)
def get_association_counts(bioentity_id, bioentity_type=None):
"""
For a given CURIE, get the number of associations by each category.
"""
count_map = {}
subject_associations = search_associations(
fq={'subject_closure': bioentity_id},
facet_pivot_fields=['{!stats=piv1}object_category', 'relation'],
stats=True,
stats_field=[
'{!tag=piv1 calcdistinct=true distinctValues=false}object'
])
object_associations = search_associations(
fq={'object_closure': bioentity_id},
facet_pivot_fields=['{!stats=piv1}subject_category', 'relation'],
stats=True,
stats_field=[
'{!tag=piv1 calcdistinct=true distinctValues=false}subject'
])
subject_facet_pivot = subject_associations['facet_pivot'][
'object_category,relation']
object_facet_pivot = object_associations['facet_pivot'][
'subject_category,relation']
parse_facet_pivot(subject_facet_pivot, count_map)
parse_facet_pivot(object_facet_pivot, count_map)
if bioentity_type == 'gene':
if CATEGORY_NAME_MAP['gene'] in count_map:
count_map.pop(CATEGORY_NAME_MAP['gene'])
# get counts for all ortholog associations
ortholog_associations = search_associations(
fq={'subject_ortholog_closure': bioentity_id},
facet_pivot_fields=['{!stats=piv1}object_category', 'relation'],
stats=True,
stats_field=[
'{!tag=piv1 calcdistinct=true distinctValues=false}object'
])
ortholog_pivot_counts = ortholog_associations['facet_pivot'][
'object_category,relation']
for category in ortholog_pivot_counts:
type = category['value']
if type == 'gene':
if 'pivot' in category:
for relation in category['pivot']:
if relation['value'] == INTERACTS_WITH:
# Ortholog-Interactions
count_map[CATEGORY_NAME_MAP[
'ortholog-interaction']] = relation['stats'][
'stats_fields']['object']['countDistinct']
else:
key = 'ortholog-{}'.format(type)
count_map[CATEGORY_NAME_MAP[key]] = category['stats'][
'stats_fields']['object']['countDistinct']
return count_map
def get(self, id):
"""
Returns associations for an entity regardless of the type
"""
return search_associations(subject=id,
user_agent=USER_AGENT,
**core_parser.parse_args())
def get(self, object):
"""
Returns list of matching associations pointing to a given object (target)
"""
args = parser.parse_args()
return search_associations(object=object, **args)
def test_disease_assocs():
payload = search_associations(subject=HUMAN_SHH,
object_category='disease'
)
print(str(payload))
assocs = payload['associations']
assert len(assocs) > 0
def get(self):
"""
Generalized search over complete corpus of associations
"""
args = parser.parse_args()
return search_associations(user_agent=USER_AGENT, **args)
def get(self):
"""
Generalized search over complete corpus of associations
"""
args = parser.parse_args()
return search_associations(**args)
def get(self, id):
"""
Returns associations to GO terms for a gene
"""
return search_associations(
subject_category='gene', object_category='function',
subject=id, invert_subject_object=True, **core_parser.parse_args())
def get(self, subject):
"""
Returns list of matching associations starting from a given subject (source)
"""
args = parser.parse_args()
return search_associations(subject=subject, **args)
def get(self, id):
"""
Returns interactions for a gene
"""
return search_associations(
subject_category='gene', object_category='gene',
relation='RO:0002434', subject=id, **core_parser.parse_args())
def get_counts(entities=None, object_category=None, min_count=1, **kwargs):
"""
given a set of entities (genes, diseases, etc), finds the number of entities associated with each descriptor in a given category.
