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

Kevin B. Cohen kevin.cohen at gmail.com
Fri May 31 08:59:38 PDT 2013


Thank you, Simon.

Kev

On Fri, May 31, 2013 at 2:06 AM, Simon Kocbek <simon at dbcls.rois.ac.jp> wrote:
> 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
>



-- 
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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