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[bioontology-support] procedures CPT
Huser, Vojtech MD PhD
huser.vojtech at marshfieldclinic.org
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 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<mailto:support at bioontology.org> will answer questions if you get stuck etc.
On Thu, May 13, 2010 at 2:41 PM, Nigam Shah <nigam at stanford.edu<mailto: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
<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
<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.
On Thu, May 13, 2010 at 1:09 PM, Murphy, Shawn N. <SNMURPHY at partners.org<mailto:SNMURPHY at partners.org>> wrote:
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 kumc.edu<mailto:vpagadala at kumc.edu>]
Sent: Thursday, May 13, 2010 12:21 PM
To: members at i2b2aug.org<mailto:members at i2b2aug.org>
Cc: Arvinder Choudhary
Subject: procedures CPT
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,
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