RE: ctakes-web-rest changes

Hi Tim, Thanks for taking your time out and checking this. Have left my comments in the JIRA issue. Sorry that I could not improvise on the REST module which is more suitable for our business needs due to lack of domain expertise. Regards, Gandhi -Original Message- From: Miller, Timoth

RE: Compiling Ctakes from Subversion

Hi Peter, I use Java 1.8.0_171. Checked out the source code from - https://svn.apache.org/repos/asf/ctakes/trunk I don’t get any compilation issue in ctakes-temporal module running the command - " mvn clean install" Regards, Gandhi -Original Message- From: Peter Abramowitsch Sent: Su

RE: Adding LabValueFinder to Piper file leads to MESSAGE LOCALIZATION FAILED error

Hi Rumpa, I guess you are using cTAKES 4.0.0 user installation setup which does not have LabValueFinder implementation. Try building ctakes core jar from cTAKES SVN trunk and try again. It should work fine. Regards, Gandhi -Original Message- From: Rumpa Giri Sent: Wednesday, October 3

RE: [Request for information] - how do I become a committer?

Thanks for providing the access James. @Rumpa, The broken link is corrected now. Regards, Gandhi -Original Message- From: James Masanz Sent: Friday, October 26, 2018 10:04 PM To: dev@ctakes.apache.org Subject: Re: [Request for information] - how do I become a committer? Great to hear y

RE: missing medication mentions (tika cTAKESParser)

Hi Patrick, If the default CVD works fine, then we may have to look at tika app implementation on how it processes the cTAKES output. It required you can come up with your parser. Please check this link for more info on custom parser - https://github.com/GoTeamEpsilon/ctakes-rest-service/blob/

RE: Question regarding Dictionary Creator GUI

ve to set the fast dictionary parameter exactly. Can you point me towards the right direction? Thanks, Brihat On Wed, Oct 10, 2018 at 12:11 AM Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Hi Brihat, > > Is your 'CTAKES_HOME' environment variable p

RE: Question regarding Dictionary Creator GUI

Hi Brihat, Is your 'CTAKES_HOME' environment variable pointing to the right directory? Also I could see that you are trying to execute runDictionaryCreator.sh available under the checked out codebase from SVN. Did you build the complete cTAKES code before executing this? Regards, Gandhi -

RE: ctake web service [EXTERNAL]

manually connect when processing (re)starts. I am really busy these days, and this is just an off-the-cuff idea, but if anybody out there can tackle this please let the devlist know about it. Sean -Original Message- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent

RE: ctake web service

Hi Kathy, Sometime back we encountered this issue and the problem seems to be DB connections getting timed out. Currently we are using the following implementations: "org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary" and "org.apache.ctakes.dictionary.lookup2.concept.JdbcC

RE: Family history identification in cTAKES

at 8:21 AM, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Hi All, > > Does cTAKES provides any annotators or any other mechanism to extract > out family history information of a patient? > > For e.g, if the input is "Patient has Cancer. His mother

Family history identification in cTAKES

Hi All, Does cTAKES provides any annotators or any other mechanism to extract out family history information of a patient? For e.g, if the input is "Patient has Cancer. His mother has arthritis". Is there a way to extract out arthritis as family disease history? This email and any files transm

RE: API to integrate programmatically

Hi Ravi, Please refer to the following github repository - https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest This is a beta version of the cTAKES REST service implementation. Hope it helps. -Original Message- From: Ravindranath Oruganti Sent: Friday, July

RE: UMLS credentials don't seem to let me run UMLS process XML files

Hi Ken, Similar issues are creeping up very frequently off late. Though I’m not sure what exactly is the issue here, in one of the recent mail chains Dmitriy has mentioned the following: We had similar issues back in February (you can search the email archive). I was under impression that this

RE: Run cTAKES continuously

trivial change, the system has to re-do a large amount of downloading and building. On Thu, Jun 14, 2018 at 4:53 PM, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Hi Ted, > > Try building 'ctakes-web-rest' module in https://github.com/ > GoTea

RE: Run cTAKES continuously

. I also found that Tika has a cTAKES REST API, but unfortunately it loads the model on each request. On Wednesday, June 13, 2018, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Hi Ted, > > The implementation suggested by Peter is already available in >

RE: Run cTAKES continuously

Hi Ted, The implementation suggested by Peter is already available in https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest Building this project will give you a WAR file which you need to deploy in Tomcat. Regards, Gandhi -Original Message- From: Peter Abra

RE: Batching Queries in Ctakes Web Rest

Even if you send it in batch, the processing will be sequential I guess. You may have to run multiple instances of REST service to process huge volume of records. Regards, Gandhi -Original Message- From: Zakir Saifi [mailto:zakir.sa...@raxa.com] Sent: Monday, May 21, 2018 4:23 PM To: de

