README

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.