Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/bluebrain/bluima

Natural Language Processing Toolkit for Neuroscience

https://github.com/bluebrain/bluima

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.0%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Natural Language Processing Toolkit for Neuroscience

Basic Info
  • Host: GitHub
  • Owner: BlueBrain
  • License: apache-2.0
  • Language: Java
  • Default Branch: master
  • Size: 210 MB
Statistics
  • Stars: 27
  • Watchers: 10
  • Forks: 15
  • Open Issues: 0
  • Releases: 0
Created almost 12 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

Bluima:: UIMA components at BlueBrain

Build Status

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-Cdric 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 BLUIMAHOME, e.g. (in your .bashprofile):

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

Acknowledgment

The development of this software was supported by funding to the Blue Brain Project, a research center of the cole polytechnique fdrale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.

Copyright (c) 2024 Blue Brain Project/EPFL

Owner

  • Name: The Blue Brain Project
  • Login: BlueBrain
  • Kind: organization
  • Email: bbp.opensource@epfl.ch
  • Location: Geneva, Switzerland

Open Source Software produced and used by the Blue Brain Project

GitHub Events

Total
  • Watch event: 2
  • Member event: 1
  • Push event: 1
  • Fork event: 1
Last Year
  • Watch event: 2
  • Member event: 1
  • Push event: 1
  • Fork event: 1

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 229
  • Total Committers: 4
  • Avg Commits per committer: 57.25
  • Development Distribution Score (DDS): 0.354
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
renaud r****d@a****g 148
Marco Antognini a****o@g****m 76
Erick Cobos e****s@e****h 4
jdcourcol j****l@h****r 1
Committer Domains (Top 20 + Academic)
epfl.ch: 1 apache.org: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 1
  • Total pull requests: 8
  • Average time to close issues: about 2 hours
  • Average time to close pull requests: about 21 hours
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 1.13
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • renaud (1)
Pull Request Authors
  • mantognini (7)
  • renaud (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

