Hi,
We have deployed ctakes temporal demo application in Tomcat server and its
downloaded from
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo
While testing the demo locally, we could see some differences in the output as
compared to the hosted temporal example URL's ou
ile the demo
links everything to the false timex "2-3". Which one is better is a matter
that some could debate. The temporal models are constantly changing in trunk,
and the masters of the models might be able to recommend versions.
Sean
-Original Message-
From: Ga
HI All, we have deployed temporal demo application available under
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo locally
and referring to dictionaries(RxNORM,SnoMED) loaded in MySQL DB. We are trying
to extract out disease terms using this application.
When we tried
Hi All, Could someone please throw some light on this and help me out?
Regards,
Gandhi
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Saturday, September 09, 2017 11:52 PM
To: dev@ctakes.apache.org
Subject: Filtering disease term precisely
ustom dictionary you can add medDRA terms.
https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Saturday, September 09, 2017 2:22 PM
To: dev@ctakes.apache.org
Subject:
source
type in the umls, such as snomed, rxnorm and meddra. You do not need to select
terms individually, it is mostly a "bulk import". You can use the same db
script that you created to convert the hsql to mysql.
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mail
Hi All,
We are using the pipeline code as mentioned in
https://github.com/healthnlp/examples/blob/master/ctakes-temporal-demo/src/main/java/org/apache/ctakes/web/client/servlet/Pipeline.java
for the cTAKES web application we are building. But in our case, the
measurements and quantities are ide
Hi Sean,
Thanks again for the prompt response. Appreciate your input on adding
DrugMentionAnnotator. Actually, we are relying on pretty printer output just to
understand the analysis. Our logic to extract disorders and findings are based
on the XML file generated by
https://github.com/healthnl
You must have the HtmlTextWriter at the end of your pipeline to produce html
files. To keep the xml file output, place "add FileTreeXmiWriter" at the end
of the piper.
> Apologizes for too many
No worries, we are happy to have your interest!
Sean
-Original Message-
Fr
Hi, Could someone help me out on the below queries please?
Regards,
Gandhi
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, September 19, 2017 8:51 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying
dates [EXTERNAL]
Hi Gandhi,
I don't have time to go through all of this right now, but I will try to get to
it soon.
Make sure that you are running the latest version in trunk.
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wedn
you might need to modify both DateFSM and DateParser.
On Tue, Sep 19, 2017 at 11:20 AM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi Sean,
>
> Thanks again for the detailed and prompt response. We were able to run
> the piper GUI as per your advice.
er 20, 2017 8:50 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]
[SUSPICIOUS]
Hi Gandhi,
I don't have time to go through all of this right now, but I will try to get to
it soon.
Make sure that you are running the latest version i
* {@inheritDoc}
*/
@Override
public void process( final JCas jCas ) throws AnalysisEngineProcessException
{
LOGGER.info( "Processing ..." );
// Place AE processing code here
LOGGER.info( "Finished." );
}
}
-Original Message-
From: Gandhi Rajan N
us: 3px;
border-radius: 3px;
background-color: #000;
background-color: hsla(0, 0%, 20%, 0.9);
color: #fff;
content: attr(TIP);
text-align: center;
font-size: 14px;
line-height: 1.2;
}
[TIP]:hover::before,
[TIP]:hover::after {
visibility: visible;
-ms-filter: "progid:DXImageTransform.M
you have a jira account and permissions for the ctakes project.
An administrator may need to set that up for you.
Thanks,
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Thursday, September 28, 2017 4:09 AM
To: dev@ctakes.apache.org
Subj
ne coreference chains discovered in your full paragraph,
> and one of those will have superscript 1s.
>
> >
> > Could someone have a look and know your thoughts please?
> Thank you for creating the jira and the patch. I am sure that
> somebody will take a look.
>
> Tha
ns help
find more true positives (as in your examples), can we verify that they
won't create false positives?
Tim
On Fri, 2017-09-29 at 06:25 +, Gandhi Rajan Natarajan wrote:
> Hi Sean,
>
> Thanks again for the response. I guess its mistake from my side that
> I
ncern at a glance is that these additions help find more true
positives (as in your examples), can we verify that they won't create false
positives?
