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
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:
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 annotations
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.
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.
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
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
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
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
