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From "John Green" <john.travis.gr...@gmail.com>
Subject Re: ctakes-vm.apache.org
Date Wed, 02 Apr 2014 22:24:21 GMT
Great! 




Let me clean it up this weekend and ill throw it out onto my github. Will post link soon;
nlt cob this weekend.




JG

—
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On Wed, Apr 2, 2014 at 1:53 PM, andy mcmurry <mcmurry.andy@gmail.com>
wrote:

> Yes! Impeccable timing. Where can we find the python source?
> On Apr 2, 2014 8:33 AM, "John Green" <john.travis.green@gmail.com> wrote:
>> 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
>>
>> --
>> Sent from Mailbox for iPhone
>>
>> 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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