RE: Query on ctakes

Hi, As far as I know, there is no annotations available in cTAKES to extract person specific details as I checked with Sean earlier. May be he can elaborate more on this. Regards, Gandhi -Original Message- From: IBIL Global [mailto:ibilglob...@gmail.com] Sent: Wednesday, May 09, 2018 1

RE: issues with line endings

Hi Tim, Though I'm not an expert in git, I guess there is a setting to turn off this feature of auto correcting line endings in git-svn. Just have a look at this link - https://dzone.com/articles/git-showing-file-modified-even and see if it helps. Regards, Gandhi -Original Message- F

RE: Ctakes not running on docker

Hi Zakir, I could see that you are using customDictionary.xml as dictionary descriptor. Does that XML file contains valid jdbcUrl property? Regards, Gandhi -Original Message- From: Zakir Saifi [mailto:zakir.sa...@raxa.com] Sent: Tuesday, May 01, 2018 11:32 AM To: dev@ctakes.apache.org

RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]

HI Sean, I guess he meant about annotators like Negation annotator, Context annotator etc.. and its short description if I'm right for the write-up. Regards, Gandhi -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Monday, April 30, 2018 8:28 PM To: d

RE: Question about piper system

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

RE: Rest API

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

RE: consequences of change to typesystem [EXTERNAL]

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

RE: How to change and build project source code?

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-

RE: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

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

RE: Query on LabValueFinder

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

RE: How to change and build project source code?

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

RE: How to change and build project source code?

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-

Query on LabValueFinder

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

RE: Regarding Duration of a given symptom

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

RE: Build failure in Ctakes developer installation

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

RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

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

RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

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

RE: Query on ctakes [EXTERNAL]

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

RE: Output formats - CPE - cTAKES - Persist in database

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

RE: UmlsUserApprover Error [EXTERNAL]

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]

RE: Fast UMLS dictionary lookup description

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

RE: using umls dictionary lookup offline [EXTERNAL]

, 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

RE: using umls dictionary lookup offline

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:

RE: Regarding cTAKES Tlinks [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

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

RE: Regarding cTAKES Tlinks [EXTERNAL]

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

Regarding cTAKES Tlinks

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"

RE: Issue Regarding cTakes Installation

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

RE: Can we build CollectionReader from database [EXTERNAL]

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

RE: Unable to understand the importance of attributes in IdentifiedAnnotations

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

RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern [EXTERNAL]

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

RE: Custom Dictionary connected to mysql

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 -

RE: Custom Dictionary connected to mysql

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

RE: Custom Dictionary connected to mysql

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

RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

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

RE: cTAKES Rest Service Development - Dictionary GUI MySQL Progress + 1 Concern

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

RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

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

RE: cTAKES as REST service [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]

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

RE: cTAKES as REST service [EXTERNAL]

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

RE: cTAKES as REST service [EXTERNAL]

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

RE: Regarding cTakes version upadtion [EXTERNAL]

> 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

RE: Regarding cTakes version upadtion

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

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

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

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

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

RE: ResourceInitializationException in DefaultJCasTermAnnotator

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, &

RE: ResourceInitializationException in DefaultJCasTermAnnotator

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

RE: Having trouble creating the first annotator.

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

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

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

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

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

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

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,

RE: cTAKES as REST service [EXTERNAL]

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

RE: cTAKES as REST service [EXTERNAL]

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

RE: YTEX Assistance required RE: Test case failure [EXTERNAL]

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

RE: YTEX Assistance required RE: Test case failure [EXTERNAL]

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

Test case failure

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

RE: cTAKES Jenkins build is successful.

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

RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

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

RE: Disable yTEX and Regression tests on Jenkins [EXTERNAL]

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

RE: Disable yTEX and Regression tests on Jenkins

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

RE: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

, 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

RE: source code of user installation of cTakes. [EXTERNAL] [SUSPICIOUS]

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

RE: cTAKES as REST service [EXTERNAL]

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

RE: source code of user installation of cTakes.

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

RE: source code of user installation of cTakes.

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

RE: cTAKES as REST service [EXTERNAL]

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, &

RE: cTAKES as REST service [EXTERNAL]

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

RE: cTAKES as REST service [EXTERNAL]

--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

RE: cTAKES as REST service

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

RE: cTAKES as REST service [EXTERNAL]

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

cTAKES as REST service

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.

RE: false positive

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

RE: Queries on custom annotators [EXTERNAL]

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

RE: steps to upgrade to the latest version of umls and snomed

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

Queries on custom annotators

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

RE: HSQLDB out of memory with custom dictionary

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>

RE: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

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.

RE: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

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

RE: HSQLDB out of memory with custom dictionary

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. > >

RE: HSQLDB out of memory with custom dictionary

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

RE: HSQLDB out of memory with custom dictionary

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: HSQLDB out of memory with custom dictionary

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

RE: HSQLDB out of memory with custom dictionary

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

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

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

RE: Enabling drugner pipeline and identifying dates [EXTERNAL] [SUSPICIOUS]

: 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

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