Tim
On Fri, 2017-09-29 at 06:25 +0000, Gandhi Rajan Natarajan wrote:
> Hi Sean,
>
> Thanks again for the response. I guess its mis
: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, October 03, 2017 4:26 AM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]
[SUSPICIOUS]
Hi Tim/Sean,
Is this an action item on us? If yes, Could someone give us some valid
tient , This patient , This patient , this patient , this
patient , this patient , this patient
This is a bug in the html writer that I will need to fix.
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, October 03, 2017 4:26 AM
To: d
: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, October 03, 2017 12:21 PM
To: dev@ctakes.apache.org
Subject: RE: Enabling drugner pipeline and identifying dates [EXTERNAL]
[SUSPICIOUS]
Hi Sean,
Will this JIRA issue -
https://urldefense.proofpoint.com/v2/url?u
ting us use your example note!
>
> Sean
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Tuesday, October 03, 2017 12:21 PM
> To: dev@ctakes.apache.org
> Subject: RE: Enabling drugner pipeline and identifying date
Hi Mathew,
I feel using MySQL Db would be better idea than using in-memory HSQLDB. In
fact, this also comes handy when you are planning to deploy ctakes as a web
application as in our case.
Regards,
Gandhi
-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Sun
hewvit...@gmail.com]
Sent: Monday, October 09, 2017 10:41 AM
To: dev@ctakes.apache.org
Subject: Re: HSQLDB out of memory with custom dictionary
Gandhi,
Thank you for the reply. Do you have any documentation on how to accomplish
this?
Thanks,
Matthew Vita
www.matthewvita.com
On Sun, Oct 8, 2017
TABLE SNOMEDCT_US (
CUI BIGINT NOT NULL,
SNOMEDCT_US BIGINT NOT NULL
);
CREATE INDEX IDX_SNOMEDCT_US ON SNOMEDCT_US (CUI);
Quick question: do you use the AIR table?
Thanks,
Matthew Vita
www.matthewvita.com
On Mon, Oct 9, 2017 at 1:14 AM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.co
re-load them.
My question for you are:
2. What configuration file do I change to switch to use the new database?
3. Do you think I can use SQL server instead of MySQL? My SQL seems to run
faster.
Thank
Kathy
On Tue, Oct 10, 2017 at 2:34 AM, Gandhi Rajan Natarajan <
gandhi.natara...@ar
57 PM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi Kathy,
>
> Good to hear from you. Please find the response below.
>
> NOTE: This is based on my experience with cTAKES so far. Please
> correct me if someone find the answers to be wrong.
>
>
Hi Sirisha,
I tried executing this in my windows machine and it works fine. The execution
also creates the output folder itself. So as Sean suggested this could be an
issue with file permissions or folder creation permissions.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailt
nts "output" to be a
subdirectory in the ctakes installation then a leading slash '/' cannot be used.
Cheers,
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, October 11, 2017 2:09 PM
To: dev@ctakes.apache.
I'm very appreciated your help.
Kathy
On Wed, Oct 11, 2017 at 5:14 PM, Kathy Ferro
wrote:
> Gandhi and Matthew,
>
> Thank you for the information.
>
> Kathy
>
> On Wed, Oct 11, 2017 at 1:35 AM, Gandhi Rajan Natarajan <
> gandhi.natara...@arisglobal.com>
Hi All,
We have wrote a custom annotation to identify the pharma company names,
integrated it with cTAKES and it works fairly well with CVD. But when I tried
integrating the same in my extended web application that uses
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo as
Hi Rajeev,
All you got to do is to use latest dictionary generator GUI to generate snomed
2017 scripts. We tried this and loaded to MySQL DB and it works. For more info
you can check the recent thread on 'HSQLDB out of memory with custom
dictionary' under
http://mail-archives.apache.org/mod_mb
Gandhi,
For 1) Just to be sure, you are running your pipeline using xml descriptor
files?
For 2) Consider using FileLocator.getAsStream(..).
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Saturday, October 14, 2017 3:52 AM
To: dev
Hi Abilash,
I'm not sure how much it will make sense. But in our custom annotator we wrote
on top of cTAKES, we resolved this false positives to an extent by using
commonly used English words metadata available from OpenNLP.
Regards,
Gandhi
-Original Message-
From: abilash.mat...@cogni
Hi All,
We have extended the cTAKES web application available under
https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo and
added our custom annotator. We have tested the same and it works fine with CVD.
