Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] SPARQL - getting all predicates for an ontology

Simon Kocbek simon at dbcls.rois.ac.jp
Tue May 14 20:39:26 PDT 2013


Hi Manuel, 

 

thank you for your answer. 

 

Do you recommend any workaround for this limitation? There are also other
queries that won't work correctly as a result. For example:

 

"SELECT ?p, (COUNT(?p) as ?pCount)

WHERE {

  GRAPH <http://bioportal.bioontology.org/ontologies/RCD> {

    ?s ?p ?o .

  }

}

GROUP BY ?p"

 

also returns only 1200000 predicates, however there is no indication that
the query had been interrupted. I believe users should be informed about
this somehow. 

 

Are these kind of limitations documented somewhere? 

 

Thanks, 

Simon

 

From: manuelso [mailto:manuelso at stanford.edu] 
Sent: Wednesday, May 15, 2013 12:59 AM
To: Simon Kocbek
Cc: support at bioontology.org
Subject: Re: [bioontology-support] SPARQL - getting all predicates for an
ontology

 

Hi Simon,

 

Unbound predicate queries are very inefficient and hit query timeouts. They
tend to not return all the answers. Probably the query is being stopped by
server always at the same point returning the same number.

 

It is not a bug it is just a configuration we have to assure that no query
uses too many resources.

 

Manuel

 

 

On May 14, 2013, at 12:38 AM, "Simon Kocbek" <simon at dbcls.rois.ac.jp> wrote:





Hi BioPortal,

 

I have a problem with getting the number of predicates for larger ontologies
through the SPARQL interface.

 

The following query:

 

SELECT (COUNT(?p) as ?pCount)

WHERE {

  GRAPH < <http://bioportal.bioontology.org/ontologies/%5bontology%5d>
http://bioportal.bioontology.org/ontologies/[ontology]> {

    ?s ?p ?o .

  }

}

 

will always return the same number (i.e., 1200000) for large [ontology]
values (e.g, SNOMEDCT, RCD, NCBITAXON).

 

Is this a bug?

 

Thanks,

Simon

 

_______________________________________________
bioontology-support mailing list
 <mailto:bioontology-support at lists.stanford.edu>
bioontology-support at lists.stanford.edu
 <https://mailman.stanford.edu/mailman/listinfo/bioontology-support>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20130515/efcc0215/attachment.html>


More information about the bioontology-support mailing list