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[bioontology-support] procedures CPT

Trish Whetzel whetzel at stanford.edu
Mon May 17 13:09:17 PDT 2010


Hi Vojtech,

I have included Nigam on this thread to point you to the code sample.

Best regards,
Trish


On May 17, 2010, at 1:03 PM, Huser, Vojtech MD PhD wrote:

> Dear BioOntology team,
>
> We are trying to implement the code below (in bold), but ran into  
> some problems. perhaps it would be best to look at the code as  
> suggested by Nigam.
> Could you email us the code, please?
>
> Vojtech
>
>
>
>
> From: drnigam at gmail.com [mailto:drnigam at gmail.com] On Behalf Of  
> Nigam Shah
> Sent: Thursday, May 13, 2010 17:13
> To: members at i2b2aug.org
> Cc: Venkata Pagadala; Arvinder Choudhary; Murphy, Shawn N.
> Subject: Re: procedures CPT
>
> PS: A little history and future work ...Last fall, we (NCBO and  
> i2b2) did a bunch of tests - which led to the prototype Shawn  
> mentioned - primarily to make sure that our web service outputs  
> contain all the information that the i2b2 ontology cell would need.  
> The plan for future work is to make an ontology manager that can do  
> the steps I mentioned from within the i2b2 workbench. Till, that  
> happens using the services directly will do the job .. support at bioontology.org 
>  will answer questions if you get stuck etc.
>
> -Nigam.
>
> On Thu, May 13, 2010 at 2:41 PM, Nigam Shah <nigam at stanford.edu>  
> wrote:
> Thanks Shawn. The prototype code is still available and will dump  
> out any ontology in NCBO in the i2b2 format. Conceptually it is very  
> simple and does the following:
>
> 1 - you specify an ontology to extract (or a root node that you want  
> to extract the branch under)
>
> 2 - the code simply calls the services at: http://www.bioontology.org/wiki/index.php/NCBO_REST_services
>     - specifically "get term" http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_term_for_latest_ontology_version_id
>     - and then recursively "get children" http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_parents.2Fchildren_of_a_given_concept_in_the_latest_version_of_a_given_ontology
>
> 3 - parses the XML using a few XPATH expressions and writes out the  
> information the information in the i2b2 format.
>
>
> That's about it. I am happy to share the code .. but its simple  
> enough that most people can just write their own routines in their  
> favorite language.
>
> Regards,
> Nigam.
>
>
> On Thu, May 13, 2010 at 1:09 PM, Murphy, Shawn N. <SNMURPHY at partners.org 
> > wrote:
> Hi Venkata,
>
> The only way to add vocabulary items through tools is in the "Edit"  
> View of the ontology of the i2b2 workbench that was added in 1.5.   
> We will be adding a more robust ontology manager in the future  
> working with the NCBO team.
>
> For now, you can contact Nigam (NCBO) and see what state a prototype  
> tool he made for us might be in.
>
> Thanks,
> Shawn.
>
> From: Venkata Pagadala [mailto:vpagadala at kumc.edu]
> Sent: Thursday, May 13, 2010 12:21 PM
> To: members at i2b2aug.org
> Cc: Arvinder Choudhary
> Subject: procedures CPT
>
> Hello everyone,
>
> We are using I2B2 version 1.4 and we are trying to setup CPT's in  
> the procedures hierarchy in addition to ICD9 hierarchical levels.  
> Can anyone please guide us how to set up the hierarchy or do we have  
> a place we can download the hierarchical levels to our  
> concept_dimension and i2b2metadata tables?
>
> Thanks for your help,
> Venkata Pagadala
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org



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