modules/bluima_abbreviations/pom.xml maven
  • ${project.groupId}:bluima_utils ${project.version}
modules/bluima_banner/pom.xml maven
  • ${project.groupId}:bluima_utils ${project.version}
  • banner:dragontool 20111108-SNAPSHOT
  • banner:heptag 20111108-SNAPSHOT
  • banner:medpost 20111108-SNAPSHOT
  • mallet:mallet 0.4
  • mallet:mallet-deps 0.4
modules/bluima_bbp/pom.xml maven
  • com.googlecode.combinatoricslib:combinatoricslib 2.0 compile
  • ${project.groupId}:bluima_abbreviations 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_banner 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_commons 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_corpora ${project.version}
  • ${project.groupId}:bluima_db 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_elasticsearch 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_fusion 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_jsre 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_lexica ${project.version}
  • ${project.groupId}:bluima_mongodb 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_neuroner 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_opennlp 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_oscar4 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_pdf 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_protein_concentrations 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_pubmed_ws 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_reference_classifier 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_regions 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_scripting 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_text2pmid 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_topic_models 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_units 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_utils ${project.version}
  • ${project.groupId}:bluima_xml 1.0.2-SNAPSHOT
  • org.la4j:la4j 0.4.9 test
modules/bluima_commons/pom.xml maven
  • ${project.groupId}:bluima_utils ${project.version}
  • bioadi:bioadi 0.1
  • bioadi:j-seqalign 0.1
  • bioadi:sptoolkit 0.1
  • com.cybozu.labs:langdetect 1.2.2
  • edu.mit:jwi 2.2.3
  • edu.ucdenver.ccp:biolemmatizer-core 1.1
  • edu.ucdenver.ccp:biolemmatizer-uima 1.1
  • hu.u_szeged.rgai.bio.uima:linnaeus 2.0
  • mallet:mallet 0.4
  • org.wiki.harvester.dependency:morphadorner 1.0
  • ${project.groupId}:bluima_scripting ${project.version} test
  • ${project.groupId}:bluima_test_helper ${project.version} test
modules/bluima_corpora/pom.xml maven
  • ${project.groupId}:bluima_utils ${project.version}
  • ${project.groupId}:bluima_xml ${project.version}
modules/bluima_db/pom.xml maven
  • ${project.groupId}:bluima_abbreviations 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • mysql:mysql-connector-java 5.1.20
  • org.hibernate:hibernate-annotations 3.5.6-Final
  • org.hibernate:hibernate-c3p0 3.5.6-Final
  • org.hibernate:hibernate-ehcache 3.5.6-Final
  • org.javalite:activejdbc 1.4.8
modules/bluima_elasticsearch/pom.xml maven
  • ch.epfl.bbp.nlp:bluima_utils 1.0.2-SNAPSHOT
  • org.elasticsearch:elasticsearch 1.3.4
  • ch.epfl.bbp.nlp:bluima_lexica 1.0.2-SNAPSHOT test
  • ch.epfl.bbp.nlp:bluima_opennlp 1.0.2-SNAPSHOT test
  • ch.epfl.bbp.nlp:bluima_scripting 1.0.2-SNAPSHOT test
modules/bluima_fusion/pom.xml maven
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_lexica 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_opennlp 1.0.2-SNAPSHOT test
modules/bluima_jsre/pom.xml maven
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • commons-cli:commons-cli 1.2
  • commons-digester:commons-digester 2.1
  • tw.edu.ntu.csie:libsvm 3.17
  • ${project.groupId}:bluima_commons 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_corpora 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_opennlp 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_scripting 1.0.2-SNAPSHOT test
modules/bluima_jython/pom.xml maven
  • ${project.groupId}:bluima_utils ${project.version}
  • org.python:jython-standalone 2.5.2
modules/bluima_lexica/pom.xml maven
  • ${project.groupId}:bluima_opennlp 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • ch.epfl.bbp.nlp:bluima_xml 1.0.2-SNAPSHOT
modules/bluima_mongodb/pom.xml maven
  • ${project.groupId}:bluima_utils ${project.version}
  • org.mongodb:mongo-java-driver 2.8.0
modules/bluima_neuroner/pom.xml maven
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_db 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_opennlp 1.0.2-SNAPSHOT test
modules/bluima_opennlp/pom.xml maven
  • ${project.groupId}:bluima_utils ${project.version}
  • de.jules:jules-utilities 2.1.1
  • net.sf.trove4j:trove4j 2.0.2
  • ${project.groupId}:bluima_test_helper ${project.version} test
modules/bluima_oscar4/pom.xml maven
  • ${project.groupId}:bluima_utils ${project.version}
  • uk.ac.cam.ch.wwmm.oscar:oscar4-api 4.1
modules/bluima_pdf/pom.xml maven
