Silk Workbench - error when generating links

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Amrapali Zaveri

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Jun 6, 2016, 6:55:18 PM6/6/16
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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

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Jun 7, 2016, 4:36:28 AM6/7/16
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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

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Jun 7, 2016, 2:24:05 PM6/7/16
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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

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Jun 7, 2016, 4:17:40 PM6/7/16
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