But we are facing problems while trying to expose this as rest service.
odules?
Thanks,
Sean
-Original Message-----
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, October 25, 2017 9:20 AM
To: dev@ctakes.apache.org
Subject: cTAKES as REST service [EXTERNAL]
Hi All,
We have extended the cTAKES web application availab
interests you and we can schedule a Google Hangouts to talk about what work is
left (I estimate that I will be done in a month and a half).
Please do note that this solution is 100% free/open source :)
Thanks,
Matthew Vita
www.matthewvita.com
On Wed, Oct 25, 2017 at 6:20 AM, Gandhi Rajan
--Original Message-----
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, October 25, 2017 7:33 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]
Hi Sean,
Thanks for the instant response. Will try to upgrade to Spring 4 and keep you
po
haring the process!
Sean
-Original Message-----
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Thursday, October 26, 2017 3:02 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]
Hi Sean,
I'm glad to inform that I was able to upgrade cTAKES
ks to you and Mathew both!
>
> Sean
>
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
> Sent: Sunday, October 29, 2017 5:44 AM
> To: dev@ctakes.apache.org
> Subject: RE: cTAKES as REST service [EXTERNAL]
>
> Hi Sean,
&
Hi Bhagwat,
The source code of cTAKES is available under
https://svn.apache.org/repos/asf/ctakes/trunk
Regarding the resources to start off, cTAKES official site documentations
should be fine.
I also feel, mailing list is the one stop shop for all your other detailed
queries.
Regards,
Gandhi
that gives this result for a clinical
note. Could you please point me to the project, where can I see to it in the
ctakes-trunk or so.
On 30 October 2017 at 16:36, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi Bhagwat,
>
> The source code of cTAKES is
ps://issues.apache.org/jira/browse/CTAKES-473
[3] - https://issues.apache.org/jira/browse/CTAKES-188
On Sun, Oct 29, 2017 at 11:36 PM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Matthew,
>
> Looking forward to hear from you. Please let me know if there are a
ording to the guidelines in the user-install guide..
> It gives me descent result in the left pane of the UI.
> Now I am looking for the source-code that gives this result for a
> clinical note. Could you please point me to the project, where can I
> see to it in the ct
, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi Bhagwat,
>
> I'm not sure if it will help you. But I extended the code available in
> https://github.com/healthnlp/examples/tree/master/ctakes-temporal-demo
> to get the XML output and parsed the req
Hi Sean,
I can take it up if someone is willing to guide me on this.
Regards,
Gandhi
-Original Message-
From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
Sent: Wednesday, November 08, 2017 9:45 PM
To: dev@ctakes.apache.org
Subject: Disable yTEX and Regression tests on Jenkins
ndeep
Hi Gandhi,
Many thanks for volunteering. I am slammed with work right now, but if anybody
else can also help out ...
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Thursday, November 09, 2017 12:43 AM
To
f7d4gTao&m=l0_Tnqk6P-iMIhPUpRO8RiW-eImTKvJDGishYy1Jk-o&s=-PwjGWv5MEFT_1Jui9b27fdgkKfFRa29hts-FMalo8I&e=
On Nov 13, 2017 10:41, "Finan, Sean"
wrote:
> Thanks Gandhi!
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal
Great job Alex. In fact it is a great milestone. Cheers
Regards,
Gandhi
-Original Message-
From: Alexandru Zbarcea [mailto:al...@apache.org]
Sent: Friday, November 17, 2017 6:04 AM
To: Apache cTAKES Dev
Subject: cTAKES Jenkins build is successful.
Hi,
The job:
https://builds.apache.or
Hi All,
I did a fresh check out of cTAKES code from SVN to work on Spring upgrade
patch. But I have one failed test case in ctakes-ytex-uima module. The error
trace is as follows,
---
Test set: org.apache.ctakes.ytex.ui
ators/DateAnnotatorTest/testParseDate/
On Sat, Nov 18, 2017 at 12:11 PM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:
> Is anybody that was involved with ytex still out there?
>
> -Original Message-
> From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisgloba
Hi Alex,
I tried out a fresh checkout from SVN and git. Tried a full build in both
setups and DateAnnotatorTest fails consistently for me. Did you changed build
order or something in pom to fix it?
Regards,
Gandhi
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara
t 30, 2017 at 8:46 PM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi Alex and Sean,
>
> Thanks for the acknowledgement.
