The original query:
SELECT ?it1 ?st1 ?p01 ?x01 ?p02 ?x02 ?p03 WHERE {?it1 ?st1 <http://bio2rdf.org/omim_vocabulary:Gene> . ?it1 ?p01 ?x01 . ?x01 ?p02 ?x02 . <http://bio2rdf.org/pharmgkb:PA446359> ?p03 ?x02 . FILTER (isIRI(?it1) && isIRI(?x01) && isIRI(?x02)) FILTER (?it1 != ?x01) FILTER (?it1 != ?x02) FILTER (?x01 != ?x02) FILTER (str(?p01) NOT IN ("http://rdfs.org/ns/void#inDataset", "http://bio2rdf.org/omim_vocabulary:refers-to", "http://bio2rdf.org/omim_vocabulary:article", "http://bio2rdf.org/omim_vocabulary:mapping-method", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "http://www.w3.org/2000/01/rdf-schema#subClassOf", "http://bioportal.bioontology.org/ontologies/umls/hasSTY")) FILTER (str(?p02) NOT IN ("http://rdfs.org/ns/void#inDataset", "http://bio2rdf.org/omim_vocabulary:refers-to", "http://bio2rdf.org/omim_vocabulary:article", "http://bio2rdf.org/omim_vocabulary:mapping-method", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "http://www.w3.org/2000/01/rdf-schema#subClassOf", "http://bioportal.bioontology.org/ontologies/umls/hasSTY")) FILTER (str(?p03) NOT IN ("http://rdfs.org/ns/void#inDataset", "http://bio2rdf.org/omim_vocabulary:refers-to", "http://bio2rdf.org/omim_vocabulary:article", "http://bio2rdf.org/omim_vocabulary:mapping-method", "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "http://www.w3.org/2000/01/rdf-schema#subClassOf", "http://bioportal.bioontology.org/ontologies/umls/hasSTY")) FILTER (str(?st1) IN ("http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "http://www.w3.org/2000/01/rdf-schema#subClassOf", "http://bioportal.bioontology.org/ontologies/umls/hasSTY"))} LIMIT 10
==Test 1 ==
FedX:
Rewriting the query by filling the predicate parts:
select ?s1 ?o1 ?o2 where{ ?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/omim_vocabulary:Gene>. ?s1 <http://bio2rdf.org/omim_vocabulary:phenotype> ?o1. ?o1 <http://bio2rdf.org/omim_vocabulary:x-snomed> ?o2. <http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-SnoMedCT> ?o2. }
select ?s1 ?o1 ?o2 where{ ?s1 ?p1 <http://bio2rdf.org/omim_vocabulary:Gene>. ?s1 <http://bio2rdf.org/omim_vocabulary:phenotype> ?o1. ?o1 <http://bio2rdf.org/omim_vocabulary:x-snomed> ?o2. <http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-SnoMedCT> ?o2. }
select ?s1 ?o1 ?o2 where{ ?s1 ?P1 <http://bio2rdf.org/omim_vocabulary:Gene>. ?s1 ?P2 ?o1. ?o1 <http://bio2rdf.org/omim_vocabulary:x-snomed> ?o2. <http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-SnoMedCT> ?o2. }
ALl of these three queries can be finished within 5 seconds.
select ?s ?p1 ?o1 ?o2 where{ ?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/omim_vocabulary:Gene>. ?s ?p2 ?o1. ?o1 ?p3 ?o2. <http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-SnoMedCT> ?o2.}
Error while using the FedX CLI. System will exit. Details: -1
As for the original query,the following error occurs:
Exception in thread "pool-31-thread-2" Exception in thread "Union Scheduler_12" java.lang.OutOfMemoryError?: Java heap space
==Test 2 ==
Virtuoso:
select ?s1 ?o1 ?o2 where{ service<http://pharmgkb.bio2rdf.org/sparql> {<http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-SnoMedCT> ?o2.} service<http://omim.bio2rdf.org/sparql> { ?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/omim_vocabulary:Gene>. ?s1 <http://bio2rdf.org/omim_vocabulary:phenotype> ?o1. ?o1 <http://bio2rdf.org/omim_vocabulary:x-snomed> ?o2.} }
OK!
select ?s1 ?o1 ?o2 where{ service<http://omim.bio2rdf.org/sparql> { ?s1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/omim_vocabulary:Gene>. ?s1 <http://bio2rdf.org/omim_vocabulary:phenotype> ?o1. ?o1 <http://bio2rdf.org/omim_vocabulary:x-snomed> ?o2.} service<http://pharmgkb.bio2rdf.org/sparql> {<http://bio2rdf.org/pharmgkb:PA446359> <http://bio2rdf.org/pharmgkb_vocabulary:x-SnoMedCT> ?o2.} }
wrong!
Virtuoso RDFZZ Error DB.DBA.SPARQL_REXEC('http://pharmgkb.bio2rdf.org/sparql', ...) has received result with unexpected variable name 'stubvar11'
Conclusion
1. Virtuoso requires explicitly specified Service keyword, namely SPARQL endpoints;
2. Even with the explicitly specified SPARQL endpoints, queries may not get an ideal result.
添付ファイル
- bio2RDF.ttl (3.7 KB) - 登録者 wu 10 年 前.
- SPARQL federated query.pdf (0.5 MB) - 登録者 wu 10 年 前.