バージョン 1 から バージョン 2 における更新: ~FederatedQuery

更新日時:

2014/08/21 10:18:44 (10 年 前)

更新者:

wu

コメント:

--

~FederatedQuery

@@ -1 @@
-Test
+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.
+}
+
+}}}
+
+Both of the two queries can be finished within 5 seconds.
+
+
+{{{
+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.
+}
+
+}}}
+
+
+
+
+==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.