The result is a tuple (cmap, results), where cmap is a dict of TERM:COUNT
"""
if entities is None:
entities = []
results = search_associations(
subjects=entities,
subject_direct=True,
rows=0,
facet_fields=[M.IS_DEFINED_BY, M.SUBJECT_TAXON, M.SUBJECT_CATEGORY],
object_category=object_category,
facet_mincount=3, # TODO
facet_limit=-1,
json_facet={
'categories': {
'limit': -1,
'type': 'terms',
'field': M.OBJECT_CLOSURE,
'facet': {
'uniq_subject': "unique(subject)"
}
}
},
**kwargs)
buckets = results['facets']['categories']['buckets']
cmap = {}
for bucket in buckets:
if bucket['uniq_subject'] >= min_count:
cmap[bucket['val']] = bucket['uniq_subject']
return (cmap, results)
def get(self, subject_category='gene', object_category='gene'):
"""
Returns list of matching associations
"""
args = parser.parse_args()
return search_associations(subject_category, object_category, **args)
def test_disease2gene():
payload = search_associations(subject=LSD,
subject_category='disease',
object_category='gene')
assocs = payload['associations']
for a in assocs:
print(str(a))
assert len(assocs) > 0
def get(self, id):
"""
Returns expression events for a gene
"""
return search_associations(
subject_category='gene', object_category='anatomical entity',
object=id, **core_parser.parse_args())
def test_species_facet():
payload = search_associations(subject_category='gene',
object_category='phenotype',
facet_fields=['subject_taxon', 'subject_taxon_label'],
rows=0)
fcs = payload['facet_counts']
print(str(fcs))
assert 'H**o sapiens' in fcs['subject_taxon_label'].keys()
def get(self, id):
"""
Returns the association with a given identifier.
An association connects, at a minimum, two things, designated subject and object,
via some relationship. Associations also include evidence, provenance etc.
"""
return search_associations(id=id, user_agent=USER_AGENT)
def get(self, subject_category):
"""
Returns list of matching associations for a given subject category.
"""
args = self.parser.parse_args()
return search_associations(subject_category=subject_category,
user_agent=USER_AGENT,
**args)
def get(self, id):
"""
Returns genes associated with a disease
"""
args = core_parser.parse_args()
return search_associations(
subject_category='disease', object_category='gene',
subject=id, invert_subject_object=True, **core_parser.parse_args())
def test_go_assocs():
"""
Test basic association search functionality
"""
payload = search_associations(subject=TWIST_ZFIN,
object_category='function')
assocs = payload['associations']
assert len(assocs) > 0
def get(self, id):
"""
Returns phenotypes associated with a genotype
"""
return search_associations(
subject_category='genotype', object_category='phenotype',
subject=id, **core_parser.parse_args())
def get(self, id):
"""
Return diseases associated with orthologs of a gene
"""
return search_associations(fq={'subject_ortholog_closure': id},
object_category='disease',
**core_parser.parse_args())
def get(self, id):
"""
Returns associations between a lit entity and a genotype
"""
return search_associations(subject_category='literature',
object_category='genotype',
subject=id,
**core_parser.parse_args())
def get(self, id):
"""
Returns genes associated with a variant
"""
# TODO: invert
return search_associations(
subject_category='variant', object_category='gene',
subject=id, **core_parser.parse_args())
def test_func_objects():
results = search_associations(subject=TWIST_ZFIN,
fetch_objects=True,
rows=0,
object_category='function')
objs = results['objects']
print(objs)
assert DVPF in objs
assert len(objs) > 1
def test_pheno_objects():
results = search_associations(subject=TWIST_ZFIN,
fetch_objects=True,
rows=0,
object_category='phenotype')
objs = results['objects']
print(str(objs))
assert len(objs) > 1
assert 'ZP:0007631' in objs
def test_pheno_assocs():
payload = search_associations(subject=TWIST_ZFIN,
object_category='phenotype')
assocs = payload['associations']
assert len(assocs) > 0
for a in assocs:
print(str(a))
assocs = [a for a in assocs if a['subject']['id'] == TWIST_ZFIN]
assert len(assocs) > 0
def get(self, id):
"""
Returns genes associated with a pathway
"""
args = core_parser.parse_args()
return search_associations(
subject_category='gene', object_category='pathway',
object=id, **core_parser.parse_args())
def get(self, id):
"""
Returns diseases associated with a genotype
"""
# TODO: invert
return search_associations(
subject_category='genotype', object_category='disease',
subject=id, **core_parser.parse_args())
