Re: Travis for testing

Does cTakes use Jenkins? If not, I would like to volunteer in the > > > configuration of it. > > > What sort of bureaucracy hoops should I jump through to be able work on > > > this :) > > > > Here is the Apache Jenkins: https://builds.apache.org > > > > Searching for "ctakes", I found two jobs there. > > > > Cheers, > > > > -- Richard > > > -- jay vyas

Re: Docker

Dockerizing ctakes as a build was useful at one time for sure. If running as a microservice remember the size of the image is problematic ; you don't want it on lots of different nodes if using something like kubernetes. Also remember to make sure you run with Xmx args so that cgroups done const

Re: Migration to Git

ARG sorry I meang GIT would be preferred :).. Anyways, in the interim, Pull Requests are welcome, and I'm sure Pei will happily merge them for you :) :) :) On Thu, Oct 22, 2015 at 10:42 AM, jay vyas wrote: > Hi suneel. Great idea... Someday hopefully :) > > (1) Feel free to su

Re: Migration to Git

ince most other Apache projects > have already migrated over? It would be easier to submit/review patches on > Git than SVN. > -- jay vyas

Re: Packaging Ctakes Application

copies you may have > created and notify me immediately by replying to this email. Thank you. > > > > Geisinger Health System utilizes an encryption process to safeguard > Protected Health Information and other confidential data contained in > external e-mail messages. If email is encrypted, the recipient will receive > an e-mail instructing them to sign on to the Geisinger Health System Secure > E-mail Message Center to retrieve the encrypted e-mail. > -- jay vyas

Re: End to end ctakes example app

0:52 AM, Savova, Guergana < guergana.sav...@childrens.harvard.edu> wrote: > Jay, > Do you mean something like this: > http://52.26.219.218:8080/index.jsp > > --guergana > > -Original Message- > From: Jay Vyas [mailto:jayunit100.apa...@gmail.com] > Sen

Re: CTAKES-377 : Upgrade to Java 8

+1 for sure > On Sep 18, 2015, at 10:06 AM, Ted Strall wrote: > > Going to Java 8 can provide a lot of benefit to an application like cTAKES. > The new features added to Java 8 are a game changer in terms of doing data > pipelining. The streams functionality and the ability to do functional >

End to end ctakes example app

Is there a end 2 end ctakes app that can be used to demonstrate all the core Portions of it? We built the bigpetstore app in bigtop to do this. And we have a data generator. Maybe time to do something similar for ctakes

Re: Boston cTAKES Hackathon?

Yes I'd love to. How about some lightning talks also to start the night off? I know Harvard is using ctakes for some stuff. > On Sep 16, 2015, at 4:23 PM, Pei Chen wrote: > > Hi, > I hope everyone had a great summer. I just wanted to resurrect the > Docker integration idea. > Anyone interested

Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives

Yes this is very interesting work. - If we have access to a large corpus of de identified records we can recession test the ctakes platform. - I can help collaborate on a regression testing framework if someone else wants to help Maintain it. > On Jul 24, 2015, at 11:12 AM, Pei Chen wrote:

Re: UmlsConcept subject

nabled in the clinical pipeline until this > new Subject Classifier is fixed? > > Thanks, > Tomasz > -- jay vyas

Re: Integration of Tika with cTAKES

This is awesome; thanks! For some of the new ctakes projects where fplks bc are aiming at using it with big data tooling, the till abstraction might be super useful. On Jun 6, 2015 8:19 PM, "Mattmann, Chris A (3980)" < chris.a.mattm...@jpl.nasa.gov> wrote: > Hey cTAKES peeps! > > We went ahead a

Re: [VOTE] Release Apache cTAKES 3.2.2 (rc2)

s-2D3.2.2-2Dsrc.tar.gz.md5&d=BQMDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=7L5MUxlkhMYDS-BUpfA2NU3vIPZgSwZqSyMm4dfICQg&s=MVx9tZTThRbARCWwhF6H8gGzoq2Lxt0YNIHegaVudQY&e=> >> >> /.zip.md5 >> >> >> >> The signature of the tarball can be found at: >> >> https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/apache-ctakes-3.2.2-src.tar.gz.asc >> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__dist.apache.org_repos_dist_dev_ctakes_ctakes-2D3.2.2-2Drc2_apache-2Dctakes-2D3.2.2-2Dsrc.tar.gz.asc&d=BQMDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=7L5MUxlkhMYDS-BUpfA2NU3vIPZgSwZqSyMm4dfICQg&s=2Q67800RBncc6aNG4pYiWEoEUb651gpFoOXXMlNHJLM&e=> >> >> /.zip.asc >> >> >> >> Apache cTAKES' KEYS file, containing the PGP keys used to sign the release: >> >> https://dist.apache.org/repos/dist/release/ctakes/KEYS >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__dist.apache.org_repos_dist_release_ctakes_KEYS&d=BQMDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=7L5MUxlkhMYDS-BUpfA2NU3vIPZgSwZqSyMm4dfICQg&s=Z2mFjX2pyjO3sFfi6q2LxZRjc_uh6E_HMS5kEC1QaFg&e=> >> >> >> >> Please vote on releasing these packages as Apache cTAKES 3.2.2. The vote is >> >> open for at least the next 72 hours. >> >> >> >> The vote passes if at least three binding +1 votes are cast. >> >> [ ] +1 Release the packages as Apache cTAKES 3.2.2 >> >> [ ] -1 Do not release the packages because... >> >> >> >> Also, the convenience binary can be found at: >> >> https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/apache-ctakes-3.2.2-bin.tar.gz.md5 >> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__dist.apache.org_repos_dist_dev_ctakes_ctakes-2D3.2.2-2Drc2_apache-2Dctakes-2D3.2.2-2Dbin.tar.gz.md5&d=BQMDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=7L5MUxlkhMYDS-BUpfA2NU3vIPZgSwZqSyMm4dfICQg&s=yC9TgSVlyFJd1Q5HyUaNPdp7tTevjTbONipoSLql72I&e=> >> >> /.zip >> >> >> >> >> >> >> > -- jay vyas

