Hi Paul,
To my knowledge, in order to use any UMLS dictionary, the script needs to
authenticate the user with the NLM servers. In order to make this work in our
closed environment, we had to do two things:
1. Set up a proxy to relay the authentication and protect the sensitive data
2. Poi
Hi John,
There have been a couple of presentations at the recent ApacheCon:
https://www.apachecon.com/acah2020/tracks/ctakes.html
Cheers,
Gundolf.
From: John Doe
Reply-To: "user@ctakes.apache.org"
Date: Tuesday, November 17, 2020 at 08:48
To: "user@ctakes.apache.org"
Subject: Scaling out cTAK
Hi,
I am seeing the same behavior. But I am not sure if it is really a dictionary
issue.
Look here:
http://browser.ihtsdotools.org/?perspective=full&conceptId1=404684003&edition=en-edition&release=v20180131&server=http://browser.ihtsdotools.org/api/v1/snomed&langRefset=9000509007
When I
Hi Tiffany,
It seems like your installation cannot find file sno_rx_16ab.xml in
resources/org/apache/ctakes/dictionary/lookup/fast/. This file is part of the
additional resources. Please double-check that you have installed them properly.
Cheers,
Gundolf.
From: Tiffany Buu
Reply-To: "user@ct
. Are you using
it?
Cheers,
Gundolf.
From: Ankit Bisht
Date: Friday, June 8, 2018 at 09:20
To: "Schenk, Gundolf"
Cc: "user@ctakes.apache.org"
Subject: Re: Regardng Apache cTakes
Hello Gundolf,
I have attached the snapshot of the error which I am getting.
Also check my l
double check and post the exact
error message you are getting.
Cheers,
Gundolf.
From: Ankit Bisht
Date: Friday, June 8, 2018 at 08:12
To: "user@ctakes.apache.org" , "Schenk, Gundolf"
Subject: Re: Regardng Apache cTakes
Hello Gundolf,
Thanks for replying back. Yes, I fo
Hi Ankit,
Have you followed this guide?
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide
What exactly do you mean by “open it”?
Cheers,
Gundolf.
From: Ankit Bisht
Reply-To: "user@ctakes.apache.org"
Date: Wednesday, June 6, 2018 at 20:22
To: "user@ctakes.apach
Hi Reed,
Did you enable UMLS?
I am also not quite happy with the result. When I run this test sentence in the
DefaultClinicalPipeline I am getting 4 IdentifiedAnnotation (AnnotationIndex ->
uima.tcas.Annotation ->
org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation).
Namely, Procedu
HI Reed,
Perhaps, this should go to the developers list.
I am getting those test errors, too. Curious to hear any thoughts about why
they happen.
If you just want an installation you can skip the tests by using
-DskipTests=false
and a zip or tar.gz file should be produced at the end of the compi
I would be very interested to learn more about his, too. Any insight
appreciated. Thanks!
From: "Mullane, Sean *HS"
Reply-To: "user@ctakes.apache.org"
Date: Tuesday, March 20, 2018 at 11:11
To: "'user@ctakes.apache.org'"
Subject: RE: Extract relation among entities in cTAKES
It seems Liam’s
ave installed and enabled UMLS for cTAKES (and it’s working for the default
clinical pipeline). Do I have to do step 6) for YTEX to work properly perhaps?
Cheers,
Gundolf.
From: "Mullane, Sean *HS"
Date: Monday, March 5, 2018 at 17:04
To: "Schenk, Gundolf" , "user@cta
)
Unclear to me, what might cause it. Any thoughts welcome!
Cheers,
Gundolf.
From: "Schenk, Gundolf"
Reply-To: "user@ctakes.apache.org"
Date: Monday, March 5, 2018 at 15:12
To: "user@ctakes.apache.org"
Subject: Re: YTEX installation
This increased the loggi
ization of annotator class
"org.apache.ctakes.ytex.uima.annotators.DBConsumer" failed. (Descriptor:
)
Seems to me that some classes were not found?
Is my $CLASSPATH correct?
> echo $CLASSPATH
/mnt/apache-ctakes-4.0.0/desc/:/mnt/apache-ctakes-4.0.0/resources/:/mnt/apache-ctakes-4.0.0/l
.
