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] procedures CPT

Huser, Vojtech MD PhD huser.vojtech at
Mon May 17 13:03:05 PDT 2010

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?


From: drnigam at [mailto:drnigam at] On Behalf Of Nigam Shah
Sent: Thursday, May 13, 2010 17:13
To: members at
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<mailto:support at> will answer questions if you get stuck etc.

On Thu, May 13, 2010 at 2:41 PM, Nigam Shah <nigam at<mailto:nigam at>> 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:
<>    - specifically "get term"
    - and then recursively "get children"

<>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.


On Thu, May 13, 2010 at 1:09 PM, Murphy, Shawn N. <SNMURPHY at<mailto:SNMURPHY at>> 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.


From: Venkata Pagadala [mailto:vpagadala at<mailto:vpagadala at>]
Sent: Thursday, May 13, 2010 12:21 PM
To: members at<mailto:members at>
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

The information in this e-mail is intended only for the person to whom it is

addressed. If you believe this e-mail was sent to you in error and the e-mail

contains patient information, please contact the Partners Compliance HelpLine at . If the e-mail was sent to you in error

but does not contain patient information, please contact the sender and properly

dispose of the e-mail.

The contents of this message may contain private, protected and/or privileged information.  If you received this message in error, you should destroy the e-mail message and any attachments or copies, and you are prohibited from retaining, distributing, disclosing or using any information contained within.  Please contact the sender and advise of the erroneous delivery by return e-mail or telephone.  Thank you for your cooperation.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list