def resolve_display(self):
diseases = list(set(self.store.subjects(RDF.type, PHENO.Disease)))
diseases_iris = list(map(lambda i: str(i), diseases))
mim_disease = list(
set(filter(lambda x: find_valueset(x) == 'OMIM', diseases_iris)))
mim_indices = lookup_es.find_entity_by_iris(mim_disease, 'OMIM')
logger.info("Resolving iris; total:%d|found:%d", len(mim_disease),
len(mim_indices))
self.add_label(mim_disease, mim_indices)
decipher_disease = list(
set(filter(lambda x: find_valueset(x) == 'DECIPHER',
diseases_iris)))
decipher_indices = lookup_es.find_entity_by_iris(
decipher_disease, 'DECIPHER')
logger.info("Resolving iris; total:%d|found:%d", len(decipher_disease),
len(decipher_indices))
self.add_label(decipher_disease, decipher_indices)
ordo_disease = list(
set(filter(lambda x: find_valueset(x) == 'ordo', diseases_iris)))
ordo_indices = lookup_es.find_entity_by_iris(ordo_disease, 'ordo')
logger.info("Resolving iris; total:%d|found:%d", len(ordo_disease),
len(ordo_indices))
self.add_label(ordo_disease, ordo_indices)
self.add_phenotype_label()
self.add_evidence_label()
def map_entity(self, iri):
result = lookup_es.find_entity_by_iris([iri], 'NCBITAXON')
if len(result) > 0:
result[0]['valueset'] = self.valueset['valueset']
return result[0]
logger.info("not found: %s", iri)
def create_phenotype_filter(self, phenotype_iri, concept_iri,
include_subclass):
if phenotype_iri and include_subclass and not concept_iri:
ontology = find_valueset(phenotype_iri)
result = find_entity_by_iris([phenotype_iri], ontology)
label = result[0]['label'][0]
label = "'" + label + "'" if len(label.split(' ')) > 1 else label
label = label.lower()
return ("\n ?association rdf:predicate obo:RO_0002200 . \
\n VALUES ?phenotype { \
\n OWL subeq <" + self.PHENOME_SERVICE_URL + "> <" +
ontology + "> { \
\n " + label + " \
\n } \
\n } . \
\n ?association rdf:object ?phenotype . \
\n ?phenotype rdfs:label ?phenotypeLabel . \
\n ?association rdf:subject ?concept . \
\n ?concept rdfs:label ?conceptLabel .")
elif phenotype_iri and not concept_iri:
return ('\n ?association rdf:predicate obo:RO_0002200 . \
\n ?association rdf:object <' + phenotype_iri + '> . \
\n <' + phenotype_iri + '> rdfs:label ?phenotypeLabel . \
\n ?association rdf:subject ?concept . \
\n ?concept rdfs:label ?conceptLabel .')
elif not phenotype_iri and not concept_iri:
return ('\n ?association rdf:predicate obo:RO_0002200 . \
\n ?association rdf:object ?phenotype. \
\n ?phenotype rdfs:label ?phenotypeLabel . \
\n ?association rdf:subject ?concept . \
\n ?concept rdfs:label ?conceptLabel .')
else:
return ''
def add_phenotype_label(self):
phenotypes = list(set(self.store.subjects(RDF.type, PHENO.Phenotype)))
phenotypes_iris = list(map(lambda i: str(i), phenotypes))
hp_phenotypes = list(
set(filter(lambda x: find_valueset(x) == 'HP', phenotypes_iris)))
hp_indices = lookup_es.find_entity_by_iris(hp_phenotypes, 'HP')
logger.info("Resolving iris; total:%d|found:%d", len(hp_phenotypes),
len(hp_indices))
self.add_label(hp_phenotypes, hp_indices)
mp_phenotypes = list(
set(filter(lambda x: find_valueset(x) == 'MP', phenotypes_iris)))
mp_indices = lookup_es.find_entity_by_iris(mp_phenotypes, 'MP')
logger.info("Resolving iris; total:%d|found:%d", len(mp_phenotypes),
len(mp_indices))
self.add_label(mp_phenotypes, mp_indices)
def resolve_display(self):
gene = list(set(self.store.subjects(RDF.type, PHENO.Gene)))
gene_iris = list(map(lambda i:str(i), gene))
gene_indices = lookup_es.find_entity_by_iris(gene_iris, 'MGI')
logger.info("Resolving iris; total:%d|found:%d", len(gene_iris), len(gene_indices))
self.add_label(gene_iris, gene_indices)
self.add_phenotype_label()
self.add_evidence_label()
def resolve_display(self):
metabolites = list(set(self.store.subjects(RDF.type, PHENO.Metabolite)))
metabolites_iris = list(map(lambda i:str(i), metabolites))
logger.info("Resolving iris; total:%d", len(metabolites_iris))
metabolites_indices = lookup_es.find_entity_by_iris(metabolites_iris, 'CHEBI')
self.add_label(metabolites_iris, metabolites_indices)
self.add_phenotype_label()
self.add_evidence_label()
def resolve_display(self):
diseases = list(set(self.store.subjects(RDF.type, PHENO.Disease)))
diseases_iris = list(map(lambda i:str(i), diseases))
logger.info("Resolving iris; total:%d", len(diseases_iris))
diseases_indices = lookup_es.find_entity_by_iris(diseases_iris, 'DOID')
self.add_label(diseases_iris, diseases_indices)
self.add_phenotype_label()
self.add_evidence_label()
def resolve_display(self):
pathogens = list(set(self.store.subjects(RDF.type, PHENO.Pathogen)))
pathogen_iris = list(map(lambda i:str(i), pathogens))
logger.info("Resolving iris; total:%d", len(pathogen_iris))
pathogen_indices = lookup_es.find_entity_by_iris(pathogen_iris, 'NCBITAXON')
self.add_label(pathogen_iris, pathogen_indices)
self.add_phenotype_label()
self.add_evidence_label()
def resolve_display(self):
genes = list(set(self.store.subjects(RDF.type, PHENO.Gene)))
genes_iris = list(map(lambda i: str(i), genes))
mgi_gene = list(
set(filter(lambda x: find_valueset(x) == 'MGI', genes_iris)))
mgi_indices = lookup_es.find_entity_by_iris(mgi_gene, 'MGI')
logger.info("Resolving iris; total:%d|found:%d", len(mgi_gene),
len(mgi_indices))
self.add_label(mgi_gene, mgi_indices)
ncbi_gene = list(
set(filter(lambda x: find_valueset(x) == 'NCBIGene', genes_iris)))
ncbi_indices = lookup_es.find_entity_by_iris(ncbi_gene, 'NCBIGene')
logger.info("Resolving iris; total:%d|found:%d", len(ncbi_gene),
len(ncbi_indices))
self.add_label(ncbi_gene, ncbi_indices)
self.add_phenotype_label()
self.add_evidence_label()
def post(self, request, format=None):
try:
entity_iris = request.data['iri']
valueset = None
if 'valueset' in request.data:
valueset = request.data['valueset']
if not entity_iris:
raise RuntimeException("'iri' property is required")
result = lookup_es.find_entity_by_iris(entity_iris, valueset)
return Response(result)
except Exception as e:
logger.exception("message")
def add_evidence_label(self):
evidences = list(set(self.store.objects(None, OBO.RO_0002558)))
evidence_iris = list(map(lambda i: str(i), evidences))
logger.info("Resolving iris; total:%d", len(evidence_iris))
evidence_indices = lookup_es.find_entity_by_iris(evidence_iris, 'ECO')
self.add_label(evidence_iris, evidence_indices)