From: "Mullane, Sean *HS"
Date: Monday, March 5, 2018 at 12:36
To: "Schenk, Gundolf" , "user@ctakes.apache.org"
Subject: RE: YTEX installation
You could try setting the log level to DEBUG in log4j.xml if you haven’t
already, then re-run the pipeline. You should
-To: "user@ctakes.apache.org"
Date: Monday, March 5, 2018 at 10:43
To: "Schenk, Gundolf" , "user@ctakes.apache.org"
Subject: RE: YTEX installation
Have you done step 7 listed here? (
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation )
If so, maybe check
Hi Sean,
Thanks for your reply. I think, I did set the DB access parameters correctly.
This was already done for the DB creation and has worked there. Any other
thoughts?
Cheers,
Gundolf.
From: "Mullane, Sean *HS"
Date: Monday, March 5, 2018 at 10:21
To: "Schenk, G
he.org"
Date: Saturday, March 3, 2018 at 02:15
To: "user@ctakes.apache.org"
Subject: RE: YTEX installation
HI Gundolf,
Try using – “add org.apache.ctakes.ytex.uima.annotators.DBConsumer”
Also “documentMapperService” bean should be available in your application
context.
Regar
"user@ctakes.apache.org"
Date: Friday, February 23, 2018 at 15:13
To: "user@ctakes.apache.org"
Subject: Re: YTEX installation
might help...
https://code.google.com/archive/p/ytex/downloads
On 02/23/2018 05:45 PM, Schenk, Gundolf wrote:
Hi,
Does anyone know how to export the res
Hi,
Does anyone know how to export the resulting XMI files to a sql database
efficiently? I found the YTEX DBConsumer module but I am not able to install
YTEX properly as the links the the zip files seem to be outdated/broken at:
https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installati
Hi Gandhi,
I am using Java 9.0.1 successfully. Perhaps there is a different reason for
Queenie’s error?
Cheers,
Gundolf.
From: Gandhi Rajan Natarajan
Reply-To: "user@ctakes.apache.org"
Date: Monday, February 5, 2018 at 7:42 AM
To: "user@ctakes.apache.org"
Subject: RE: Error loading UMLS fast
Hi,
Me too would like to have a fuzzy matching in cTAKES. Do we have anything like
it? Or is the typical approach to use a preprocessor to correct for
misspellings, clean up/standardize interpunction and such?
Would be great to read any thoughts on this.
Cheers,
Gundolf.
From: Desteny Child
Hi,
The authentication works for me.
Don, did you try
C:\apache-ctakes-4.0.0>bin\runctakesCVD.bat -Dctakes.umlsuser=donflinn
-Dctakes.umlspw="yourpassw@rd"
Cheers,
Gundolf.
On 1/19/18, 11:57 AM, "Miller, Timothy"
wrote:
I'm having trouble loading the url in my browser too. Could be th
5 11:28 HSqlDb
In that subdirectory, you should see files with names like lvg2008*
Offhand I'm not sure about the drugner engine is part of the default Clinical
Pipeline. I'll have to take a look at that.
On Thu, Jan 18, 2018 at 12:24 PM, Schenk, Gundolf
mailto:gundolf.sch...@ucsf.
1312589 lvg2008.script
This might help you get started with the meaning of the annotations:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Assertion
On Tue, Jan 16, 2018 at 2:52 PM, Schenk, Gundolf
mailto:gundolf.sch...@ucsf.edu>> wrote:
Dear Tim and James,
Many than
x27;m not sure what to recommend.
Sorry for the delayed response.
Tim
From: Schenk, Gundolf mailto:gundolf.sch...@ucsf.edu>>
Sent: Friday, January 12, 2018 5:18 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Re: Errors when executing AggregatePla
anyone?
On 1/8/18, 11:47 AM, "Schenk, Gundolf" wrote:
Hi,
I am new to cTAKES (and NLP) and I am trying to extract clinically relevant
information from electronic freetext records.
I am running the default Clinical Pipeline. But I have a few general
questions for und
Hi,
I am new to cTAKES (and NLP) and I am trying to extract clinically relevant
information from electronic freetext records.
I am running the default Clinical Pipeline. But I have a few general questions
for understanding and for some error output I am seeing.
1) what is the difference between
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