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

Simon Kocbek simon at dbcls.rois.ac.jp
Fri May 31 01:06:13 PDT 2013


Hi Kevin, 

you might find the following fact interesting. If you try to sort the result
with the ORDER BY keyword, the query actually returns more than 1.200.000
hits where applicable.

So the following query:

"SELECT  ?p, (COUNT(?p) as ?pCount)
WHERE {
  GRAPH <http://bioportal.bioontology.org/ontologies/SNOMEDCT> {
    ?s ?p ?o .
  }
}
group by ?p order by (?pCount)"

returns all (?) 13.644.855 predicates for SNOMEDCT

Hope it helps.

Thanks, 
Simon

-----Original Message-----
From: Kevin B. Cohen [mailto:kevin.cohen at gmail.com] 
Sent: Wednesday, May 15, 2013 3:42 AM
To: Simon Kocbek
Cc: support at bioontology.org
Subject: Re: [bioontology-support] SPARQL - getting all predicates for an
ontology

Hi, Simon,

I have run into the same problem (with SNOMED, specifically).  Trish was
very helpful in finding a solution for me.

Kev

On Tue, May 14, 2013 at 1:38 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
>



--
Kevin Bretonnel Cohen, PhD
Biomedical Text Mining Group Lead, Computational Bioscience Program, U.
Colorado School of Medicine
303-916-2417 (cell) 303-377-9194 (home)
http://compbio.ucdenver.edu/Hunter_lab/Cohen



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