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

Simon Kocbek simon at dbcls.rois.ac.jp
Tue May 21 01:37:20 PDT 2013


Hi Manuel, 

 

thank you for your answer. 

 

Since I still wish to count numbers of specific/all predicates in a single
ontology, I've decided to download ontologies as RDF/XML and parse them
myself. I use the download service as described here:

http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#RDF_Downlo
ad_Service

 

However, I have another question. For example, according to SPARQL query,
FBdv contains 132 prefLabel relations/predicates
(http://bioportal.bioontology.org/metadata/def/prefLabel). When I search for
this relation in the downloaded ontology (vid: 1016), I cannot find any.
Some other relations that I am interested in (e.g., subclassOf, label) agree
with the SPARQL query.

 

Could you please explain this behaviour?

 

Thanks, 

Simon

 

From: manuelso [mailto:manuelso at stanford.edu] 
Sent: Monday, May 20, 2013 12:11 PM
To: Simon Kocbek
Cc: support at bioontology.org
Subject: Re: [bioontology-support] SPARQL - getting all predicates for an
ontology

 

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>
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@ <http://stanford.edu> stanford.edu] 
Sent: Wednesday, May 15, 2013 12:59 AM
To: Simon Kocbek
Cc:  <mailto:support at bioontology.org> 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" <
<mailto:simon at dbcls.rois.ac.jp> 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

 

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