Re: CTAKES mirroring on github.

ens.harvard.edu] > > Sent: Tuesday, February 17, 2015 12:31 PM > > To: dev@ctakes.apache.org > > Subject: Re: CTAKES mirroring on github. > > > > Is there any existing resource to help people who want to use git > > understand the right workflow to contribute to ctak

Re: cTAKES and UMLS web service

orant of cTAKES as well. I have never set it up or > even > > used it. After installation we would need to expose it in a Rest web > > service. Many considerations there (DoS attacks, etc). Recommendations > > welcome! > > > > Does it make sense to anyone to concomitantly expose search of UMLS as a > > webservice? Would this require a separate Solr/Elasticsearch instance? > > > > Dave Donohue > > > -- jay vyas

Re: cTAKES and UMLS web service

This is a fabulous idea. Are you able to invest in some cloud resources for hosting? If so I think Project atomic might be a great way to deploy Ctakes as a service on containers. > On Mar 9, 2015, at 6:26 AM, David Donohue wrote: > > Hi everyone > I am working on a free and open source Perso

Re: Running cTakes in parallel

We also have a spark implementation in the ctakes sandbox you can use (for up to date see jayunit100/SparkStreamingApps on gh). Sent from my iPhone > On Feb 25, 2015, at 2:17 PM, Finan, Sean > wrote: > > Hi Michelle, > > When it comes to >> multiple instances of cTakes in parallel > You can

Re: CTAKES mirroring on github.

im > > > On 02/17/2015 12:23 PM, jay vyas wrote: > > Hi CTakes. Looks like infra finally got onto the JIRA i made for this a > > while back. They are currently working on fixing a couple of minor > > glitches w/ the mirroring (not showing all commits)... but there now

CTAKES mirroring on github.

Hi CTakes. Looks like infra finally got onto the JIRA i made for this a while back. They are currently working on fixing a couple of minor glitches w/ the mirroring (not showing all commits)... but there now is a mirror for CTakes on github. https://github.com/apache/ctakes -- jay vyas

Re: revamping the Apache cTAKES website

r > >> the Lord your God is with you wherever you go." ~Joshua 1:9 On Fri, Dec > 5, 2014 at 11:21 AM, Savova, Guergana < > guergana.sav...@childrens.harvard.edu> wrote: > >>> cTAKES-ers, > >>> > >>> we would like to start working on updating the Apache cTAKES website > >>> - some of the information there is already stale and needs refreshing. > >>> Do you have ideas on website design, content, etc.? Would you like to > >>> contribute to the effort? We are planning to start working on the > >>> website the week of Dec 15. > >>> > >>> Cheers, > >>> --Guergana > >>> > >>> > -- jay vyas

Re: Scaling cTakes

> Protected Health Information and other confidential data contained in > external e-mail messages. If email is encrypted, the recipient will receive > an e-mail instructing them to sign on to the Geisinger Health System Secure > E-mail Message Center to retrieve the encrypted e-mail. > > -- jay vyas

Re: Announcement: UMLS MedGen-MySQL dataset now available as open access download

+1000 on this! Great lets make a jira!!! > On Nov 11, 2014, at 5:02 PM, andy mcmurry wrote: > > Hello! > > https://bitbucket.org/invitae/medgen-mysql (Apache Licensed ASL2) > > We just released a new library containing a huge chunk of UMLS concepts > which are available without registering ac

Re: CTakes on github.

> > On Thu, Oct 30, 2014 at 12:40 PM, jay vyas > wrote: > > > Hi Pei : I Agree with (A) - the hybrid approach, so anyone can use both, > or > > and git.apache.org has working github mirroring. > > > -- jay vyas

Re: CTakes on github.

Hi Pei : I Agree with (A) - the hybrid approach, so anyone can use both, or and git.apache.org has working github mirroring.

CTakes on github.

Hi CTakes. I notice we dont have a github presence yet. Maybe we can file an INFRA ticket for this ? -- jay vyas

Re: cTakes output predictability

dded. > > I would like to work towards addressing this issue by changing those areas > of the code where it matters to use a LinkedHashMap instead. > > Is this something the community would be interested in and find helpful? > > Thanks, > > Bruce Tietjen > Perfect Search Corp. > -- jay vyas

Re: Boston cTAKES Meetup

Shall we create an umbrella jira ? > On Sep 23, 2014, at 6:26 AM, Prakash Poudyal wrote: > > It will be great if you could broadcast the gathering, talk, etc. I wish I > would be there, but it is very hard tor is not possible for me to be there. > > Prakash Poudyal > Portugal > > On Tue, Sep 2