...@algotec.co.il wrote:
Thank you, Vijay.
However, I am still encountering with the crash.
Best,
Oranit.
-Original Message-
From: vijay garla [mailto:vnga...@gmail.com]
Sent: Monday, July 13, 2015 5:53 PM
To: dev@ctakes.apache.org
Subject: Re: The SegmentRegexAnnotator of Ytex
see
see https://cwiki.apache.org/confluence/display/CTAKES/User%27s+Guide
best,
vj
On Mon, Jul 13, 2015 at 2:50 AM, Oranit Dror ora...@algotec.co.il wrote:
Hello,
I am using ctakes 3.2.2. and recently I have tried to apply the YTEX
pipeline. Particularly, I am interested in the
much!
Best regards,
Tim
*From:* Tsung-Ting Kuo [mailto:ts...@ucsd.edu]
*Sent:* Thursday, June 11, 2015 11:10 AM
*To:* 'Vijay Garla'
*Cc:* dev@ctakes.apache.org
*Subject:* RE: Question about YTEX
Thanks a lot, I followed the instructions and run “ytexweb.sh” script and
successfully
for YTEX’s help)? I saw
“ctakes-ytex-web-3.2.2-classes.jar” in the “lib” folder, but I am not sure
how to deploy it as a web service.
Best regards,
Tim
*From:* Vijay Garla [mailto:vijay.ga...@yale.edu]
*Sent:* Wednesday, June 10, 2015 12:10 PM
*To:* ts...@ucsd.edu
*Cc:* Vijay Garla; dev
As guergana mentioned ctakes has a rule based negation detection module.
In addition ytex adds a negex based analysis engine. Both approaches are
very sensitive to sentence splitting (see previous threads on alternative
sentence splitters).
An additional advantage of rule based negation is you
I don't know what the difference between PAR/CHD (parent/child) and RB/RN
(broader/narrower) is supposed to be. some umls source vocabularies use
PAR/CHD only/predominantly (e.g. SNOMED-CT), others use RB/RN (e.g.
RXNORM). You can use and experiment with whatever relationships you want
(I think
The error is caused by not finding the required properties files/xml config
files.
There are some issues with the ytex setup scripts for the 3.2 release; I
have fixed that in trunk. I am updating the 3.2 installation guide with
the patched setup scripts.
It's not clear to me if you're running
Hi John,
Looking at the code, that error is due to the concept graph 'umls' not
being loaded. by default, ytex is configured to use the sct-rxnorm concept
graph.
Can you see if this works:
Why not use the i2b2 corpora?
On Monday, September 29, 2014, Dligach, Dmitriy
dmitriy.dlig...@childrens.harvard.edu wrote:
Maybe creating a made-up set of sentences would be an option? That way we
could agree on the annotation of concrete cases. Although this would be
more of a unit test
That is an expected error having to do with the fact that UMLS isn't
installed in the test database that get's fired up for unit tests. That is
actually a warning (and should be interpreted as an error only if you do
have UMLS set up)
On Mon, Aug 25, 2014 at 9:02 PM, Pei Chen chen...@apache.org
Can you try this:
copy
https://code.google.com/p/ytex/source/browse/trunk/workspace/examples/fracture/cui/export.template.xml
to CTAKES_HOME\desc\ctakes-ytex\fracture\cui.xml
replace %DB_SCHEMA% with your database schema name (value of db.schema in
your ytex.properties file)
Then from a command
so much for putting up with my issues
-Clayton
On Wed, Jul 30, 2014 at 2:48 PM, vijay garla vnga...@gmail.com wrote:
Can you try this:
copy
https://code.google.com/p/ytex/source/browse/trunk/workspace/examples/fracture/cui/export.template.xml
to CTAKES_HOME\desc\ctakes-ytex
My guess is that this exception is coming out of the DictionaryLookup (it
creates a connection and holds on to it for the life of the AE).
If it is coming out of the DBCollectionReader/DBConsumer you're in luck, as
those use a connection pool, and you can configure it to check the
connection upon
You can add the DBConsumer to any pipeline, or add it to any CPE config.
See
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+-+YTEX+DBConsumer
You will have to set up ctakes to and your database as documented here:
and look again.
Thank you for your time Vijay,JG
—
Sent from Mailbox for iPhone
On Tue, Jul 15, 2014 at 8:26 AM, vijay garla vnga...@gmail.com wrote:
You can add the DBConsumer to any pipeline, or add it to any CPE config.
