Silk Workbench - error when generating links

[Amrapali Zaveri]

Hello,

I am trying to interlink two datasets using the Silk Workbench. When I run "Generate Links", I get these two errors:

SELECT DISTINCT ?a ?v0

WHERE {

?y <http://bio2rdf.org/taxonomy_vocabulary:scientific-name> ?name .

?a a <http://bio2rdf.org/taxonomy_vocabulary:Resource> .

OPTIONAL {

?a <http://bio2rdf.org/taxonomy_vocabulary:anamorph> ?v0 .

}

} ORDER BY ?a OFFSET 0 LIMIT 1000

Error Message: 'Virtuoso 42000 Error The estimated execution time 23076402 (sec) exceeds the limit of 400000 (sec).

Even though I restricted the Link Limit to 1, I still get this error.

Please let me know how I can overcome this.

Thanks.

Regards,

Amrapali

[Jindřich Mynarz]

Hi Amrapali,

this is a problem of Virtuoso, not of Silk. It may be related to erroneous estimation of query execution time in Virtuoso (see https://github.com/openlink/virtuoso-opensource/issues/535#issuecomment-187787567 or https://github.com/openlink/virtuoso-opensource/issues/229). If you have the queried Virtuoso instance under your control, you may try to increase the MaxQueryCostEstimationTime parameter in the virtuoso.ini configuration file. If that doesn't work, I suggest you raise this issue on the Virtuoso support channels (virtuos...@lists.sourceforge.net or https://github.com/openlink/virtuoso-opensource/issues).

- Jindřich

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[Amrapali J Zaveri]

Thanks Jindrich. I have another question: Why is the SPARQL query adding the OPTIONAL part? I did not specify it anywhere.

Thanks.

Regards,
Amrapali Zaveri, PhD

Dumontier Lab, Stanford University

Twitter: @amrapaliz

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[Jindřich Mynarz]

AFAIK, Silk wraps each property path (https://github.com/silk-framework/silk/blob/master/doc/Linking.md#property-paths) that you specify in <Input/> in OPTIONAL (https://github.com/silk-framework/silk/blob/master/silk-plugins/silk-plugins-rdf/src/main/scala/org/silkframework/plugins/dataset/rdf/sparql/SparqlPathBuilder.scala#L38-L45), since the path may not be present.

- Jindřich