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[bioontology-support] Problem with subtreerootconceptid in REST request

Dan Bolser dan.bolser at gmail.com
Wed May 15 09:53:43 PDT 2013


Hah!

I only just spotted that topic_0083 (Alignment) isn't below
topic_0003! It's been moved to below oboInOwl:ObsoleteClass.

If I try the subtree restriction using 'data_0006', it works as
expected. This also works:
http://rest.bioontology.org/bioportal/search/?query=alignment&ontologyids=1498&isexactmatch=true&subtreerootconceptid=oboInOwl:ObsoleteClass&apikey=YourAPIKey


Cheers,
Dan.

On 17 December 2012 17:46, Dan Bolser <dan.bolser at gmail.com> wrote:
> 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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>>
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>>
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>>
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