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[bioontology-support] Problem with subtreerootconceptid in REST request

Dan Bolser dan.bolser at gmail.com
Mon Dec 17 09:46:01 PST 2012


On 17 December 2012 16:10, Trish Whetzel <whetzel at stanford.edu> wrote:
> Hi Dan,
>
> This appears to be working now. The proper format of the web service call
> is:
> http://rest.bioontology.org/bioportal/search/?query=Alignment&ontologyids=1498&isexactmatch=false&subtreerootconceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0003&apikey=YourAPIKey
> This call returns 8 results.
>
> Note that the parameter "isexactmatch" is set to false to match terms that
> contain the string 'alignment' versus looking for the exact string
> 'alignment' within the 'topic' subtree.

Hi Trish,

Thanks for this update. Unfortunately, when I look in detail, I think
something is still wrong.

With either an 'isexactmatch=true' [1] or 'isexactmatch=false' [2] a
query for 'Alignment' returns the topic_0083. Note that this conceptId
is in the 'topic' subtree (topic_0003). If I add the appropriate
'subtree' clause to either of those queries [3,4] topic_0083 is *not*
returned. In the former case, nothing is returned, in the latter case
8 results are returned, but none of them are topic_0083.

So it looks like the latter case is working, but really it isn't... as
far as I can tell.


Cheers,
Dan.

[1] http://rest.bioontology.org/bioportal/search/?query=alignment&ontologyids=1498&isexactmatch=true&apikey=YourAPIKey
[2] http://rest.bioontology.org/bioportal/search/?query=alignment&ontologyids=1498&isexactmatch=false&apikey=YourAPIKey
[3] http://rest.bioontology.org/bioportal/search/?query=alignment&ontologyids=1498&isexactmatch=true&subtreerootconceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0003&apikey=YourAPIKey
[4] http://rest.bioontology.org/bioportal/search/?query=alignment&ontologyids=1498&isexactmatch=false&subtreerootconceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0003&apikey=YourAPIKey


P.S. For convenience, it appears that you can use the conceptShortId
in the URL (gives the same result as using the conceptId):
http://rest.bioontology.org/bioportal/search/?query=alignment&ontologyids=1498&isexactmatch=false&subtreerootconceptid=topic_0003&apikey=YourAPIKey



> Also, the value for the parameter
> "subtreerootconceptid" needs to be uri-encoded as described in the wiki
> documentation for this parameter.
>
> Best,
> Trish
>
>
>
> On Nov 21, 2012, at 2:11 PM, Trish Whetzel wrote:
>
> 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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