BRAvo is a web interface that aims to assemble regulatory networks.
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.
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/
This software is built on top of the following Java dependencies :
- JENA (https://jena.apache.org)
- GSON (https://github.com/google/gson)
- Jersey (https://jersey.java.net)
- Log4J (https://logging.apache.org/log4j/2.0/)
- Commons CLI (https://commons.apache.org/proper/commons-cli/)
- Commons Lang (https://commons.apache.org/proper/commons-lang/)