读取 Turtle 文件并使用 SPARQL 查询图形

Question

I am in a learning phase of SPARQL so excuse if the question sounds basic. I am exploring SPARQLWrapper to connect to a SPARQL endpoint to fetch some data. Below is the query.

sparql = SPARQLWrapper("http://patho.phenomebrowser.net/sparql/") #endpoint link

sparql.setQuery("""

PREFIX SIO: <http://semanticscience.org/resource/SIO_>
PREFIX RO: <http://purl.obolibrary.org/obo/RO_>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT distinct ?PA_ID ?pathogen  ?D_ID ?disease ?disease_pathogen_evidence_code  ?P_ID ?phenotype ?disease_phenotype_evidence_code  
FROM <http://patho.phenomebrowser.net>
WHERE
  {
    ?D_ID SIO:000255 ?o1 .
    ?o1 RO:0002558 ?EC1_ID . 
    ?o1 RO:0002200 ?P_ID .
    ?D_ID SIO:000255 ?o .
    ?o RO:0002558 ?EC2_ID .
    ?o RO:0002556 ?PA_ID .
    ?PA_ID rdfs:label ?pathogen.
    ?P_ID rdfs:label ?phenotype .
    ?D_ID rdfs:label ?disease .
    ?EC1_ID rdfs:label ?disease_phenotype_evidence_code .
    ?EC2_ID rdfs:label ?disease_pathogen_evidence_code .

  } limit 50 
""")

sparql.setReturnFormat(JSON)
results = sparql.query().convert()

for result in results["results"]["bindings"]:
    print(result["pathogen"]["value"])

The query above work fine. Is there a way to load or read a Turtle file and then use SPARQLWrapper to query the graph?

Answer 1

To be able to query a graph with SPARQLWrapper, you need to load this graph in a SPARQL endpoint. Such an endpoint could be hosted locally, eg:

sparql = SPARQLWrapper("http://localhost/sparql")

The documentation lists how certain endpoints can be used with SPARQLWrapper: SPARQL Endpoint Implementations

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Instead of using SPARQLWrapper, you could consider using RDFLib (which gets used by SPARQLWrapper, and comes from the same developers), which allows you to query endpoints (using SERVICE ) as well as files (no need to load them in an endpoint).