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

manuelso manuelso at stanford.edu
Sun May 19 20:11:09 PDT 2013


Hi Simon,

You are right we should notify the users about incomplete answers. We have an action item for this that should be addressed soon. However we can only do this on the UI front-end and not on programatic queries because HTTP SPARQL program does not have a neat way to handle this. This is a known issue in or community see related discussion here [1].

Re: Documentation on incomplete results see "Partial or Incomplete results" here [2]

Best,

Manuel

[1] http://lists.w3.org/Archives/Public/public-lod/2013Apr/0198.html
[2] http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal



On May 14, 2013, at 8:39 PM, Simon Kocbek <simon at dbcls.rois.ac.jp> wrote:

> 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/[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
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>  

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