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
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 code
Virtuoso 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 ;
2014-05-28 15:02 GMT+02:00 Rumi <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 Kocis
>
>
>
> I 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
>
>
>
>
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