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From "John Green" <john.travis.gr...@gmail.com>
Subject RE: ctakes-vm.apache.org
Date Sat, 05 Apr 2014 19:15:13 GMT
Thanks Pei.




Sure, that would be great, add me.




Jg

—
Sent from Mailbox for iPhone

On Fri, Apr 4, 2014 at 10:15 AM, Chen, Pei <Pei.Chen@childrens.harvard.edu>
wrote:

> John,
> You should have committer rights now... I would suggest opening a Jira item just so that
it can be tracked.
> But you should be able create a subdir within https://svn.apache.org/repos/asf/ctakes/sandbox
and do an svn commit.
> As a side note: ctakes-vm.apache.org has been created now.  John, let me know if you
would like to added as list of maintainers.
> We can use that machine to host any of the demo's.
> It requires passwordless ssh so you'll need to ssh-keygen and save them via http://id.apache.org.
> --Pei
>> -----Original Message-----
>> From: John Green [mailto:john.travis.green@gmail.com]
>> Sent: Thursday, April 03, 2014 6:05 PM
>> To: dev@ctakes.apache.org
>> Cc: dev@ctakes.apache.org
>> Subject: RE: ctakes-vm.apache.org
>> 
>> 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
>> >>> >>
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