See
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES
, and some made-up terms, not
SNOMED-CT or the other sources taken from UMLS. If that is not correct,
then I agree there is a problem with what is being shipped in lucene
indexes.
-- James
-Original Message-
From: vijay garla [mailto:vnga...@gmail.com]
Sent: Wednesday, July 09, 2014 9:30 AM
- not sure if that can
be related).
Here's a screenshot of my CPE (using ytex):
[image: Inline image 1]
On Wed, Jul 2, 2014 at 10:48 PM, vijay garla vnga...@gmail.com wrote:
Hi clayton,
I assume you are running the fracture_demo.xml cpe - is that correct?
The CPE GUI should give you the option
. When running the CVD I have
access to a log file within the gui, but that does not seem to be present
here. Is there a specific place that this log file is saved?
On Tue, Jul 8, 2014 at 3:14 AM, vijay garla vnga...@gmail.com wrote:
Hi Clayton,
The screenshot is not coming through via
a way to deploy it this
way local.
Thanks again,
JG
On Wed, Jul 2, 2014 at 10:58 PM, vijay garla vnga...@gmail.com
javascript:; wrote:
The ytexWeb application tries to look up concepts from terms using the
ytex
dictionary lookup table, which is a small subset of the UMLS. Can you
try
Hi clayton,
I assume you are running the fracture_demo.xml cpe - is that correct? The
CPE GUI should give you the option to set the analysis batch. (see attached
screenshot). That being said, the analysis_batch is not required (it will
default to the current date). Can you attach the log file?
a hint at where
to
check Ill investigate.
Thanks!
JG
On Sun, Jun 29, 2014 at 8:56 PM, vijay garla vnga...@gmail.com wrote:
Hi John,
YTEX ships with 3 concept graphs (see
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+-+Semantic+Similarity
):
- sct
that shipped watered down versions? And if
not, why are my concepts coming up short? If you give me a hint at where to
check Ill investigate.
Thanks!
JG
On Sun, Jun 29, 2014 at 8:56 PM, vijay garla vnga...@gmail.com wrote:
Hi John,
YTEX ships with 3 concept graphs (see
https
I think one major issue with ctakes in a web server is thread safety. I
know that LVG is not thread safe, and it isn't clear what the status is on
other components.
On Tue, Apr 29, 2014 at 9:20 AM, John Green john.travis.gr...@gmail.comwrote:
Pei - I meant as a web app, can we keep the
...
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-surefire-plugin:2.12:test (default-test) on
project ctakes-ytex-uima:
There are test failures.
-Original Message-
From: vijay garla [mailto:vnga...@gmail.com]
Sent: Sunday, April 27, 2014 10:56 PM
To: dev@ctakes.apache.org
%
I didn't see anything about the Similarity Benchmark on the new pages.
Is
that still part of ytex?
-- james
-Original Message-
From: vijay garla [mailto:vnga...@gmail.com]
Sent: Sunday, March 16, 2014 8:53 PM
To: dev@ctakes.apache.org
Subject: YTEX Doc
on the Semantic+Similarity page use cd CTAKES_HOME
but later use %CTAKES_HOME%
so it looks like you meant cd %CTAKES_HOME%
I didn't see anything about the Similarity Benchmark on the new pages. Is
that still part of ytex?
-- james
-Original Message-
From: vijay garla [mailto:vnga
Hello All,
I've made a first cut at moving and updating the YTEX docs over from google
code to the cTAKES confluence site.
This is a first cut, and I'm trying to keep the YTEX docs separated, as it
is not yet in trunk/released, and I don't want to mess up any existing docs.
see
Hi John,
Thanks for this. I've updated the YTEXPipeline, fixed the lvg paths in
SetupAUIFirstWord.
If you want to re-run SetupAUIFirstWord (not necessary unless you are using
the stemmed words for dictionary lookup), just svn update, rebuild
ctakes-ytex-uima, and copy the jar to the lib dir of
at this point?
As you mentioned earlier, it's largely complementary.
[I was just thinking of saving effort to maintain the separate branch and
for simplicity for dev...]
--Pei
-Original Message-
From: vijay garla [mailto:vnga...@gmail.com]
Sent: Wednesday, February 05, 2014 9:30 PM
(I assume this will complete
without issues as long as the umls schema hasn't changed from 2012).
what trial and error did you have to go through to build the distro?
