[jira] [Created] (CTAKES-375) Including gene mappings in UMLS

["Pei Chen (JIRA)" <ji...@apache.org>]

Pei Chen created CTAKES-375:
-------------------------------

             Summary: Including gene mappings in UMLS
                 Key: CTAKES-375
                 URL: https://issues.apache.org/jira/browse/CTAKES-375
             Project: cTAKES
          Issue Type: Improvement
            Reporter: Pei Chen
            Priority: Minor


Hello cTakers

My name is iker Huerga and I'm a software engineer/data scientist at Memorial Sloan Kettering in NYC. I've been using cTakes for a while now in some of my projects and I'd like to contribute the gene/mutations module to the project

I have more than 8 years of Java experience and have contributed to other apache projects in the past such as Apache Lucene and more recently Apache Ignite. If someone can create the JIRA ticket and assign it to me (ihuerga) I'll start working on it

Thanks
Iker

> On Sep 1, 2015, at 9:40 PM, "Savova, Guergana" <Gu...@childrens.harvard.edu> wrote:
> 
> Hi Chris,
> We have not focused on the gene mappings because gene mentions were not very frequent in the clinical narrative until several years ago. However, as genes/mutations and proteins have become actionable items in both diagnosing and treatment, we do have plans to add a module for gene/mutations/protein mentions in the very near future. We are likely to start with cancer since that domain offers most actionable information and is consistently recorded in pathology notes. Contributions are more than welcome.
> 
> Is this helping? 
> Cheers,
> --Guergana
> 
> -----Original Message-----
> From: Mattmann, Chris A (3980) [mailto:chris.a.mattmann@jpl.nasa.gov] 
> Sent: Tuesday, September 1, 2015 7:16 PM
> To: dev@ctakes.apache.org
> Subject: Including gene mappings in UMLS
> 
> Hey cTAKES community,
> 
> 
> 
> Is there any particular reason that you guys didn’t do the mappings
> 
> for genes (which exists in UMLS) - but doesn’t seem to exist as
> 
> cTAKES concept identifiers (CIDs)?
> 
> 
> 
> Are there any plans to include this in a future release of Apache
> 
> cTAKES? We were just wondering.
> 
> 
> 
> Thanks all!
> 
> 
> 
> Cheers,
> 
> Chris
> 
> 
> 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> Chris Mattmann, Ph.D.
> 
> Chief Architect
> 
> Instrument Software and Science Data Systems Section (398)
> 
> NASA Jet Propulsion Laboratory Pasadena, CA 91109 USA
> 
> Office: 168-519, Mailstop: 168-527
> 
> Email: chris.a.mattmann@nasa.gov
> 
> WWW:  https://urldefense.proofpoint.com/v2/url?u=http-3A__sunset.usc.edu_-7Emattmann_&d=BQIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=Dq_pRYxsnlvTlbBj114Dbfhjvu-Ps3J0sV5YYJj-S3o&s=NWXiQ1BQ4rFG345QMhfFcVwsFIiy9cmd_8KD9rlGh1w&e= 
> 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> Adjunct Associate Professor, Computer Science Department
> 
> University of Southern California, Los Angeles, CA 90089 USA
> 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
> 
> 
> 
> 
> 




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