How to handle SPARQL-FED queries for SPARQL endpoints with no OPTION() clause supported?

Suppose the following sample scenario:

  1. Assume the following SPARQL-FED query:

    PREFIX wp: <http://vocabularies.wikipathways.org/wp#> 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 <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 . } } }

  2. Execute the query from Virtuoso sparql endpoint
  3. As result you should get the following error:

    Virtuoso 37000 Error SP031: SPARQL compiler: SERVICE <https://www.ebi.ac.uk/fgpt/atlasrdf/sparql> at line 18 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, one should be able to use the following command to interrogate a target SPARQL endpoint (if initial SPARQL-FED fails):


So in our example it would be:

LOAD SERVICE  <https://www.ebi.ac.uk/fgpt/atlasrdf/sparql> DATA ;