-vj
On Wed, Feb 5, 2014 at 5:33 PM, vijay garla vnga...@gmail.com wrote:
Hi Vlad,
sorry that the instructions aren't clear
?
If the last statement is correct, there are missing parts in i.e the UMLS
install steps that are linked from the new ctakes 3.1.1 document.
Thanks,
vlad
On Friday, January 3, 2014 10:21:52 PM UTC-5, vijay garla wrote:
Hello All,
I have finished an initial cut at the port of YTEX to cTAKES 3.1.1
For clarity, I'd like to stress that the opennlp sentence model distributed
with ctakes today does 'work' with sentences that span newlines - as I
understand it, this model ignores newline tokens (or newlines are not
provided as features to that model).
I believe the improvements Tim and others
components such as negation
might be another discussion?] --Pei
On Jan 20, 2014, at 12:46 PM, vijay garla vnga...@gmail.com wrote:
The sentence detection opennlp model used by ctakes does not split
sentences at newlines - there is additional logic in the takes
sentence splitter that does
The issue is indeed the sentence splitter - negation is limited to words
within the sentence, and if newlines are considered sentence boundaries, it
doesn't work properly (splitting on newlines breaks many other things as
well). The YTEX branch includes a sentence splitter that does not
-Original Message-
From: vijay garla [mailto:vnga...@gmail.com]
Sent: Wednesday, January 15, 2014 11:34 AM
To: dev@ctakes.apache.org
Subject: Re: svn commit: r1551805 -
/ctakes/branches/ytex/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/i2b2/api
)
at java.awt.EventDispatchThread.run(Unknown Source)
On Saturday, January 4, 2014 9:06:52 AM UTC+5:45, vijay garla wrote:
Hello All,
I have finished an initial cut at the port of YTEX to cTAKES 3.1.1. Most
of the YTEX functionality has been ported and integrated with cTAKES
/tree/trunk/
[3] https://cwiki.apache.org/confluence/display/CTAKES/cTAKES
-Original Message-
From: vijay garla [mailto:vnga...@gmail.com]
Sent: Friday, January 03, 2014 10:23 PM
To: ytex-us...@googlegroups.com; ctakes-...@incubator.apache.org
Subject: YTEX cTAKES 3.1.1 ready
changes mainly adding additional
fields? Just planning ahead especially for proposed type system changes...
--Pei
-Original Message-
From: vijay garla [mailto:vnga...@gmail.com javascript:;]
Sent: Monday, November 25, 2013 5:07 PM
To: ctakes-...@incubator.apache.org javascript
No need to write any new annotator, just point
org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator at the
UMLS HSQL DB.
The UMLS password check is a very weak chastity belt. For ytex, we make
umls resources available via a UTS password protected website - to get the
resources the
For the YTEX port, I've taken a few baby steps ... I've filed some jira
tickets with patches:
CTAKES-253https://issues.apache.org/jira/browse/CTAKES-253
and CTAKES-252 https://issues.apache.org/jira/browse/CTAKES-252, more
coming soon.
I have a question regarding testing: it seems to me that the
* ctakes-ytex-uima-res
resources for ytex analysis engines
Alternatively, I can add ctakes-ytex-uima and ctakes-ytex-uima-res to
existing projects (don't know where they would fit).
Best,
Vijay
On Thu, Oct 3, 2013 at 7:06 PM, vijay garla vnga...@gmail.com wrote:
Hi Pei,
The WSD annotator
Hello All,
I'd like to contribute ytex to ctakes. YTEX's main feature is the
ability to store *any* ctakes (or uima) annotation in a relational
database (in a relational format), and the ability to export these
annotations to ML packages (weka, libsvm, matlab, R). All of this is
purely
gchat: ksa...@gmail.com
linkedin: www.linkedin.com/in/ksarma
On Thu, Oct 3, 2013 at 5:50 AM, vijay garla vnga...@gmail.com wrote:
Hello All,
I'd like to contribute ytex to ctakes. YTEX's main feature is the
ability to store *any* ctakes (or uima) annotation in a relational
database
We released code on using cTAKES to annotate clinical text and SVMs that
use the annotations to classify clinical text from the CMC 2007 and I2B2
2008 challenges:
We did the cmd 2007 with cTAKES 2.5:
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