>
> As mentioned earlier in the thread, I have sent the github link -
> https://github.com/gandhirajan/cTAKES/tree/master/Spri
module.
Regards,
Gandhi
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Sunday, November 19, 2017 4:20 AM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service [EXTERNAL]
Hi,
I have attached the patch file for cTAKES Spring upgrade in
Hi Sean,
When we try to deploy cTAKES as web application, it always looks for
sno_rx_16ab.xml by default on server start. So do you mean we should also have
sno_rx_16ab.xml as well as custom xml file in the resources folder all the time?
Regards,
Gandhi
-Original Message-
From: Finan,
efly explained at the bottom of the wiki page:
https://cwiki.apache.org/confluence/display/CTAKES/Dictionary+Creator+GUI
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 10:44 AM
To: dev@ctakes.apache.org
Su
if there was an option for response from the HtmlTextWriter,
but I don't know how quick and easy that would be to implement.
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Tuesday, November 21, 2017 1:36 PM
To: dev@ctakes.apache.org
Hi Ritwik,
I'm not able to find the link of Sean's response for this same question which
we asked sometime back. So I'm attaching his response once again for you as
follows:
> Iis there any doc or guide on how to start writing our own annotator?
There are two example annotators in the ctakes-e
Hi Ritwik,
If you run the demo app in Jetty server using 'mvn jetty:run' command as
mentioned in this link - http://healthnlp.github.io/examples/ ,it should work
fine.
In Tomcat deployment, the HSQL in-memory DB implementation is the issue. You
may have to use MySQL DB to make it work in Tomca
was the
sno_rx_16ab file due to which this particular error was coming. Now I am able
to fetch the result using tomcat. Once again thankyou for the solution.
Regards
Ritwik
On Wed, Nov 29, 2017 at 4:56 PM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi Ritwik,
&
in earlier approach so that it
improves the performance?
Regards,
Gandhi
-Original Message-----
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Wednesday, November 22, 2017 1:35 AM
To: dev@ctakes.apache.org
Subject: RE: Use of custom Dictionary Descriptor file [EXTERNA
JCasPool.
JCasPool pool = new JCasPool( 100, engine );
For each post
JCas jcas = pool.getJCas( -1 );
jcas.setDocumentText(analysisText);
engine.process( jcas );
pool.releaseJCas( jcas );
Sean
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent
Hey Sunder,
Do you have the required files in your webapp resources folder?
The below error shows the required files are missing:
Caused by:
java.io.FileNotFoundException:
\org\apache\ctakes\temporal\ae\eventevent\20150630\model.jar (The system cannot
find the path specified) at java.io.FileInp
> org.eclipse.jetty.servlet.ServletHandler.initialize(
> ServletHandler.java:791)
> at
> org.eclipse.jetty.servlet.ServletContextHandler.startContext(
> ServletContextHandler.java:265)
> at
> org.eclipse.jetty.webapp.WebAppContext.startContext(
> WebAppContext.java:1242)
> at
> org.eclipse.jetty.server.handler.ContextHandl
ject: RE: cTAKES as REST service [EXTERNAL]
Hi All,
Have completed cTAKES Spring upgrade changes and checked in the same to SVN.
Please revert in case of any issues.
@Alex, Thanks a lot for taking time out and providing your review comments on
Spring upgrade. Really appreciate it.
Now it will e
Could someone help me out on the resources cleanup atleast if not review?
Regards,
Gandhi
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Monday, December 04, 2017 10:05 PM
To: dev@ctakes.apache.org
Subject: RE: cTAKES as REST service
s,
> > >
> > > I'm still getting back into the swing of things after my trip (I'm
> > > on business traveling at the moment, here in the states). I will
> > > be jumping right back into cTAKES REST development next week
> > > personally and with
lence/lack of updates!!! Very excited to see
> > what Gandhi's updates are looking like and enriching the JSON
> > response payload.
> >
> > Thanks,
> >
> > Matthew Vita
> > www.matthewvita.com
> >
> > On Tue, Dec 5, 2017 at 10:24
Hi Matthew,
It's indeed a great news. Glad you cracked it. Cheers.
Regards,
Gandhi
-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Monday, December 18, 2017 11:53 AM
To: dev@ctakes.apache.org; Sandeep Byatha Gururaja rao
; Shane Chesnutt
Subject: cTAKES Res
very helpful.