  • ${project.groupId}:bluima_abbreviations 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • ${project.groupId}:pdf_glyph_mapping 1.0.2-SNAPSHOT
  • com.snowtide:pdftextstream 2.6.4
  • org.bouncycastle:bcmail-jdk16 1.46
  • org.jdom:jdom2 2.0.5
modules/bluima_protein_concentrations/pom.xml maven
  • ${project.groupId}:bluima_banner 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_commons 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_corpora ${project.version} test
  • ${project.groupId}:bluima_db 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_fusion 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_lexica 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_opennlp 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_pdf 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_pubmed_ws 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_regions 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_scripting 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_units 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_xml 1.0.2-SNAPSHOT test
modules/bluima_pubmed_ws/pom.xml maven
  • ${project.groupId}:bluima_utils ${project.version}
  • gov.nih.nlm.ncbi:eutils 2.0
  • org.apache.axis2:axis2-adb 1.5.4
  • org.apache.axis2:axis2-transport-http 1.5.4
  • org.apache.axis2:axis2-transport-local 1.5.4
modules/bluima_rabbit/pom.xml maven
  • ${project.groupId}:bluima_scripting 1.0.1
  • ${project.groupId}:bluima_utils 1.0.1
  • com.rabbitmq:amqp-client 3.5.3
modules/bluima_references_classifier/pom.xml maven
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • cc.mallet:mallet 2.0.7
modules/bluima_regions/pom.xml maven
  • ${project.groupId}:bluima_lexica 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_topic_models 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • ${project.groupId}:mallet_utils 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_commons ${project.version} test
  • ${project.groupId}:bluima_corpora ${project.version} test
  • ${project.groupId}:bluima_opennlp 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_pdf ${project.version} test
  • ${project.groupId}:bluima_scripting 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_test_helper ${project.version} test
  • ${project.groupId}:bluima_units ${project.version} test
modules/bluima_scripting/pom.xml maven
  • ${project.groupId}:bluima_jython 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • org.beanshell:bsh 2.0b5
modules/bluima_text2pmid/pom.xml maven
  • ${project.groupId}:bluima_db 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_pdf 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • org.apache.lucene:lucene-analyzers-common 4.9.1
  • org.apache.lucene:lucene-core 4.9.1
  • org.apache.lucene:lucene-queryparser 4.9.1
modules/bluima_topic_models/pom.xml maven
  • ${project.groupId}:bluima_opennlp 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • cc.mallet:mallet 2.0.7
  • com.github.scopt:scopt_${scala.main.version} 3.2.0
  • org.scala-lang:scala-library ${scala.version}
  • org.scala-tools.testing:specs_${scala.main.version} 1.6.9 test
  • org.scalatest:scalatest_${scala.main.version} 2.2.0 test
modules/bluima_typesystem/pom.xml maven
  • org.apache.uima:ruta-core ${ruta.version}
  • junit:junit ${junit.version} test
modules/bluima_units/pom.xml maven
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • ${project.groupId}:bluima_opennlp 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_pdf 1.0.2-SNAPSHOT test
  • ${project.groupId}:bluima_test_helper ${project.version} test
  • ${project.groupId}:bluima_xml 1.0.2-SNAPSHOT test
modules/bluima_utils/pom.xml maven
  • com.googlecode.combinatoricslib:combinatoricslib 2.0
  • org.apache.xmlbeans:xmlbeans 2.5.0
modules/bluima_xml/pom.xml maven
  • ${project.groupId}:bluima_utils 1.0.2-SNAPSHOT
  • jaxen:jaxen 1.1.4
  • org.apache.commons:commons-vfs2 2.0
  • org.codehaus.woodstox:wstx-asl 4.0.6
  • org.jdom:jdom2 2.0.5
modules/pom.xml maven
  • ch.epfl.bbp.nlp:blue_commons 1.0.2-SNAPSHOT
  • ch.epfl.bbp.nlp:bluima_typesystem 1.0.2-SNAPSHOT
  • ch.qos.logback:logback-classic 1.0.6
  • com.google.guava:guava 18.0
  • org.apache.commons:commons-math3 3.0
  • org.apache.uima:ConceptMapper 2.3.1
  • org.apache.uima:RegularExpressionAnnotator 2.3.2-BBP
  • org.apache.uima:SnowballAnnotator 2.3.1
  • org.apache.uima:ruta-core ${ruta.version}
  • org.slf4j:jcl-over-slf4j 1.6.5
  • org.slf4j:slf4j-api 1.6.5
  • junit:junit ${junit.version} test
pom.xml maven
utils/blue_commons/pom.xml maven
  • junit:junit ${junit.version} test
utils/bluima_test_helper/pom.xml maven
  • junit:junit ${junit.version}
utils/mallet_utils/pom.xml maven
  • cc.mallet:mallet 2.0.7
  • junit:junit ${junit.version} test
utils/pdf_glyph_mapping/pom.xml maven
  • org.xml-cml:pdf2svg-dev 0.1-SNAPSHOT
  • junit:junit ${junit.version} test
modules/bluima_utils/src/main/resources/bart/brat-v1.3_Crunchy_Frog/server/lib/simplejson-2.1.5/setup.py pypi