python snippet to test sparql queries (use in REPL)

sparql-query.py

# python snippet to test sparql queries


# set up the graph
import rdflib
_rdfGraph = rdflib.ConjunctiveGraph()
_rdfGraph.parse('tests/data/datasets/dataset1/phenotypes/cgd/cgd-test.ttl', format='n3')


# substitute your query here
query = """
PREFIX OBAN: <http://purl.org/oban/>
PREFIX OBO: <http://purl.obolibrary.org/obo/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT
    ?association
    ?environment
    ?environment_label
    ?feature
    ?feature_label
    ?phenotype
    ?phenotype_label
    (GROUP_CONCAT(?source; separator="|") AS ?sources)
    ?evidence_type
    WHERE {
        ?association  a OBAN:association .
        ?association    OBO:RO_0002558 ?evidence_type .
        ?association    OBO:RO_has_environment ?environment   .
        OPTIONAL { ?association  dc:source ?source } .
        ?association    OBAN:association_has_subject ?feature .
        ?association    OBAN:association_has_object ?phenotype .
        ?environment  rdfs:label ?environment_label  .
        ?phenotype  rdfs:label ?phenotype_label  .
        ?feature  rdfs:label ?feature_label  .
        FILTER (?phenotype = <http://ohsu.edu/cgd/30ebfd1a>)
        }
GROUP  BY ?association
ORDER  BY ?association
"""


# query and print
associations = _rdfGraph.query(query)

for row in associations.bindings:
  print(row)