Hello,
Is there a way to flag the medical record number when running a ctakes job?
Thanks,
Andrew Sehr
Enterprise Architect
Indiana University Health
950 N Meridian St, Indianapolis, IN 46204
317-963-0249
as...@iuhealth.org
Hi Andrew,
I'm not sure if this is what you are looking for, but you can look at the
org.apache.ctakes.typesystem.type.structured.MetaData class, which has a
setPatientID(long) method.
org.apache.ctakes.core.util. SourceMetadataUtil has a getPatientNum(JCas)
method.
I don't know of any good ex
Does someone have the DictionaryTool jar available? I'm having trouble
creating the jar file from the project and would like to be able to create an
updated UMLS fast dictionary for 2015.
Thanks,
Brandon
IMPORTANT WARNING: The information in this message (and the documents attached
to it, if
Can anybody out there think of a reason why we shouldn't upgrade to Java 8?
Please comment on Jira.
https://issues.apache.org/jira/browse/CTAKES-377
Thanks,
Sean
Hi Brandon,
I can send you a jar or commit one pre-built. What goes wrong when you try to
build the tool?
Sean
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 1:23 PM
To: 'dev@ctakes.apache.org'
Subject: Fast Dictionary Upd
Hi Sean,
That'd be great.
I think I'm building it incorrectly because after I build the jar and try to
run specifying DictionaryCreator2 as the main class it says it can't find it.
I'm not too familiar with Java and building projects/jars so it could be my
ignorance causing the problem.
Than
Hi Brandon,
I just checked in a bin/dictionarytool.zip
It should have everything that you need (.jar, lib/, data/).
java -cp dictionarytool.jar;lib/*
org.apache.ctakes.dictionarytool.DictionaryCreator2 [args]
Should do the trick.
To recreate a 2015 version of the current ctakes dictionary, the a
Thanks Sean, much appreciated. To clarify the example below would create the
dictionary for use for the rare word approach?
Thanks,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 2:16 PM
To: dev@ctakes.apache.o
+1 upgrading to Java 8; been using it unofficially locally.
On Wed, Sep 16, 2015 at 1:37 PM, Finan, Sean
wrote:
> Can anybody out there think of a reason why we shouldn't upgrade to Java 8?
> Please comment on Jira.
>
> https://issues.apache.org/jira/browse/CTAKES-377
>
> Thanks,
> Sean
>
>
Yes, that will make the rare word dictionary in a memory-based hsql database -
the same as the default for the dictionary-lookup-fast module.
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 2:42 PM
To: dev@ctakes.apache.org
Su
Ok, hopefully one last question.
Based on your example everything runs, however the Anat and Snomed runs don't
produce any valid CUIs but RXNorm does. I'm not sure if this has anything to
do with it but every UMLS source read is against MRSTY.
Here's my command
java -cp dictionarytool.jar;l
I'm not sure that I understand your question. As I sent it, the anat, snomed
and rxnorm are not separate runs. The args line I sent earlier is for a single
run that will create a dictionary with snomed and rxnorm terms. The anatomy
tui list has a special use in correctly processing snomed cod
Sorry for not being clearer in my question.
All 3 run when the command is issued, but when anat and snomed run nothing is
output to the bsv file whereas with RXNorm 74,421 CUIs are written. So my
dictionary only ends up being RXNorm CUIs and doesn't include snomed.
Does that clarify?
Thanks,
If this can helps, I had to replace 'SNOMEDCT' with 'SNOMEDCT_US' in
CtakesSources.txt.
On Wed, Sep 16, 2015 at 2:33 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> I'm not sure that I understand your question. As I sent it, the anat,
> snomed and rxnorm are not separate runs. The
I'm not sure. What 3 are you talking about? There should only be a single run.
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 3:38 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Sorry for not being clearer
Thank you! I believe that was a change post 2011! You should actually be ok
with both SNOMEDCT and SNOMEDCT_US in CtakesSources.txt
Cheers,
Sean
-Original Message-
From: Maite Meseure Hugues [mailto:meseure.ma...@gmail.com]
Sent: Wednesday, September 16, 2015 3:43 PM
To: dev@ctakes.ap
I tried changing as suggested.
Below is what I see for the snomed piece, but for RXNorm it writes terms at the
end.
Reading list of Source Types from ./data/default/CtakesSources.txt
File Lines 1 list of Source Types 1
Reading list of Tuis from ./data/tiny/CtakesSnomedTuis.txt
File Lines 24
Hi,
I hope everyone had a great summer. I just wanted to resurrect the
Docker integration idea.
Anyone interested in joining a small hackathon with the single goal of
deploying cTAKES in a docker container.
One of the evenings 6pm?
--Pei
I am interested in participating!
Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
britt.fi...@wiredinformatics.com
> 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
>
Ah, now I see what you mean. Can you do a grep on your MRCONSO.RRF for
"SNOMEDCT" ?
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 4:04 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
I tried changing as
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
Yes, it finds "SNOMEDCT_US".
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015 5:17 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
Ah, now I see what you mean. Can you do a grep on your MRCONSO.RRF for
"
I have exactly the same problem with the tool.
A grep on MRCONSO.RRF for "SNOMEDCT" or for "SNOMEDCT_US" shows many lines.
From: Geise, Brandon D. [bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 5:05 PM
To: dev@ctakes.apache.org
Subject: RE: Fa
And you added "SNOMEDCT_US" to data/tiny/CtakesSources.txt ?
-Original Message-
From: Tomasz Oliwa [mailto:ol...@uchicago.edu]
Sent: Wednesday, September 16, 2015 7:13 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
I have exactly the same problem with the tool.
A grep
Sean,
I added that and still had the same issue.
Thanks,
Brandon
_
From: Finan, Sean
mailto:sean.fi...@childrens.harvard.edu>>
Sent: Wednesday, September 16, 2015 7:56 PM
Subject: RE: Fast Dictionary Update
To: mailto:dev@ctakes.apache.org>>
And you added "SNOMEDCT_
Did you add it to data/default/ CtakesSources.txt ?
If not then you need to specify -src ./data/tiny/CtakesSources.txt
Sorry for any confusion.
As soon as my inet isn't overloaded I'll download 2015AA and see if I can build
a dictionary.
-Original Message-
From: Geise, Brandon D. [mail
No, I had changed it on the Tiny source file. I just changed the default file
and it looks to be running as expected now.
Thank you for all your help and patience,
Brandon
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, September 16, 2015
Excellent!
-Original Message-
From: Geise, Brandon D. [mailto:bdge...@geisinger.edu]
Sent: Wednesday, September 16, 2015 9:55 PM
To: dev@ctakes.apache.org
Subject: RE: Fast Dictionary Update
No, I had changed it on the Tiny source file. I just changed the default file
and it looks to
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