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[bioontology-support] Problem with subtreerootconceptid in REST request

Dan Bolser dan.bolser at gmail.com
Wed Nov 21 13:45:26 PST 2012


I notice EDAM is in this list with status 28:
http://rest.bioontology.org/obs/ontologies?apikey=sekret

and that this appears to be working:
http://rest.bioontology.org/bioportal/viewextractor/47814?apikey=sekret&conceptid=EDAM_topic%3A0003

although nothing has been returned after several minutes, even trying
with a much smaller tree:
http://rest.bioontology.org/bioportal/viewextractor/47814?apikey=sekret&conceptid=EDAM_topic%3A0199

So I'm no closer to working out the problem :-/


Cheers,
Dan.

On 21 November 2012 21:23, Dan Bolser <dan.bolser at gmail.com> wrote:
> Hi,
>
> I'm trying to do a REST search with subtreerootconceptid [1] because
> my search term 'Alignment' matches several branches of the EDAM
> ontology. For example:
> http://rest.bioontology.org/bioportal/search?apikey=sekret&ontologyids=1498&isexactmatch=true&query=Alignment
>
> Returns the following three concepts:
> * EDAM_data:1916
> * EDAM_topic:0083
> * EDAM_operation:2928
>
> In this particular search, I only want to return concepts in the
> 'topic' branch of the EDAM ontology, so I'm trying the following (and
> various permutations thereof):
> http://rest.bioontology.org/bioportal/search?apikey=sekret&ontologyids=1498&isexactmatch=true&query=Alignment&subtreerootconceptid=EDAM_topic%3A0003
>
> Nothing I've tried seems to work, returning zero hits instead of the
> previous three. This seems to be the right way to specify the 'topic'
> branch, being the subtree of the topic node:
> http://bioportal.bioontology.org/ontologies/47814/?p=terms&conceptid=EDAM_topic%3A0003
>
> Am I doing something wrong?
>
>
> Many thanks for any suggestions,
> Dan.
>
> [1] http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Search_BioPortal


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