Enabling drugner pipeline and identifying dates

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

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

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

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

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 adv

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

pache.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 in trunk. Sean -Original Message- Fr

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

he 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- From: Gandhi Raja

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

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: Wednesday

RE: Enabling drugner pipeline and identifying dates [EXTERNAL]

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

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

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

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

> -----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 dates [EXTERNAL] > [SUSPICIOUS] > > Hi Sean,

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

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

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: Filtering disease term precisely from EventMention and loading MedDRA library for cTAKES

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

Filtering disease term precisely from EventMention and loading MedDRA library for cTAKES

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

RE: Filtering disease term precisely from EventMention and loading MedDRA library for cTAKES [EXTERNAL]

y 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: Filtering disea

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

tml I don't know if 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@ctake

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

rue 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 dint send the complete te

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

: 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

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

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

verride public void process( final JCas jCas ) throws AnalysisEngineProcessException { LOGGER.info( "Processing ..." ); // Place AE processing code here LOGGER.info( "Finished." ); } } -Original Message- From: Gandhi Rajan Natarajan [mailto:gandhi.natara

RE: HSQLDB out of memory with custom dictionary

: 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 at 3:14 AM, Gandhi Rajan

RE: HSQLDB out of memory with custom dictionary

, 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. > > 1

RE: HSQLDB out of memory with custom dictionary

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...@arisglobal.com> wrote: > H

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

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: Use of custom Dictionary Descriptor file [EXTERNAL]

a 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: 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

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: 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

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

t;> Great, that's 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? >>> >

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

RE: Custom Dictionary connected to mysql

Rajan Natarajan <gandhi.natara...@arisglobal.com<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:

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

i'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 AM, Gandhi Rajan Natarajan < > > Gandhi.Nata ra...@arisglobal

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

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 a new team mate from the open source team. > > > > &

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:

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:

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

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: dev

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

Sean" <sean.fi...@childrens.harvard.edu> wrote: > Thanks Gandhi! > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > Sent: Monday, November 13, 2017 10:40 AM > To: dev@ctakes.apache.org > Subject: RE: Disable yTEX and Regression tes

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: cTAKES as REST service [EXTERNAL]

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/SpringUp

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

Report/org.apache.ctakes.ytex.uima.annotators/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 Nataraj

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: Use of custom Dictionary Descriptor file [EXTERNAL]

lained 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 Subject: RE: Use

RE: Use of custom Dictionary Descriptor file [EXTERNAL]

ld be cool 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 Subjec

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

for a clinical note > according 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

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 required

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: 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: Regarding cTakes version upadtion [EXTERNAL]

extHandler.java:265) > at > org.eclipse.jetty.webapp.WebAppContext.startContext( > WebAppContext.java:1242) > at > org.eclipse.jetty.server.handler.ContextHandler. > doStart(ContextHandler.java:717) > at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:494) >

RE: cTAKES as REST service [EXTERNAL]

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 ease o

RE: cTAKES as REST service [EXTERNAL]

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 to Spring 4

RE: cTAKES as REST service [EXTERNAL]

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: 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,

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

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: cTAKES as REST service [EXTERNAL]

s? 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 available un

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:

RE: cTAKES as REST service

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 Natarajan

RE: cTAKES as REST service [EXTERNAL]

ssues.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

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-

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

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

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:

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

RE: Run cTAKES continuously

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 > https://github

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/ > GoTeamEpsilon/c

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 as REST service [EXTERNAL]

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 posted about

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

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]

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

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

ator" >in that piper file. The 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? > &

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

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 Natarajan

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: Custom Dictionary connected to mysql

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 - Looking fo

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

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: 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,

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 Can

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

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

RE: ctake web service [EXTERNAL]

and then 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: 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

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 -

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

, 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" <gandhi.natara...@arisglobal.com> wrote: >Hi Chen/Sean, > >As per our earlier discussion, I was under

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

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: 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: How to change and build project source code?

un 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 sure whether I

RE: Query on LabValueFinder

: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 (*) 3.7 - > 5.1 g

RE: How to change and build project source code?

MainPanel2. >> java:139) >> at >> org.apache.ctakes.gui.pipeline.MainPanel2.(MainPanel2.java:76) >> at org.apache.ctakes.gui.pipeline.PiperCreator. >> createMainPanel(PiperCreator.java:40) >> at org.apache.ctakes.gui.pipeline.PiperCreator.lambda$ >> m

RE: Query on LabValueFinder [EXTERNAL] [SUSPICIOUS]

s 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 <gandhi.natara...@arisglobal.com> Sent: Wednesday, March 28, 20

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

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.

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

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

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: Question regarding Dictionary Creator GUI

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 pointing to the

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