def find_all_phenotypes(self, concept_iri):
query = 'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \
\nPREFIX pb: <http://phenomebrowser.net/> \
\nPREFIX obo: <http://purl.obolibrary.org/obo/> \
\nSELECT ?phenotype ?phenotypeLabel \
\nFROM <http://phenomebrowser.net> \
\nWHERE { \
\n <' + concept_iri + '> obo:RO_0002200 ?phenotype . \
\n ?phenotype rdfs:label ?phenotypeLabel . \
\n} ORDER BY asc(?phenotypeLabel)'
logger.debug("Executing find all phenotypes query for a concept: %s",
concept_iri)
return (virt.execute_sparql(query, self.MIME_TYPE_JSON), query)
def find_matching_phenotypes(self, source_iri, target_iri):
query = 'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \
\nPREFIX pb: <http://phenomebrowser.net/> \
\nPREFIX obo: <http://purl.obolibrary.org/obo/> \
\nSELECT ?phenotype ?phenotypeLabel \
\nFROM <http://phenomebrowser.net> \
\nWHERE { \
\n <' + source_iri + '> obo:RO_0002200 ?phenotype . \
\n <' + target_iri + '> obo:RO_0002200 ?phenotype . \
\n ?phenotype rdfs:label ?phenotypeLabel . \
\n} ORDER BY asc(?phenotypeLabel)'
logger.debug("Executing find all associationset query")
return (virt.execute_sparql(query, self.MIME_TYPE_JSON), query)
def find_associationsets(self):
query = 'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \
\nPREFIX pb: <http://phenomebrowser.net/> \
\nPREFIX dcterms: <http://purl.org/dc/terms/> \
\nPREFIX dc: <http://purl.org/dc/elements/1.1/> \
\nSELECT ?associationset ?identifier ?label ?type ?description ?source ?download \
\nFROM <http://phenomebrowser.net> \
\nWHERE { \
\n ?associationset rdf:type pb:AssociationSet . \
\n ?associationset dc:identifier ?identifier . \
\n ?associationset rdfs:label ?label . \
\n ?associationset dc:description ?description . \
\n OPTIONAL { ?associationset dcterms:source ?source . }\
\n OPTIONAL { ?associationset pb:download ?download . } \
\n ?associationset pb:includeTypes ?type . \
\n} ORDER BY asc(?label)'
logger.debug("Executing find all associationset query")
return (virt.execute_sparql(query, self.MIME_TYPE_JSON), query)
def find_similar_concepts(self,
concept_iri,
type_iri,
order_by,
limit=100):
order_clause = self.create_orderby_clause(order_by)
query = 'PREFIX b2v: <http://bio2vec.net/function#> \
\nPREFIX b2vd: <http://bio2vec.net/dataset#> \
\n \
\nSELECT ?concept ?conceptLabel ?type ?val ?x ?y \
\nWHERE { \
\n SERVICE <https://bio2vec.cbrc.kaust.edu.sa/ds/query> { \
\n (?concept ?val ?x ?y) b2v:mostSimilar(b2vd:dataset_4 <' + concept_iri + '> ' + str(limit) + ' ' \
+ (('<' + type_iri + '>' ) if type_iri else '') + ') . \
\n } \
\n GRAPH <http://phenomebrowser.net> { \
\n ?concept a ?type . \
\n OPTIONAL { ?concept rdfs:label ?conceptLabel } .\
\n } \
\n}' + order_clause
logger.debug("Executing query for search criteria: concept_iri=" +
concept_iri)
return (virt.execute_sparql(query, self.MIME_TYPE_JSON), query)
def find(self,
concept_iri,
phenotype_iri,
concept_type_iri=None,
evidence_iris=[],
associationset_iris=None,
include_subclass=False,
limit=10,
offset=None,
order_by=None):
phenotype_stmt = self.create_phenotype_filter(phenotype_iri,
concept_iri,
include_subclass)
concept_stmt = self.create_concept_filter(concept_iri, phenotype_iri)
type_subj = '?concept' if not concept_iri else '<{iri}>'.format(
iri=concept_iri)
type_stmt = (
type_subj + ' rdf:type <' + concept_type_iri + '> .'
) if concept_type_iri else type_subj + ' rdf:type ?conceptType .'
concept_var = '?concept' if not concept_iri else '(<{iri}> as ?concept)'.format(
iri=concept_iri)
type_var = '?conceptType' if not concept_type_iri else '(<{iri}> as ?conceptType)'.format(
iri=concept_type_iri)
phenotype_var = '?phenotype' if not phenotype_iri and not include_subclass else '(<{iri}> as ?phenotype)'.format(
iri=phenotype_iri)
order_clause = self.create_orderby_clause(order_by)
page = order_clause + ' LIMIT ' + str(limit) + " OFFSET " + str(
offset) if offset else ''
graph_pattern = 'WHERE { \
\n ?association rdf:type rdf:Statement . \
' + phenotype_stmt + ' \
' + concept_stmt + ' \
\n ' + type_stmt + ' \
\n ' + self.associationset_stmt(associationset_iris) + ' \
\n ?associationset rdfs:label ?associationsetLabel . \
\n ' + self.evidence_stmt(evidence_iris) + ' \
\n ?evidence rdfs:label ?evidenceLabel . \
\n ?association dc:provenance ?prov . \
\n ?prov dc:creator ?creator . \
\n ?prov dcterms:source ?source . \
\n OPTIONAL { ?prov dcterms:created ?created . } \
\n}'
query = 'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \
\nPREFIX pb: <http://phenomebrowser.net/> \
\nPREFIX obo: <http://purl.obolibrary.org/obo/> \
\nPREFIX dcterms: <http://purl.org/dc/terms/> \
\nPREFIX dc: <http://purl.org/dc/elements/1.1/> \
\n\
\nSELECT * \
\n{\n { \
\n SELECT ?association ' + concept_var + ' ' + type_var + ' ' + phenotype_var + ' ?phenotypeLabel ?conceptLabel \
\n ?evidence ?evidenceLabel ?creator (group_concat(distinct ?source;separator=",") as ?sources) ?created \
\n ?associationset ?associationsetLabel \
\n FROM <http://phenomebrowser.net> \
\n ' + graph_pattern + page + ' \
\n } \
\n UNION { select (count(*) as ?total) \
\n FROM <http://phenomebrowser.net> \
\n ' + graph_pattern + ' \
\n }\n}'
logger.debug("Executing query for search criteria: concept_iri=" +
str(concept_iri) + "|phenotype_iri=" +
str(phenotype_iri) + "|concept_type_iri=" +
str(concept_type_iri))
# logger.debug("Query : %s", query)
if not include_subclass:
return (virt.execute_sparql(query, self.MIME_TYPE_JSON), query)
else:
return (aberowl.execute_sparql(query, self.MIME_TYPE_JSON), query)