Finding Medical terms given a string through ctakes(UMLS).

2016-10-20 Thread Ks Sunder
Hi All, Please help me on this issue, I have written below code.. package com.shyam.Test; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory; import

RE: Post co-ordinated SNOMED-CT with AggregatePlaintextFastUMLSProcessor

2016-10-20 Thread Finan, Sean
Hi Arron, Ctakes discovers text words and phrases by lookup using a subset of the UMLS https://uts.nlm.nih.gov/home.htmlctakes then assigns a code to everything that it finds. While you can employ various workarounds to remove "epilepsy" in when within "epilepsy clinic", these are not

RE: using command to generate output

2016-10-20 Thread Finan, Sean
Hi Xi, There are a number of things that I can recommend, but first I need to ask if you are using the pre-built version downloaded from the ctakes website or if you are using code. Your answer to this question will impact how I can best provide help. Sean -Original Message- From:

RE: cTAKES Couldn't find parse for:

2016-10-20 Thread Finan, Sean
Fantastic! -Original Message- From: Joern Kottmann [mailto:kottm...@gmail.com] Sent: Thursday, October 20, 2016 10:24 AM To: dev@ctakes.apache.org Subject: Re: cTAKES Couldn't find parse for: Yes, the issue is here:

RE: Newbie Question: TestClearNLPPipeLine failed

2016-10-20 Thread Finan, Sean
Hi Melvin, Thank you for reporting the test bug and going through the effort of tracking down the root. You can post a bug report on https://issues.apache.org/jira/browse/CTAKES/?selectedTab=com.atlassian.jira.jira-projects-plugin:summary-panel 1. Search emails using something like MarkMail

Post co-ordinated SNOMED-CT with AggregatePlaintextFastUMLSProcessor

2016-10-20 Thread Lacey A . S .
Hi, Just wondering if someone could point me in the direction of how ctakes produces post coordinated SNOMED-CT? Using the AggregatePlaintextFastUMLSProcessor the individual concepts come out write nicely, however if you take the following phrase "I went to the Epilepsy Clinic", I can't see

Newbie Question: TestClearNLPPipeLine failed

2016-10-20 Thread Melvin Ma
Hi, there. I am new here and have some questions. 1. For the past emails, where is a good place to search? 2. Do your guys typically use stackoverflow to discuss issues? 3. When building workspace, where we have to go to sourceforge to download them. It has the annoying HTTP redirects

RE: cTakes with Oracle JDK 8

2016-10-20 Thread Tomasz Oliwa
Bandeep, I am using the JVM from Oracle Java 8 with cTAKES. My cTAKES build from SVN is 3.2.3, but not the latest, possibly a more recent commit broke something? There is a resolved issue for JDK 8 in the JIRA https://issues.apache.org/jira/browse/CTAKES-399 , you might want to take a look at

Re: cTAKES Couldn't find parse for:

2016-10-20 Thread Joern Kottmann
Yes, the issue is here: https://issues.apache.org/jira/browse/OPENNLP-869 I think we can fix that for the upcoming 1.6.1 release. Jörn On Thu, Oct 20, 2016 at 1:57 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Sure - can you do that? > > Thanks, > Sean > > -Original

Finding Medical terms given a string through ctakes(UMLS).

2016-10-20 Thread Ks Sunder
Hi All, I have written below code.. package com.shyam.Test; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory; import org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator; import