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From andy mcmurry <mcmurry.a...@gmail.com>
Subject Re: ctakes-vm.apache.org
Date Wed, 02 Apr 2014 17:52:29 GMT
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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