Clinical Pipeline Engine using Apache cTAKES

An implementation of a clinical pipeline engine based on Apache cTAKES

License	The Apache Software License, Version 2.0
Categories	CLI User Interface Takes Web Frameworks
GroupId	it.cnr.iac
ArtifactId	ctakes-clinical-pipeline
Last Version	0.0.2
Release Date	Oct 7, 2015
Type	jar
Description	Clinical Pipeline Engine using Apache cTAKES An implementation of a clinical pipeline engine based on Apache cTAKES
Project URL	https://github.com/giuseppetotaro/ctakes-clinical-pipeline
Source Code Management	https://github.com/giuseppetotaro/ctakes-clinical-pipeline

Download ctakes-clinical-pipeline

Filename	Size
ctakes-clinical-pipeline-0.0.2.pom
ctakes-clinical-pipeline-0.0.2.jar	11 KB
ctakes-clinical-pipeline-0.0.2-tests.jar	3 KB
ctakes-clinical-pipeline-0.0.2-sources.jar	4 KB
ctakes-clinical-pipeline-0.0.2-javadoc.jar	45 KB

How to add to project

Apache Maven

<!-- https://jarcasting.com/artifacts/it.cnr.iac/ctakes-clinical-pipeline/ -->
<dependency>
    <groupId>it.cnr.iac</groupId>
    <artifactId>ctakes-clinical-pipeline</artifactId>
    <version>0.0.2</version>
</dependency>

Gradle Groovy

// https://jarcasting.com/artifacts/it.cnr.iac/ctakes-clinical-pipeline/
implementation 'it.cnr.iac:ctakes-clinical-pipeline:0.0.2'

Gradle Kotlin

// https://jarcasting.com/artifacts/it.cnr.iac/ctakes-clinical-pipeline/
implementation ("it.cnr.iac:ctakes-clinical-pipeline:0.0.2")

Apache Buildr

'it.cnr.iac:ctakes-clinical-pipeline:jar:0.0.2'

Apache Ivy

<dependency org="it.cnr.iac" name="ctakes-clinical-pipeline" rev="0.0.2">
  <artifact name="ctakes-clinical-pipeline" type="jar" />
</dependency>

Groovy Grape

@Grapes(
@Grab(group='it.cnr.iac', module='ctakes-clinical-pipeline', version='0.0.2')
)

Scala SBT

libraryDependencies += "it.cnr.iac" % "ctakes-clinical-pipeline" % "0.0.2"

Leiningen

[it.cnr.iac/ctakes-clinical-pipeline "0.0.2"]

Dependencies

compile (1)

Group / Artifact	Type	Version
org.cleartk : cleartk-ml	jar	2.0.0

provided (9)

Group / Artifact	Type	Version
org.apache.ctakes : ctakes-type-system	jar	3.2.2
org.apache.ctakes : ctakes-core	jar	3.2.2
org.apache.ctakes : ctakes-chunker	jar	3.2.2
org.apache.ctakes : ctakes-constituency-parser	jar	3.2.2
org.apache.ctakes : ctakes-context-tokenizer	jar	3.2.2
org.apache.ctakes : ctakes-dependency-parser	jar	3.2.2
org.apache.ctakes : ctakes-dictionary-lookup	jar	3.2.2
org.apache.ctakes : ctakes-dictionary-lookup-fast	jar	3.2.2
org.apache.ctakes : ctakes-assertion	jar	3.2.2

Project Modules

There are no modules declared in this project.

ctakes-clinical-pipeline

A command line tool based on Apache cTAKES in order to run the complete pipeline for annotating clinical documents in plain text format using the built in UMLS (SNOMEDCT and RxNORM) dictionaries.

Basically, this tool extends the ClinicalPipelineFactory class by adding the opportunity to run the cTAKES pipeline on arbitrary text instead of using only the static text defined into ClinicalPipelineFactory.java.

Getting started

To build the project, you can type the following command:

mvn clean install

To run the ctakes-clinical-pipeline, you can launch the following script (in /src/main/bin):

./run_ctakes.sh -i /path/to/input -o /path/to/output -u umls_user -p umls_pass [-j /path/to/jar] [-c /path/to/ctakes]

Please be sure that Apache cTAKES (both jar files and resources) is correctly installed on your machine.

Apache cTAKES

Apache cTAKES (clinical Text Analysis and Knowledge Extraction System) is an open-source natural language processing system for information extraction from electronic medical record clinical free-text. It processes clinical notes identifying types of clinical named entities.

cTAKES has been built using the Apache UIMA framework and OpenNLP toolkit. Its components are specifically trained for the clinical domain, and create rich linguistic and semantic annotations that can be utilized by clinical decision support systems and clinical research.

Apache cTAKES can be installed and configured following the instructions provided by the User Installation guide.

License

Apache License, Version 2.0

Versions

Version
0.0.2 Oct 7, 2015