Hi Andra, On 30-May-14 10:35 AM, Andra Waagmeester wrote:
Hi Rumi,That seems odd to me, because the same query on , that means that the SERVICE parts of the query changes gives results. I would expect that if the sparql endpoint at the EBI does not support the OPTION CLAUSE that there would be no results either.The query submitted at: http://www.ebi.ac.uk/rdf/services/atlas/sparql is: PREFIX up:<http://purl.uniprot.org/core/> PREFIX keywords:<http://purl.uniprot.org/keywords/> PREFIX uniprotkb:<http://purl.uniprot.org/uniprot/> PREFIX taxon:<http://purl.uniprot.org/taxonomy/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> PREFIX skos:<http://www.w3.org/2004/02/skos/core#> PREFIX owl:<http://www.w3.org/2002/07/owl#> PREFIX bibo:<http://purl.org/ontology/bibo/> PREFIX dc:<http://purl.org/dc/elements/1.1/> PREFIX xsd:<http://www.w3.org/2001/XMLSchema#> PREFIX faldo:<http://biohackathon.org/resource/faldo#> PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#> PREFIX sio: <http://semanticscience.org/resource/> PREFIX wp: <http://vocabularies.wikipathways.org/wp#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX identifiers:<http://identifiers.org/ensembl/> PREFIX atlas: <http://rdf.ebi.ac.uk/resource/atlas/> PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/> PREFIX efo: <http://www.ebi.ac.uk/efo/> SELECT DISTINCT ?wpTitle ?dbXref ?expressionValue WHERE { { SERVICE <http://95.85.25.210:8890/sparql>{ ?pwElement dcterms:isPartOf ?wpPathway . ?wpPathway dc:identifier <http://identifiers.org/wikipathways/WP455> . ?wpPathway dc:title ?wpTitle . ?pwElement wp:bdbEnsembl ?dbXref . } } ?value atlasterms:hasFactorValue ?factor . ?value atlasterms:isMeasurementOf ?probe . ?value atlasterms:pValue ?pvalue . ?value rdfs:label ?expressionValue . ?probe atlasterms:dbXref ?dbXref . ?disFactor rdfs:subClassOf+ efo:EFO_0000408 . ?disease rdf:type ?disFactor . ?disFactor rdfs:label ?label . }The query is also submitted to http://95.85.25.210:8890/sparql but doesn't choke on the option clause
When I try from http://95.85.25.210:8890/sparql the query from below, it does give the error:
Virtuoso 37000 Error SP031: SPARQL compiler: SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> at line 30 does not support OPTION (...) clause for triples so SPARQL query can not be composed Note that below you have "SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql>" and other hand, in the above query you have "SERVICE <http://95.85.25.210:8890/sparql>" Of course in the case you set as SERVICE Virtuoso sparql endpoint, it will work as Virtuoso does support the Option() .. clause.
PREFIX keywords:<http://purl.uniprot.org/keywords/> PREFIX uniprotkb:<http://purl.uniprot.org/uniprot/> PREFIX taxon:<http://purl.uniprot.org/taxonomy/> PREFIX ec:<http://purl.uniprot.org/enzyme/> PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> PREFIX skos:<http://www.w3.org/2004/02/skos/core#> PREFIX owl:<http://www.w3.org/2002/07/owl#> PREFIX bibo:<http://purl.org/ontology/bibo/> PREFIX dc:<http://purl.org/dc/elements/1.1/> PREFIX xsd:<http://www.w3.org/2001/XMLSchema#> PREFIX faldo:<http://biohackathon.org/resource/faldo#> PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#> PREFIX sio: <http://semanticscience.org/resource/> PREFIX wp: <http://vocabularies.wikipathways.org/wp#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX identifiers:<http://identifiers.org/ensembl/> PREFIX atlas: <http://rdf.ebi.ac.uk/resource/atlas/> PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/> PREFIX efo: <http://www.ebi.ac.uk/efo/> SELECT DISTINCT ?wpTitle ?dbXref ?expressionValue WHERE { { GRAPH <http://wikipathways>{ ?pwElement dcterms:isPartOf ?wpPathway . ?wpPathway dc:identifier <http://identifiers.org/wikipathways/WP455> . ?wpPathway dc:title ?wpTitle . ?pwElement wp:bdbEnsembl ?dbXref . } SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> { ?value atlasterms:hasFactorValue ?factor . ?value atlasterms:isMeasurementOf ?probe . ?value atlasterms:pValue ?pvalue . ?value rdfs:label ?expressionValue . ?probe atlasterms:dbXref ?dbXref . ?disFactor rdfs:subClassOf+ efo:EFO_0000408 . ?disease rdf:type ?disFactor . ?disFactor rdfs:label ?label . } } }When I tried the suggested work around I am getting the following error codeVirtuoso 42000 Error SQ110: Permission denied for delete from DB.DBA.RDF_QUAD (user ID = 106) SPARQL query: define sql:big-data-const 0 #output-format:text/html define sql:signal-void-variables 1 LOAD SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> DATA ;
Hm, that is strange,I have just executed from http://95.85.25.210:8890/conductor the statement successfully:
SPARQL LOAD SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> DATA; Query result: callret-0 ANYLoad service <http://www.ebi.ac.uk/rdf/services/atlas/sparql> data -- done. The endpoint <http://www.ebi.ac.uk/rdf/services/atlas/sparql> has support for define lang:dialect 1312 (hex 00000520)
No. of rows in result: 1 Best Regards, Rumi Kocis
2014-05-28 15:02 GMT+02:00 Rumi <rtsek...@openlinksw.com <mailto:rtsek...@openlinksw.com>>:Hi Andra, On 27-May-14 9:25 PM, Andra Waagmeester wrote:I am trying to run a federated query of which the individual sub graphs on the their respective SPARQL points return the expected results, however when combined I am getting the following error message: Virtuoso 37000 Error SP031: SPARQL compiler: SERVICE <https://www.ebi.ac.uk/fgpt/atlasrdf/sparql> at line 33 does not support OPTION (...) clause for triples so SPARQL query can not be composed.The error message means that the https://www.ebi.ac.uk/fgpt/atlasrdf/sparql sparql endpoint does not support OPTION clause. Basically, you should be able to use the following command to interrogate a target SPARQL endpoint (if initial SPARQL-FED fails): SPARQL LOAD SERVICE <{SPARQL-END-POINT-URL}> DATA So in your case: LOAD SERVICE <https://www.ebi.ac.uk/fgpt/atlasrdf/sparql> <https://www.ebi.ac.uk/fgpt/atlasrdf/sparql> DATA ; Best Regards, Rumi KocisI am running: Virtuoso Open Source Edition (Column Store) (multi threaded) Version 7.1.1-dev.3209-pthreads as of May 21 2014 Compiled for Linux (x86_64-unknown-linux-gnu) and the query submitted is: SELECT DISTINCT ?wpTitle ?dbXref ?expressionValue WHERE { { GRAPH <http://wikipathways>{ ?pwElement dcterms:isPartOf ?wpPathway . ?wpPathway dc:identifier <http://identifiers.org/wikipathways/WP455> . ?wpPathway dc:title ?wpTitle . ?pwElement wp:bdbEnsembl ?dbXref . } SERVICE <https://www.ebi.ac.uk/fgpt/atlasrdf/sparql> { ?value atlasterms:hasFactorValue ?factor . ?value atlasterms:isMeasurementOf ?probe . ?value atlasterms:pValue ?pvalue . ?value rdfs:label ?expressionValue . ?probe atlasterms:dbXref ?dbXref . ?disFactor rdfs:subClassOf+ efo:EFO_0000408 . ?disease rdf:type ?disFactor . ?disFactor rdfs:label ?label . } } } Anyone has an idea of what is going wrong here? Any suggestion would be highly appreciated. Regards, Andra ------------------------------------------------------------------------------ The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk _______________________________________________ Virtuoso-users mailing list Virtuoso-users@lists.sourceforge.net <mailto:Virtuoso-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/virtuoso-users
smime.p7s
Description: S/MIME Cryptographic Signature
------------------------------------------------------------------------------ Time is money. Stop wasting it! Get your web API in 5 minutes. www.restlet.com/download http://p.sf.net/sfu/restlet
_______________________________________________ Virtuoso-users mailing list Virtuoso-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/virtuoso-users
