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README.md

BRAvo : Biological netwoRk Assembly

Synopsis

BRAvo is a web interface that aims to assemble regulatory networks.

Motivations

Huge efforts address the organization of biological knowledge through linked open databases. These databases can be automatically queried to reconstruct a large variety of biological networks such as regulatory networks. Assembling networks still implies manual operations due to (i) source-specific identification of biological entities, (ii) source-specific semantics for entity-entity relationships, (iii) proliferating heterogeneous life-science databases with redundant information and (iv) the difficulty of recovering the logical flow of a biological pathway due to the bidirectionality of chemical reactions. Homogenization of biological networks is therefore costly and error-prone.

With BRAvo, we propose a framework based on Semantic Web technologies. It addresses (i) the uniform identification of multi-source biological entities, (ii) the description of labeled directed graphs through RDF, and (iii) the use of BioPAX as a semantic reference.

Requirements

  • git
  • maven
  • java8

Installation

Clone the repository

git clone https://github.com/symetric-group/bionets-demo.git

Build package with maven :

mvn install -Dmaven.test.skip=true

Run the web appliation

java -jar target/BRAvo-1.0-SNAPSHOT-bin.jar

See on http://localhost:8091/

Web interface home

Maven dependencies

This software is built on top of the following Java dependencies :

License

MIT

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