ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "John Green" <john.travis.gr...@gmail.com>
Subject RE: ctakes-vm.apache.org
Date Thu, 03 Apr 2014 22:04:00 GMT
Would love to! Ive only submitted those example notes I did though to a jira ticket. How do
I push to the sandbox dir? Any special permissions I need? 




JG

—
Sent from Mailbox for iPhone

On Wed, Apr 2, 2014 at 10:51 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu>
wrote:

> John,
> If there are no other objections, you can also put it directly in sandbox
> https://svn.apache.org/repos/asf/ctakes/sandbox/
> It may make it easier in the future if folks decided to integrate into cTAKES... and
possibly save any potential IP/License questions...
> --Pei
> ________________________________________
> From: John Green [john.travis.green@gmail.com]
> Sent: Wednesday, April 02, 2014 6:24 PM
> To: dev@ctakes.apache.org
> Subject: Re: ctakes-vm.apache.org
> 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
> —
> Sent from Mailbox for iPhone
> 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
>>> >>
Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message