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[bioontology-support] Problem with subtreerootconceptid in REST request

Trish Whetzel whetzel at stanford.edu
Wed Nov 21 14:11:15 PST 2012


Hi Dan, 

As best I can tell, there appears to be a bug when including the "subtreerootconceptid" parameter in that the searchBean information is not returned, i.e. the actual search results. When changing the param "isexactmatch" from true to false the value of "numHitsTotal" changes from 3 to 212 but with no actual results returned and I've tried this call with previous examples that now also do not return the actual search results. 

I'll submit a bug report on this issue. To help prioritize, can you provide a few details on the effect of this issue on your project, e.g. can not move forward with project or can wait a few weeks for this to be resolved. 

Trish 


On Nov 21, 2012, at 1:23 PM, Dan Bolser 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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