>>>
>>> I'll be happy to help with extracting the information needed from
>>> the CAS the easy way. Sean, am I remembering right that there was an
>>> API started for that somewhere? Or maybe that was part of DeepPhe?
>>>
>>> Tim
Not able to see any tomcat logs attached.
Do you see any errors in tomcat console?
Regards,
Gandhi
From: Chahal Arora [mailto:chahal.ar...@raxa.com]
Sent: Tuesday, December 19, 2017 6:09 PM
To: dev@ctakes.apache.org
Subject: Re: Custom Dictionary connected to mysql
Hi,
I have updated the custo
PM, Gandhi Rajan Natarajan
mailto:gandhi.natara...@arisglobal.com>> wrote:
Not able to see any tomcat logs attached.
Do you see any errors in tomcat console?
Regards,
Gandhi
From: Chahal Arora [mailto:chahal.ar...@raxa.com<mailto:chahal.ar...@raxa.com>]
Sent: Tuesday, December 19
a
Software Engineer
Raxa
On Tue, Dec 19, 2017 at 11:23 PM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi Chahal,
>
> Looking at the error trace:
> ‘javax.servlet.ServletException,java.io.IOException
> 19 Dec 2017 17:56:01 INFO RequestMappingHandlerAdapter -
Great Work Matthew. This will be very handy for cTAKEs MySQL integration.
Cheers.
Regards,
Gandhi
-Original Message-
From: Matthew Vita [mailto:matthewvit...@gmail.com]
Sent: Sunday, December 31, 2017 12:47 PM
To: dev@ctakes.apache.org
Cc: Sandeep Byatha Gururaja rao ; Shane Chesnutt
Try out this link -
"https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Assertion";
Regards,
Gandhi
-Original Message-
From: Kumari,Puja [mailto:puja.kuma...@cerner.com]
Sent: Thursday, January 04, 2018 3:11 PM
To: dev@ctakes.apache.org
Subject: Re: Unable to understand the
I guess that should be the database resource name.
You can have a look at the following file -
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java?view=markup
where you could see db resource na
Hi Neha,
I tried doing the same by checking out latest cTAKES code from SVN and build
using 'mvn clean install -Dmaven.test.skip=true'
The build was successful. Please find the console message as follows:
[INFO] ctakes-examples SUCCESS [ 1.622 s]
[INFO] Apa
Hi,
I have a question related to cTAKES Tlinks.
Is there any particular reason why
FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator is
commented in TemporalSubPipe.piper?
Also if I run the following text - "I had fever due to smoking so took
paracetomol on 12th June 2018"
ure.
Best,
Chen
On 2/12/18, 7:50 AM, "Gandhi Rajan Natarajan"
wrote:
>Hi,
>
>I have a question related to cTAKES Tlinks.
>
>Is there any particular reason why
>FullTemporalExtractionPipeline.CopyPropertiesToTemporalEventAnnotator
>is commented in TemporalSubPipe.p
he TLINK model does take some of the event
>properties (polarity, uncertainty, contextual modality, semantic types,
>etc.) for classification features. Without those features the
>classifier may lose its grip. Have you tried commenting back the line?
>
>Best,
>Chen
>
>On 2/12
Hi Razu,
You can load the UMLS data in database like MySQL and use JdbcConceptFactory
instead of UmlsJdbcConceptFactory.
Regards,
Gandhi
-Original Message-
From: Razu Sharif [mailto:razu.cse10.r...@gmail.com]
Sent: Wednesday, February 14, 2018 2:53 PM
To: dev@ctakes.apache.org
Subject:
,
JdbcDictionary and JdbcConceptFactory are probably the way to go. Just to add,
you don't need to load the dictionary into another database (mysql) to use
Jdbc* classes. They will work out-of-box with the default dictionary.
Sean
-Original Message-
From: Gandhi Rajan Nata
Hi Masoud,
In this link -
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Fast+Dictionary+Lookup,
I could see an information stating " A paper on rare word indexing is
currently in progress."
May be Sean or Tim will be able to provide info on this I feel.
