Bluima:: UIMA components at BlueBrain

About

Bluima is a natural language processing (NLP) pipeline focusing on the extraction of neuroscientific content and based on the UIMA framework. Bluima builds upon models from biomedical NLP (BioNLP) like specialized tokenizers and lemmatizers. It adds further models and tools specific to neuroscience (e.g. named entity recognizer for neuron or brain region mentions) and provides collection readers for neuroscientific corpora.

Papers

• Richardet, Renaud, Jean-Cédric Chappelier, and Martin Telefont. "Bluima: a UIMA-based NLP Toolkit for Neuroscience." Unstructured Information Management Architecture (UIMA) (2013): 34. ceur-ws.org/Vol-1038/paper_7.pdf

Dependencies

• Java JDK 7 or higher (http://www.oracle.com/technetwork/java/javase/downloads/index.html)
• Maven 3 (http://maven.apache.org/download.html#Installation)

Configure

Setup BLUIMA_HOME, e.g. (in your .bash_profile):

export BLUIMA_HOME={absolute path to Bluima}

Build

> export MAVEN_OPTS="-Xmx4G -XX:MaxPermSize=256m"
> mvn clean install -Dblue_uima_home={PATH_TO_HOME}

Get yourself a coffee. Rinse and repeat above command if error is "could not download artifacts"

If gpg signing is not setup and you simply want to skip it then you can add -Dgpg.skip=true to the maven command line options.

Maven Tests

• The reference test environment is the command line.
• Run all tests > mvn clean test
• Skip tests while building > mvn install -Dmaven.test.skip=true

Eclipse

• Tested with 4.2 and latest m2e plugin
• Make sure you have built the codebase with the above step (mvn)
• Import the module bluima_bbp with: File -> Import... -> Existing Maven Projects
• Set BLUIMA_HOME in Eclipse
• Preferences: Java > Installed JRE > Edit
• -Xms1G -Xmx4G -Dbluima_home={absolute path to Bluima}
• Test your installation (see "Getting Started" below)
• Import other modules you need with: File -> Import... -> Existing Maven Projects

Release

> cd modules/bluima
> sh release.sh

The release includes all dependencies can be deployed on any computer with a JRE (e.g. cluster).

To release to nexus: mvnt clean deploy -Dgpg.passphrase="si......" -P release

Conventions (over configuration)

• Maven projects are named bluima_{project-name}
• Class naming conventions
• UIMA Analysis Engines are named Annotator
• UIMA Collection Readers are named CollectionReader
• UIMA Cas Consumers are named Writer
• JUnit tests are named {base-class}Test

Getting Started

• launch the class ch.epfl.bbp.uima.RunPipeline in project bluima_bbp
• select a pipeline to run, e.g. examples/1_simple/simple.pipeline

Feedback

• is welcome: renaud.richardet@epfl.ch