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[bioontology-support] Query to get children.

Eamonn Maguire maguire at ebi.ac.uk
Thu Aug 20 09:13:12 PDT 2009


Hi trish et al :o)

now, this is closer to what i need :o) i didn't realise this service  
was available! if anything there is too much metadata associated with  
this query though. We'd only really metadata similar to that returned  
in bioportals search function. For a large hierarchy, this file could  
be massive particularly in an ontology with a hierarchy containing  
large numbers of axioms. You'd essentially be returning a subset of  
the OWL file in a differing XML format.

however i see that the version of EFO you are making me query with is  
old. Whenever i attempt to query with the latest version i get the  
same error that i got yesterday when i reported the problems with the  
children query returning a 'No child in hierarchy found' message.

http://rest.bioontology.org/bioportal/concepts/children/40394/efo:EFO_0000352

or

http://rest.bioontology.org/bioportal/concepts/40394/efo:EFO_0001456?email=example@example.org

Thanks,

Eamonn


On 20 Aug 2009, at 16:49, Trish Whetzel wrote:

> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>

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










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