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[bioontology-support] Ontology View

Bhandare, Aniket abhandare at path.wustl.edu
Tue Sep 21 08:34:31 PDT 2010


Thanks a lot Nigam and Trish for your help.

I will try on these lines.

 

-Aniket

 

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Monday, September 20, 2010 7:42 PM
To: Bhandare, Aniket
Cc: Nigam Shah; support
Subject: Re: Ontology View

 

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=372
148003&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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