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From "John Green" <john.travis.gr...@gmail.com>
Subject Re: ctakes-vm.apache.org
Date Wed, 02 Apr 2014 15:32:41 GMT
Andy: this is very interesting and exciting. 




I hacked out a script that makes a visually appealing representation of the aggregate pipeline
in d3js that, at least for a clinician, is a nice overall summary of the meta data generated
from the pipeline. Its really no more than a parser of the xml through the type system spitted
out into json, but when I was talking to my informatics department who didnt know much at
all about ctakes, it was a great visual summary. Its in python. I dont know if youd want it
but it might be worth having the "demo site" spit out a visually appealing graphic like this
automatically. If not in python it might be worth adapting it to whatever your using for a
platform to spit out the json for the d3js graphic im using.




John

—
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On Thu, Mar 20, 2014 at 5:31 AM, andy mcmurry <mcmurry.andy@gmail.com>
wrote:

> 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.
> --AndyMC
> 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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