def get(self, category):
"""
Summarize a set of objects
"""
args = parser.parse_args()
slim = args.get('slim')
del args['slim']
subjects = args.get('subject')
del args['subject']
# Note that GO currently uses UniProt as primary ID for some sources: https://github.com/biolink/biolink-api/issues/66
# https://github.com/monarch-initiative/dipper/issues/461
sg_dev = SciGraph(
url='https://scigraph-data-dev.monarchinitiative.org/scigraph/')
subjects = [
x.replace('WormBase:', 'WB:') if 'WormBase:' in x else x
for x in subjects
]
slimmer_subjects = []
if category == FUNCTION_CATEGORY:
# get proteins for a gene only when the category is 'function'
for s in subjects:
if 'HGNC:' in s or 'NCBIGene:' in s or 'ENSEMBL:' in s:
prots = sg_dev.gene_to_uniprot_proteins(s)
if len(prots) == 0:
prots = [s]
slimmer_subjects += prots
else:
slimmer_subjects.append(s)
else:
slimmer_subjects = subjects
if category == ANATOMY_CATEGORY:
category = 'anatomical entity'
results = map2slim(subjects=slimmer_subjects,
slim=slim,
object_category=category,
user_agent=USER_AGENT,
**args)
# To the fullest extent possible return HGNC ids
checked = {}
for result in results:
for association in result['assocs']:
taxon = association['subject']['taxon']['id']
proteinId = association['subject']['id']
if taxon == 'NCBITaxon:9606' and proteinId.startswith(
'UniProtKB:'):
if checked.get(proteinId) == None:
genes = sg_dev.uniprot_protein_to_genes(proteinId)
for gene in genes:
if gene.startswith('HGNC'):
association['subject']['id'] = gene
checked[proteinId] = gene
else:
association['subject']['id'] = checked[proteinId]
return results
def get(self, category):
"""
Summarize a set of objects
"""
args = parser.parse_args()
slim = args.get('slim')
del args['slim']
subjects = args.get('subject')
del args['subject']
# Note that GO currently uses UniProt as primary ID for some sources: https://github.com/biolink/biolink-api/issues/66
# https://github.com/monarch-initiative/dipper/issues/461
# nota bene:
# currently incomplete because code is not checking for the possibility of >1 subjects
subjects[0] = subjects[0].replace('WormBase:', 'WB:', 1)
if (subjects[0].startswith('HGNC')
or subjects[0].startswith('NCBIGene')
or subjects[0].startswith('ENSEMBL:')):
sg_dev = SciGraph(
url='https://scigraph-data-dev.monarchinitiative.org/scigraph/'
)
prots = sg_dev.gene_to_uniprot_proteins(subjects[0])
if len(prots) == 0:
prots = subjects
else:
prots = subjects
results = map2slim(subjects=prots,
slim=slim,
rows=200,
exclude_automatic_assertions=True,
object_category=category,
**args)
# To the fullest extent possible return HGNC ids
checked = {}
for result in results:
for association in result['assocs']:
taxon = association['subject']['taxon']['id']
proteinId = association['subject']['id']
if taxon == 'NCBITaxon:9606' and proteinId.startswith(
'UniProtKB:'):
if checked.get(proteinId) == None:
sg_dev = SciGraph(
url=
'https://scigraph-data-dev.monarchinitiative.org/scigraph/'
)
genes = sg_dev.uniprot_protein_to_genes(proteinId)
for gene in genes:
if gene.startswith('HGNC'):
association['subject']['id'] = gene
checked[proteinId] = gene
else:
association['subject']['id'] = checked[proteinId]
return results
def get(self):
"""
For a given gene(s), summarize its annotations over a defined set of slim
"""
args = self.function_parser.parse_args()
slim = args.get('slim')
del args['slim']
subjects = args.get('subject')
del args['subject']
# Note that GO currently uses UniProt as primary ID for some sources: https://github.com/biolink/biolink-api/issues/66
# https://github.com/monarch-initiative/dipper/issues/461
sg_dev = SciGraph(get_biolink_config()['scigraph_data']['url'])
subjects = [
x.replace('WormBase:', 'WB:') if 'WormBase:' in x else x
for x in subjects
]
slimmer_subjects = []
for s in subjects:
if 'HGNC:' in s or 'NCBIGene:' in s or 'ENSEMBL:' in s:
prots = identifier_converter.convert_gene_to_protein(s)
if len(prots) == 0:
prots = [s]
slimmer_subjects += prots
else:
slimmer_subjects.append(s)
results = map2slim(subjects=slimmer_subjects,
slim=slim,
object_category='function',
user_agent=USER_AGENT,
**args)
# To the fullest extent possible return HGNC ids
checked = {}
for result in results:
for association in result['assocs']:
taxon = association['subject']['taxon']['id']
proteinId = association['subject']['id']
if taxon == 'NCBITaxon:9606' and proteinId.startswith(
'UniProtKB:'):
if proteinId not in checked:
genes = identifier_converter.convert_protein_to_gene(
proteinId)
for gene in genes:
if gene.startswith('HGNC'):
association['subject']['id'] = gene
checked[proteinId] = gene
else:
association['subject']['id'] = checked[proteinId]
return results
def test_map2slim_golr():
results = map2slim(subjects=SUBJECTS,
slim=SLIM,
object_category='function')
assert len(results) > 0
n_found = 0
for r in results:
n_found = n_found + 1
print("Subject: {} Slim:{} Assocs:{}".format(r['subject'], r['slim'],
len(r['assocs'])))
assert n_found > 0
def get(self, category):
"""
Summarize a set of objects
"""
args = parser.parse_args()
logging.info("category is {}".format(category))
slim = args.get('slim')
del args['slim']
subjects = args.get('subject')
del args['subject']
results = map2slim(subjects=subjects,
slim=slim,
rows=200,
object_category=category,
**args)
# If there are no associations for the given ID, try other IDs.
# Note the AmiGO instance does *not* support equivalent IDs
assoc_count = 0
for result in results:
assoc_count += len(result['assocs'])
if assoc_count == 0 and len(subjects) == 1:
# Note that GO currently uses UniProt as primary ID for some sources: https://github.com/biolink/biolink-api/issues/66
# https://github.com/monarch-initiative/dipper/issues/461
# nota bene:
# currently incomplete because code is not checking for the possibility of >1 subjects
logging.info(
"Found no associations using {} - will try mapping to other IDs"
.format(subjects[0]))
sg_dev = SciGraph(
url='https://scigraph-data-dev.monarchinitiative.org/scigraph/'
)
prots = sg_dev.gene_to_uniprot_proteins(subjects[0])
if len(prots) > 0:
results = map2slim(subjects=prots,
slim=slim,
rows=200,
object_category=category,
**args)
return results
def get(self):
"""
For a given gene(s), summarize its annotations over a defined set of slim
"""
args = parser.parse_args()
slim = args.get('slim')
del args['slim']
subjects = args.get('subject')
del args['subject']
subjects = [x.replace('WormBase:', 'WB:') if 'WormBase:' in x else x for x in subjects]
results = map2slim(
subjects=subjects,
slim=slim,
object_category='anatomical entity',
user_agent=USER_AGENT,
**args
)
return results
