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From andy mcmurry <mcmurry.a...@gmail.com>
Subject Re: ctakes-vm.apache.org
Date Thu, 20 Mar 2014 09:30:45 GMT
Yes! I have been working full time on the "apt-get install" task specific
to medical genetics: http://www.ncbi.nlm.nih.gov/medgen

Right now, millions of $$$ are invested in getting phenotype concepts --
indications, diseases, problem lists -- linked to patient test results
including DNA / RNA / etc. In industry, most of the curation work is done
manually because platforms like cTAKES are not yet immediately accessible.

I have written code to
A) start automating the installer tasks for cTAKES on Ubuntu 13
B) install UMLS NLP tools metamap, semrep, semmed
C) mirror NLM content that extends UMLS annotation

*SO THAT : *

Mentions of diseases relationships -- SNOMED-CT, HPO, OMIM, GTR, UMLS --
reference the same semantic relationships in UMLS Clinical Terms and
Genetic Test Reference. This is powerful and all credit to the NLM for
creating MedGen and GTR, new crucial additions to the UMLS. To my
knowledge, these new sources have not been fully utilized by the medical
NLP community.

*I'm strongly advocating for a cTAKES VM that indexes UMLS concepts in the
same say that NCBI indexes UMLS linked Medical Genetics terms.*

Towards this goal, if other committers are interested,  I'm 100% time
committed to this problem.

*TL;DR*: at minimum, having a demo site makes cTAKES more accessible. We
should demonstrate rather than explain every feature of cTAKES. I'm working
100% on the Clinical Text +BioNLP problem. If that interests you, let me
know I'm convinced this area has huge, understudied potential.


On Tue, Mar 18, 2014 at 8:15 AM, Pei Chen <chenpei@apache.org> wrote:

> FYI:
> ASF Infra is setting up our VM for demo purposes.
> INFRA-7451
> If you need access, feel free to let us now.
> Initial maintainers: james-masanz, andymc,chenpei
> --Pei

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