Regards,
Gandhi
I guess you are running the build with test cases as I see the below messages
in my case only while running build with test cases:
>> log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [ProgressAppender]
Hi Manuel,
As far as I know cTAKES supports Pretty print and HTML format too. For more
info on this, you may have to look at the cTAKES demo webapp code under
https://github.com/healthnlp/examples/blob/master/ctakes-web-client/src/main/java/org/apache/ctakes/web/client/servlet/DemoServlet.java
Hi Amal,
If I am right, the grouping of related information together is not yet
available in cTAKES out of the box.
Also to generate output in a structured format, you can make use of HTMLWriter.
For more detailed info on this, you can check out Sean’s response for “Output
formats - CPE - cTAK
fo on this?
Regards,
Gandhi
-Original Message-
From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com]
Sent: Monday, February 12, 2018 11:00 PM
To: dev@ctakes.apache.org
Subject: RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
[SUSPICIOUS]
Thanks Sean and Ch
a system error, assuming you can identify both events("HBA1c" and
"good") correctly using the current system.
Best,
Chen
On 3/14/18, 11:20 AM, "Gandhi Rajan Natarajan"
wrote:
>Hi Chen/Sean,
>
>As per our earlier discussion, I was under the impression that t
Try disabling test cases and building it. Try using the following command:
"mvn install -Dmaven.test.skip=true"
Regards,
Gandhi
-Original Message-
From: ama...@acolade.co.in [mailto:ama...@acolade.co.in]
Sent: Friday, March 16, 2018 12:04 PM
To: dev@ctakes.apache.org
Subject: Build fai
Hi Anurag,
I believe you have to use TemporalSubPipe.piper to get duration related
information.
Regards,
Gandhi
-Original Message-
From: Anurag Shukla [mailto:anurag.shu...@raxa.com]
Sent: Monday, March 19, 2018 5:01 PM
To: dev@ctakes.apache.org
Subject: Regarding Duration of a given s
Hi All,
I'm using LabValueFinder annotator in my piper file and when I analyze the
following text:
"HEPATIC FUNCTION PANEL Result Value Ref Range Albumin 2.2 (*) 3.7 - 5.1 g/dL
Total Protein 5.5 (*) 5.8 - 8.0 g/dL Alkaline Phosphatase 844 (*) 42 - 121
IU/L" as mentioned in https://issues.ap
Hi Reed,
I'm not sure whether I got your question right. But if you make any changes in
ctakes-gui module, the updated jar files will be available under '
ctakes-gui\target' folder.
Not sure what you are looking for under 'ctakes-distribution/target'
Regards,
Gandhi
-Original Message-
how to run the project after building it (non-IDE-based install) for someone
with less maven and java experience (which I think may be my main confusion)?
On Mon, Mar 26, 2018 at 2:49 AM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi Reed,
>
> I'm not
2018 at 10:31 AM, Gandhi Rajan Natarajan <
gandhi.natara...@arisglobal.com> wrote:
> Hi All,
>
> I'm using LabValueFinder annotator in my piper file and when I analyze
> the following text:
>
>
> "HEPATIC FUNCTION PANEL Result Value Ref Range Albumin 2.2 (*) 3
ues building up,
and I will try to try to address them asap; I don't know when I'll have the
time and energy to get back to the devlist.
Feeling a bit guilty,
Sean
________
From: Gandhi Rajan Natarajan
Sent: Wednesday, March 28, 2018 8:56 AM
To
t.skip=true
>>
>> Then you can pick up the updated ctakes-gui jar file from
>> 'ctakes-gui\target' folder and replace the same in your project from
>> where you are running cTAKES.
>>
>> Regards,
>> Gandhi
>>
>>
>> -Original Message-
Hi Sean,
Please find the response from Sean Finan for the similar question I asked him
earlier:
"Ctakes doesn't really have a steadfast process for making upgrades.
You should create a jira item or use an existing one. Any commits should have
a comment/message starting with the jira item. Fo
Hi Abilash,
It is not yet available in CATKES codebase but the module is more or less
complete. You can check out the beta version of it under
https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest
We will check-in the same to CTAKES codebase after getting buy in from
Hi Peter,
I hope this link -
https://cwiki.apache.org/confluence/display/CTAKES/Piper+Files should help you
out. Also as far as I know, I doubt JsonCasSerializer has been packaged for
Piper.
Sean could elaborate more on this but I guess he is on vacation.
Regards,
Gandhi
-Original Messag
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