R2RML-mapping

(This work will be integrated into intermine repo soon)

Clone the project from github and execute:

cd intermine-R2RML-mapping
./gradlew install
./gradlew run

The mapping.ttl file is generated from the genomic_model.xml, and can then be used by R2RML implementations such as ontop.

If one wants to use ontop

mkdir ontop-cli
cd ontop-cli

wget "https://github.com/ontop/ontop/releases/download/ontop-4.0.3/ontop-cli-4.0.3.zip"
unzip ontop-cli-4.0.3.zip

# intermine uses postgresql so get the JDBC driver
cd jdbc
wget "https://jdbc.postgresql.org/download/postgresql-42.2.18.jar"

#make a file db.properties
jdbc.url=jdbc:postgresql://localhost:5432/biotestmine #Change to your settinggs
jdbc.user=${YOUR_PGSQL_USERNAME}
jdbc.password=${YOUR_PGSQL_PASSWORD}


#Then one can use 
./ontop query -m ../mapping.ttl -p db.properties -q ../queries/proteins.rq

#OR run a SPARQL endpoint
./ontop endpoint -m ../mapping.ttl -p db.properties --port 8081