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[bioontology-support] Query to get children.

Eamonn Maguire maguire at ebi.ac.uk
Fri Aug 21 10:10:55 PDT 2009


Hi Michael,

This is very useful.

Coming back to the original feature request of adding an extra  
parameter to the search query to specify a branch to search under, how  
long do you think it will take before this feature is implemented? By  
the way, I'm happy to contribute with the effort of doing it since any  
implementation I do now will simply be replaced by whatever is created  
by you guys when the actual ability to query under a branch is realised.

Any code i write now will essentially take the result of the hierarchy  
function and then filter for terms containing the string searched for  
by the user.

Thanks,

Eamonn

On 20 Aug 2009, at 19:42, Michael Dorf wrote:

> Hi Eamonn,
>
> This is the correct URL to use:
>
> http://rest.bioontology.org/obs_hibernate/ontologies
>
> The complete list of OBS services is available here:
>
> http://rest.bioontology.org/test_obs.html
>
> The Hierarchy Services subsection of this page is the one you are  
> referencing from BioPortal. For example, the service
>
> http://rest.bioontology.org/obs_hibernate/parents/MSH/C0025202
>
> is also available as
>
> http://rest.bioontology.org/bioportal/concepts/parents/MSH/C0025202  
> in a slightly different (more BioPortal-centric) XML format.
>
>
> Hope this helps.
>
> Misha
>
>
>
> From: Eamonn Maguire [mailto:maguire at ebi.ac.uk]
> Sent: Thursday, August 20, 2009 9:39 AM
> To: Trish Whetzel
> Cc: Michael Dorf; support at bioontology.org
> Subject: Re: Query to get children.
>
> 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
>
>
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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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>
> --
> *        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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--
* 	maguire at ebi.ac.uk
: 	http://www.ebi.ac.uk/~maguire
:     http://www.ebi.ac.uk/net-project










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