Mirror of Apache CTakes
Sean Finan
Sean Finan HtmlTextWriter : null check for section id
CuiListFileWriter : change from simple write to bsv table
Fhir : add basetoken, sentence, paragraph, file writer, refactoring

git-svn-id: https://svn.apache.org/repos/asf/ctakes/trunk@1846527 13f79535-47bb-0310-9956-ffa450edef68
Latest commit 64295ea Nov 13, 2018
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ctakes-assertion-res CTAKES-485 : Add thread safe default clinical pipeline Nov 26, 2017
ctakes-assertion-zoner-res CTAKES-410 updating trunk snapshot to future 4.0.1-SNAPSHOT Apr 7, 2017
ctakes-assertion-zoner CTAKES-502: Fix typos of "symptom" in several places. May 8, 2018
ctakes-assertion Fix issue where system CAS was being used instead of gold during trai… Feb 13, 2018
ctakes-chunker-res CTAKES-485 : Add thread safe default clinical pipeline Nov 26, 2017
ctakes-chunker CTAKES-485 : Add thread safe default clinical pipeline Nov 26, 2017
ctakes-clinical-pipeline-res Adding piper files for -common- pipelines Dec 14, 2017
ctakes-clinical-pipeline CTAKES-502: Fix typos of "symptom" in several places. May 8, 2018
ctakes-constituency-parser-res CTAKES-410 updating trunk snapshot to future 4.0.1-SNAPSHOT Apr 7, 2017
ctakes-constituency-parser CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-context-tokenizer CTAKES-443 : stop rebuilding the type system for every module Jun 28, 2017
ctakes-core-res CTAKES-485 : rename AdvancedTokenizer to FullTokenizer Nov 26, 2017
ctakes-core HtmlTextWriter : null check for section id Nov 13, 2018
ctakes-coreference-res adding piper files for -common- pipelines Dec 14, 2017
ctakes-coreference Changes to-date to get coref system working with cross-doc reading an… Aug 2, 2018
ctakes-dependency-parser-res remove outdated URL reference Oct 5, 2017
ctakes-dependency-parser Fix Possible NPE in headnode resolution Mar 21, 2018
ctakes-dictionary-lookup-fast-res CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-dictionary-lookup-fast CTAKES-526 : Add shutdown hook to close hsql database Oct 30, 2018
ctakes-dictionary-lookup-res CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-dictionary-lookup CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-distribution CTAKES-526 : Add shutdown hook to close hsql database Nov 7, 2018
ctakes-drug-ner-res CTAKES-410 updating trunk snapshot to future 4.0.1-SNAPSHOT Apr 7, 2017
ctakes-drug-ner CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-examples-res CTAKES-485 : rename AdvancedTokenizer to FullTokenizer Nov 26, 2017
ctakes-examples CTAKES-526 : Add shutdown hook to close hsql database Nov 7, 2018
ctakes-fhir HtmlTextWriter : null check for section id Nov 13, 2018
ctakes-gui-res Don't want negative terms (starting with "no ") Aug 8, 2017
ctakes-gui CTAKES-526 : Add shutdown hook to close hsql database Nov 7, 2018
ctakes-lvg-res CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-lvg CTAKES-415: fix relative path to .voc resources Nov 22, 2017
ctakes-ne-contexts-res CTAKES-410 updating trunk snapshot to future 4.0.1-SNAPSHOT Apr 7, 2017
ctakes-ne-contexts CTAKES-465: Fix deprecation for org.apache.uima.analysis_engine.annot… Nov 19, 2017
ctakes-pos-tagger-res CTAKES-410 updating trunk snapshot to future 4.0.1-SNAPSHOT Apr 7, 2017
ctakes-pos-tagger CTAKES-485 : Add thread safe default clinical pipeline Nov 26, 2017
ctakes-preprocessor CTAKES-465: fix usage of deprecated junit.framework Nov 20, 2017
ctakes-regression-test CTAKES - 441 : adding the ability to use drugs in addition to labs. Mar 28, 2018
ctakes-relation-extractor-res Adding piper files for -common- pipelines Dec 14, 2017
ctakes-relation-extractor CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-side-effect-res CTAKES-410 updating trunk snapshot to future 4.0.1-SNAPSHOT Apr 7, 2017
ctakes-side-effect CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-smoking-status-res CTAKES-410 updating trunk snapshot to future 4.0.1-SNAPSHOT Apr 7, 2017
ctakes-smoking-status CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-template-filler CTAKES-443 : stop rebuilding the type system for every module Jun 28, 2017
ctakes-temporal-res Adding piper files for -common- pipelines Dec 14, 2017
ctakes-temporal Fix temporal gold standard reader for new coref format. May 11, 2018
ctakes-type-system CTAKES-502: Fix typos of "symptom" in several places. May 8, 2018
ctakes-utils CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-web-rest REST implementation in cTAKES. CTAKES-473: Creating a REST/SOAP and/o… Oct 31, 2018
ctakes-ytex-res CTAKES-410 updating trunk snapshot to future 4.0.1-SNAPSHOT Apr 7, 2017
ctakes-ytex-uima CTAKES-415: add more logging to DateAnnotatorTest Dec 6, 2017
ctakes-ytex-web CTAKES-457: consistently usage of properties to manage dependency ver… Nov 30, 2017
ctakes-ytex CTAKES-488: fix WARN message for JdbcOperationsHelper Dec 5, 2017
.gitattributes CTAKES-481: fix exec-maven-plugin - use default parent pom for defaul… Nov 19, 2017
.gitignore CTAKES-482: add .gitignore and .gitattributes; remove .gitignore from… Nov 19, 2017
KEYS CTAKES-410 - Checking in public code signing key Dec 6, 2016
LICENSE keep trunk in synch with r1440105 Synchronize NOTICE and LICENSE file… Jan 29, 2013
NOTICE keep trunk in synch with r1440105 Synchronize NOTICE and LICENSE file… Jan 29, 2013
README prereq java 1.8 rather than 1.7 Apr 14, 2017
pom.xml CTAKES-526 : Add shutdown hook to close hsql database Nov 7, 2018

README

Apache cTAKES
==================================
Detail documentation can found at:
http://ctakes.apache.org

Requirements
---------------------------------------
Java 1.8 is required to run cTAKES
Maven 3.0.0 is required for building it

Running a simple pipeline in the UIMA CAS Visual Debugger
or in the Collection Processing Engine
----------------------------------------------------------------
Run bin/runctakesCVD/CPE.sh.bat
Load AE (analysis engine)
Select desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor
Enter note or other text
Run analysis engine
NOTE: The included example dictionary is very small. Try a sentence such as: 
Patient took aspirin for knee pain

Using LVG resources
----------------------------------------------------------------
Refer to the cTAKES User Install Guide or cTAKES Developer Install Guide 
for the current release of Apache cTAKES for information about obtaining 
the full LVG resource.


Using UMLS resources
----------------------------------------------------------------
Refer to the cTAKES User Install Guide or cTAKES Developer Install Guide 
for the current release of Apache cTAKES for information about obtaining 
the UMLS resources used by cTAKES.