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[bioontology-support] Query to get children.

Eamonn Maguire maguire at ebi.ac.uk
Thu Aug 20 09:38:48 PDT 2009


I can't access it no.

Eamonn
On 20 Aug 2009, at 17:35, Trish Whetzel wrote:

> The hierarchy services are currently geared towards certain versions  
> of an ontology, so 39885 is the version that has been processed to  
> generate data for the ontology hierarchy services. This version also  
> includes the 'efo:' prefix for the term while the version 40394 does  
> not.
>
> There is a service to call to get the list of ontologies that are  
> used in the ontology hierarchy service, however I have been having  
> difficulty accessing this from outside Stanford and trying to sort  
> out the reason. The URL is: http://ncbo-obs-prod1:8080/obs_hibernate/ 
> ontologies. Are you able to access this?
>
> Trish
>
>
> On Aug 20, 2009, at 9:13 AM, Eamonn Maguire wrote:
>
>> 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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>>
>

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










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