def test():
"""What do we get back for HBB"""
relations = gene_get_disease(('HGNC:4827', ))
checker = Mondo(ServiceContext.create_context())
for p, a in relations:
igc, nid = checker.is_genetic_disease(a)
print(a['id'], igc, nid)
def __init__(self, config=None, override={}):
self.service_context = ServiceContext.create_context(config)
service_context = self.service_context
self.clinical = Clinical(service_context)
#temporarly taken out because of http errors
#self.exposures = CMAQ (service_context)
self.endotype = Endotype(service_context)
self.chembio = ChemBioKS(self.service_context)
self.chemotext = Chemotext(self.service_context)
self.disease_ontology = DiseaseOntology(self.service_context)
self.pharos = Pharos(self.service_context)
self.oxo = OXO(self.service_context)
self.hpo = HPO(self.service_context)
self.hetio = HetIO(self.service_context)
self.biolink = Biolink(self.service_context)
self.mondo = Mondo(self.service_context)
self.go = GO(self.service_context)
self.tkba = TranslatorKnowledgeBeaconAggregator(self.service_context)
self.translator_registry = TranslatorRegistry(self.service_context)
self.quickgo = QuickGo(self.service_context)
self.translator = Translator(core=self)
self.hgnc = HGNC(self.service_context)
self.uberongraph = UberonGraphKS(self.service_context)
self.ctd = CTD(self.service_context)
def __init__(self, context):
super(Biolink, self).__init__("biolink", context)
# TODO, can we just use the Mondo that's inthe core already?
self.checker = Mondo(ServiceContext.create_context())
self.go = GO(ServiceContext.create_context())
class Biolink(Service):
""" Preliminary interface to Biolink. Will move to automated Translator Registry invocation over time. """
def __init__(self, context):
super(Biolink, self).__init__("biolink", context)
# TODO, can we just use the Mondo that's inthe core already?
self.checker = Mondo(ServiceContext.create_context())
self.go = GO(ServiceContext.create_context())
def process_associations(self,
r,
predicate,
target_node_type,
reverse=False):
"""Given a response from biolink, create our edge and node structures.
Sometimes (as in pathway->Genes) biolink returns the query as the object, rather
than the subject. reverse=True will handle this case, bringing back the subject
of the response, rather than the object."""
edge_nodes = []
for association in r['associations']:
pubs = []
if 'publications' in association and association[
'publications'] is not None:
for pub in association['publications']:
# Sometimes, we get back something like "uniprotkb" instead of a PMID. We don't want it.
pubid_prefix = pub['id'][:4].upper()
if pubid_prefix == 'PMID':
pubs.append(pub['id'])
if reverse:
obj = KNode(association['subject']['id'], target_node_type,
association['subject']['label'])
else:
obj = KNode(association['object']['id'], target_node_type,
association['object']['label'])
rel = {
'typeid': association['relation']['id'],
'label': association['relation']['label']
}
props = {'publications': pubs, 'relation': rel}
edge = KEdge('biolink', predicate, props)
edge_nodes.append((edge, obj))
return edge_nodes
def gene_get_disease(self, gene_node):
"""Given a gene specified as an HGNC curie, return associated diseases. """
ehgnc = urllib.parse.quote_plus(gene_node.identifier)
logging.getLogger('application').debug(
' biolink: %s/bioentity/gene/%s/diseases' %
(self.url, ehgnc))
r = requests.get('%s/bioentity/gene/%s/diseases' %
(self.url, ehgnc)).json()
return self.process_associations(r, 'gene_get_disease',
node_types.DISEASE)
def disease_get_phenotype(self, disease):
url = "{0}/bioentity/disease/{1}/phenotypes/".format(
self.url, disease.identifier)
response = requests.get(url).json()
return self.process_associations(response, 'disease_get_phenotype',
node_types.PHENOTYPE)
def gene_get_go(self, gene):
# this function is very finicky. gene must be in uniprotkb, and the curie prefix must be correctly capitalized
url = "{0}/bioentity/gene/UniProtKB:{1}/function/".format(
self.url, Text.un_curie(gene.identifier))
response = requests.get(url).json()
# return [ (a['object']['id'] , a['object']['label']) for a in response['associations'] ]
return self.process_associations(response, 'gene_get_go',
node_types.PROCESS)
def gene_get_function(self, gene):
edges_nodes = self.gene_get_go(gene)
process_results = list(
filter(lambda x: self.go.is_molecular_function(x[1].identifier),
edges_nodes))
for edge, node in process_results:
edge.predicate = 'gene_get_molecular_function'
node.identifier.replace('GO:', 'GO.MOLECULAR_FUNCTION:')
node.node_type = node_types.FUNCTION
return process_results
def gene_get_process(self, gene):
edges_nodes = self.gene_get_go(gene)
process_results = list(
filter(lambda x: self.go.is_biological_process(x[1].identifier),
edges_nodes))
for edge, node in process_results:
edge.predicate = 'gene_get_biological_process'
node.identifier.replace('GO:', 'GO.BIOLOGICAL_PROCESS:')
node.node_type = node_types.PROCESS
return process_results
def gene_get_pathways(self, gene):
url = "{0}/bioentity/gene/{1}/pathways/".format(
self.url, gene.identifier)
response = requests.get(url).json()
return self.process_associations(response, 'gene_get_pathways',
node_types.PATHWAY)
def gene_get_react_pathway(self, gene):
process_results = self.gene_get_pathways(gene)
return list(
filter(lambda en: en[1].identifier.startswith('REACT:'),
process_results))
def gene_get_kegg_pathway(self, gene):
process_results = self.gene_get_pathways(gene)
return list(
filter(lambda en: en[1].identifier.startswith('KEGG-path:'),
process_results))
def pathway_get_gene(self, pathway):
url = "{0}/bioentity/pathway/{1}/genes/".format(
self.url, pathway.identifier)
response = requests.get(url).json()
return self.process_associations(response,
'pathway_get_genes',
node_types.GENE,
reverse=True)
def gene_get_genetic_condition(self, gene):
"""Given a gene specified as an HGNC curie, return associated genetic conditions.
A genetic condition is specified as a disease that descends from a ndoe for genetic disease in MONDO."""
disease_relations = self.gene_get_disease(gene)
# checker = Mondo(ServiceContext.create_context ())
relations = []
for relation, obj in disease_relations:
is_genetic_condition, new_object_ids = self.checker.is_genetic_disease(
obj)
if is_genetic_condition:
obj.properties['mondo_identifiers'] = new_object_ids
obj.node_type = node_types.GENETIC_CONDITION
relations.append((relation, obj))
# print (" biolink relations %s" % relations)
return relations