RE: [VOTE] Release Apache cTAKES 3.2.1 (rc2)

Thanks for testing Tim. I don't think AggregatePlaintextProcessor.xml (w/o UMLS) does much actually. We can fix the descriptor xml in the next patch irrespective [1]. I updated the documentation[2] to say - if you want something simple to test, try the SentencesAndTokensAggregate.xml in the me

revamping the Apache cTAKES website

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

gold standard annotations for Apache cTAKES sample notes

Thanks to John Green, we now have sample clinical notes in cTAKES. Many thanks, John, for your effort! We will take these notes and will start generating gold annotations that could be used then to compare cTAKES output to. We are planning to include annotations for: 1. Entities with the

Re: revamping the Apache cTAKES website

Hello Guergana, I don't know that much about cTakes, but would be interested in contributing to the effort. I'm not sure if there is an interest in matching the website design of other Apache projects, but it seems that the two main designs that are being used from my arbitrary search on http://p

RE: revamping the Apache cTAKES website

Wonderful, thank you, Michelle! There will be a flurry of emails the week of Dec 15 followed by actual work, so book your calendar if possible... --Guergana -Original Message- From: Michelle Chen [mailto:michelle1919c...@gmail.com] Sent: Friday, December 05, 2014 11:48 AM To: dev@ctakes.

RE: revamping the Apache cTAKES website

There are now 4 volunteers: Michelle Chen Pei Chen Sean Finan Guergana Savova --Guergana -Original Message- From: Savova, Guergana [mailto:guergana.sav...@childrens.harvard.edu] Sent: Friday, December 05, 2014 11:56 AM To: dev@ctakes.apache.org Subject: RE: revamping the Apache cTAKES we

Re: gold standard annotations for Apache cTAKES sample notes

This is great, thanks John green ! On Dec 5, 2014 8:32 AM, "Savova, Guergana" < guergana.sav...@childrens.harvard.edu> wrote: > Thanks to John Green, we now have sample clinical notes in cTAKES. Many > thanks, John, for your effort! > > We will take these notes and will start generating gold annot

Scaling cTakes

Hi, I'm new to cTakes and the UIMA framework. I've read most of the UIMA documentation and was able to take the BagofCUIGenerator example and modify to read notes from a DB, process using the UMLS AE in the clinical-pipeline using a local DB version of UMLS, and output the CUIs to a DB. Howev

RE: Scaling cTakes

Hi Brandon, It sounds like you've got a decent pipeline set up. To increase the speed you could try swapping out use of ctakes-dictionary-lookup with ctakes-dictionary-lookup-fast in the AE. Check ctakes-clinical-pipeline/desc/[ae]/AggregatePlaintextFastUMLSProcessor.xml for an example. As

RE: Scaling cTakes

Hi Brandon, Our estimate of how long it takes to process a document is under a second with the fast dictionary lookup I believe. Sean can provide more details. --Guergana -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Friday, December 05, 2014 1:21

RE: Scaling cTakes

Thanks Sean. I'll take a look and see if this speeds the pipeline up. Thanks, Brandon -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Friday, December 05, 2014 1:14 PM To: dev@ctakes.apache.org Subject: RE: Scaling cTakes Hi Brandon, It sounds like

Re: Scaling cTakes

on a tangential note, we do have example of running ctakes in a massively parallel system like spark/hadoop. https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-spark-streaming-twitter/ if you're problem is embarrasingly parallelizable, you can use mapreduce/spark to distribute your app using

RE: Scaling cTakes

Thanks Jay, I'll have to take a look at this too. -Original Message- From: jay vyas [mailto:jayunit100.apa...@gmail.com] Sent: Friday, December 05, 2014 2:40 PM To: dev@ctakes.apache.org Subject: Re: Scaling cTakes on a tangential note, we do have example of running ctakes in a massivel

Re: gold standard annotations for Apache cTAKES sample notes

Thank you for the thanks! If its at all helpful, I can expand the note base at some point. Best, JG — Sent from Mailbox On Fri, Dec 5, 2014 at 11:32 AM, Savova, Guergana wrote: > Thanks to John Green, we now have sample clinical notes in cTAKES. Many > thanks, John, for your effort! > We wi

RE: revamping the Apache cTAKES website

I would like to second the bootstrap recommendation, with the additional recommendation of django for the backend. It is an amazing platform for rapid development and easy updating. JG — Sent from Mailbox On Fri, Dec 5, 2014 at 12:15 PM, Savova, Guergana wrote: > There are now 4 volunteers: