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From andy mcmurry <mcmurry.a...@gmail.com>
Subject Re: ctakes-vm.apache.org
Date Mon, 07 Apr 2014 21:41:52 GMT
On a mac here, also having trouble logging in to the VM.
Looking more into the keys situation.

On mac, there is this problem: "no support for PKCS#11"
Which I'm working to resolve.




On Sat, Apr 5, 2014 at 12:15 PM, John Green <john.travis.green@gmail.com>wrote:

> 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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