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[bioontology-support] Ontology View

Trish Whetzel whetzel at stanford.edu
Mon Sep 20 17:42:29 PDT 2010


Hi Aniket,

Currently the auto-complete widget does not include the feature you  
mention, however I added this as a feature request.  In the interim,  
you can use the View Extraction web service ( http://www.bioontology.org/wiki/index.php/View_Extraction 
  ) to extract all children of the concept "Ethnic group" as a subtree  
from SNOMED CT and then load this subtree as a View of SNOMED CT ( http://bioportal.bioontology.org/ontologies/42789#views 
  ).

Details on the View Extraction web service are described here:
http://www.bioontology.org/wiki/index.php/View_Extraction

and therefore the corresponding URL to extract the "Ethnic group"  
subtree is:
http://rest.bioontology.org/bioportal/viewextractor/42789/?conceptid=372148003&ontologyname=http://testing.org/ethnic-group.owl&delay=10

Trish

PS - cc'ing support at bioontology.org to log this request


On Sep 8, 2010, at 1:43 PM, Bhandare, Aniket wrote:

> Hi Trish,
>
> I tried using Ontology widget auto-complete dropdown for term search  
> in ontology.
> I tried option "get the preferred name for a term". To do so we  
> specify ontology id in the class attribute of html input tag. In my  
> case, I tried it with SNOMEDCT ontology and so  
> class="bp_form_complete-1353-name"
>
> I was wondering if it's possible to limit options in a dropdown to a  
> particular term. E.g. Say in my application I want to show a  
> dropdown to select one of "Ethnic group" values. It’s a valid term  
> in SNOMEDCT with id 372148003. So can I specify this term id along  
> with ontology id in class attribute of html input tag to limit  
> permissible values in dropdown? If no, is there any other way to  
> accomplish this?
> Please let me know your inputs on this.
>
> Thanks,
> Aniket
>
> From: Nigam Shah [mailto:nigam at stanford.edu]
> Sent: Thursday, August 26, 2010 12:15 PM
> To: Nagarajan, Rakesh
> Cc: Bhandare, Aniket; McIntosh, Leslie; Trish Whetzel
> Subject: Re: Ontology View
>
> Hi Rakesh, Aniket and Leslie,
>
> You can use any method/tool of your choice to create a view. If the  
> ontology you want to create a view of is in OWL, you can use Protege  
> to create the view. Once you have the view, you can upload it by  
> simply going to bioportal at: http://bioportal.bioontology.org/ontologies 
>  and clicking on the ontology of which you have created a view. For  
> example, if you create a view of the NCIT, and you click on NCIT (in  
> the first column in the table at: http://bioportal.bioontology.org/ontologies) 
>  .. you will reach:
>
> http://bioportal.bioontology.org/ontologies/42838 ... go to the  
> "views" tab and click on "create new view" link to submit your file.
>
> Trish Whetzel (cc'ed) can help if you run into any issues.
>
> Regards,
> Nigam.
>
> On Thu, Aug 26, 2010 at 9:26 AM, Nagarajan, Rakesh  
> <rakesh at wustl.edu> wrote:
> Nigam,
>     It was great seeing your presentation yesterday.  We are  
> interested in creating a view of a larger ontology one of our  
> collaborators will soon load into BioPortal.  Can you point Aniket/ 
> Leslie, CCed, to documentation on how we can do this and then load  
> this view back into BioPortal?
>
> Thanks,
> Rakesh
>

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