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[bioontology-support] Query to get children.

Eamonn Maguire maguire at ebi.ac.uk
Thu Aug 20 03:58:53 PDT 2009


Thanks trish,

So now my next question relates to the metadata. In the result from http://rest.bioontology.org/bioportal/concepts/children/39885/efo:EFO_0000352 
  we have a result which looks like this:

<classBean>
     <ontologyVersionId>39885</ontologyVersionId>
     <id>efo:EFO_0000493</id>
     <relations>
         <entry>
             <string>Level</string>
             <int>1</int>
         </entry>
     </relations>
</classBean>

now, this doesn't give me much in terms of anything i can use straight  
away. can i request the addition of the concept name and concept short  
name like you have in the main search result to avoid making many  
additional queries to find out what EFO_0000493 actually is.

For those of you in this email who don't know the use-case we want to  
implement, i'll give you a quick overview.

inside isacreator we offer people the choice of querying either a  
recommended ontology (provided through a configuration tool) or to  
search the whole ontology. the latter case is already fulfilled by  
BioPortal obviously :o) in the case of querying a recommended  
ontology(ies) you also have what we would need if we just wanted to  
query for terms matching 'protocol' for example in OBI or EFO through  
supplying ontology ids. However, what if i wanted to restrict the  
search space as well as the ontology, meaning restricting the search  
to a certain part of one or more ontologies. e.g., in EFO http://bioportal.bioontology.org/visualize/40394 
  when a search is made, only the terms under 'process (EFO_0001433)'  
should be searched for.

I have already requested via trish an extra parameter in BioPortals  
search query to allow one to provide an ontology term id or unique  
name (dependent on the ontology being used) to restrict the search  
space to a particular part of the ontology.

the query would look like this:

http://rest.bioontology.org/bioportal/search/protocol/?ontologyids=39885&searchBranch=EFO_0001433

not only would such a search be greatly advantageous to us, but it  
could also speed up searches made by others on bioportal since the  
search space is restricted!

i hope this is clear,

thanks for all your great efforts thus far!!

Eamonn


On 19 Aug 2009, at 17:26, Trish Whetzel wrote:

> There was a change in the identifiers for EFO a few versions back.  
> The change is that there was an extra 'efo' in the fully qualified  
> term name.
>
> The term id in version 39885 is: http://bioportal.bioontology.org/visualize/39885/efo:EFO_0000001
> The term id in version 40394 is: http://bioportal.bioontology.org/visualize/40394/EFO_0000001
>
> So using http://rest.bioontology.org/bioportal/virtual/children/1136/efo:EFO_0000352 
> , will get the child term of clinical history or http://rest.bioontology.org/bioportal/concepts/children/39885/efo:EFO_0000352 
>  will work.
>
> Trish
>
>
>
> On Aug 19, 2009, at 6:16 AM, Eamonn Maguire wrote:
>
>> Hi Trish,
>>
>> Just a quick question.
>>
>> I'm having trouble getting the "Get parents/children of a given  
>> concept in a specific ontology version" query to work properly. For  
>> instance, I thought that making the following queries should work,  
>> but they return a message saying that no children exist in the  
>> hierarchy when they clearly do.
>> http://rest.bioontology.org/bioportal/concepts/children/40394/EFO_0000352
>>
>> i get the same message using the virual ontology equivalent of this  
>> method
>> http://rest.bioontology.org/bioportal/virtual/children/1136/EFO_0000352
>>
>> any ideas?
>>
>> thanks,
>> Eamonn
>> --
>> * 	maguire at ebi.ac.uk
>> : 	http://www.ebi.ac.uk/~maguire
>> :     http://www.ebi.ac.uk/net-project
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>

--
* 	maguire at ebi.ac.uk
: 	http://www.ebi.ac.uk/~maguire
:     http://www.ebi.ac.uk/net-project










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