Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Query to get children.

Trish Whetzel whetzel at stanford.edu
Thu Aug 20 09:35:47 PDT 2009


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
>
>
>
>
>
>
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20090820/ebe79350/attachment.html>


More information about the bioontology-support mailing list