GPML2RDF

GPML2RDF creates RDF for WikiPathways [1,2]. Use cases, examples SPARQL queries, downloads, etc, are available from the WikiPathways RDF Portal: http://rdf.wikipathways.org/

Installation

Setup

Clone or download this repository, and then import as an "Existing Java Project" in Eclipse.

There are two dependencies. You can make them available to Maven using the instructions below.

Start from the GPML2RDF folder for both the WikiPathways API client, and PathVisio Core

PathVisio Core

git clone https://github.com/egonw/pathvisio-1.git
cd pathvisio-1
git checkout -b patch/bridgedb3.0.21 origin/patch/bridgedb3.0.21
ant clean core.jar
mvn install:install-file -Dfile=modules/org.pathvisio.core.jar -DgroupId=org.pathvisio \
  -DartifactId=pathvisio-core -Dversion=3.4.0-bridgedb-3.0.22-1 -Dpackaging=jar

WikiPathways API client

git clone https://github.com/wikipathways/wikipathways-api-client-java.git
cd wikipathways-api-client-java
cd org.wikipathways.client
mvn -Dmaven.test.failure.ignore=true clean install

Compiling

There is a pom.xml and you can compile the code with:

cd WP2RDF
mvn clean install

A single archive with all dependencies can be created with:

mvn package

Try different pathways

Add GPML file in resources directory --> Open WP2RDF class --> Change pathwayFile location

1.Waagmeester A, Kutmon M, Riutta A, Miller R, Willighagen EL, Evelo CT, Pico AR. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLOS Computational Biology. 2016 Jun;12(6):e1004989+. Available from: https://doi.org/10.1371/journal.pcbi.1004989
2.Miller RA, Kutmon M, Bohler A, Waagmeester A, Evelo CT, Willighagen EL. Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions. Yoon BJ, editor. PLoS ONE. 2022 Apr 18;17(4):e0263057. Available from: https://doi.org/10.1371/journal.pone.0263057