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[bioontology-support] Query to get children.

Trish Whetzel whetzel at stanford.edu
Thu Aug 20 08:49:59 PDT 2009


Hi Eamonn,

The last I talked to the developers on the design of the bean from the  
hierarchy services the information I received is that the hierarchy  
service needs to be used with the concept service, e.g. http://rest.bioontology.org/bioportal/concepts/39885/efo:EFO_0000352?email=example@example.org 
, to generate the additional term information.

Misha, can you add more on this design decision and whether the  
preferred term field can be added to the bean from the ontology  
hierarchy service?

Thanks,
Trish


On Aug 20, 2009, at 3:58 AM, Eamonn Maguire wrote:

> 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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