gff2rdf ======= The goal of this project is to provide an easy way to convert the genome annotation of some crops (here Arabidopsis, potato and Tomato) into a semantic format. The genome annotation is accessible via gff files (tab separated values). These files are read and converted into RDF. The RDF model generated by this tool is used by the marker2seq project available for tomato at: http://www.plantbreeding.wur.nl/BreeDB/marker2seq/ Installation ============ * Clone this repository: git clone https://github.com/PBR/gff2RDF.git * Compile the sources: cd gff2rdf mvn install This step will download all the dependencies using maven, this may take a while. * Run the produced jar file: java -jar target/gff2rdf2-1.0.jar -h This will display the help and explain how to use this utility. Usage ===== Simply calling the jar file with the right argument (ie: the specie you are interested in) will download the data file, read them and generate the RDF model. The data downloaded will be stored on the working directory on folder called: At_files for Arabidopsis Tomato_files for tomato Potato_files for potato This avoid to re-download the files every time the program is ran. The argument --force-download however allows to re-download the files if wished. The generated model will be write into a file "genemodel.rdf" in the same directory as the data downloaded (see above). From there, you can upload the RDF file into a triple store such as: Virtuoso: http://www.openlinksw.com/wiki/main/Main or Sesame: http://www.openrdf.org/ Dependencies ============ The dependencies are listed in the pom.xml but this program is written and meant to be use under Java 1.6 or higher. License ======= This project is licensed under the new BSD license.