Setting up PDXIntegrator¶
PDXIntegrator is a Java program that requires at least Java version 8.
Note that for now, we are using a private fork of the ontolib library for parsing the NCIT obo file. Go to https://github.com/monarch-initiative/OLPG and enter the following commands (notify Peter if you need access).
$ git clone https://github.com/monarch-initiative/OLPG
$ cd OLPG
$ mvn install
This will put the OLPG library files into your local maven repository (.m2 directory) and let you build PDXIntegrator.
PDXIntegrator is provided as a maven project. The quickest way to set it up is to clone the project from the GitHub site at https://github.com/TheJacksonLaboratory/PDXintegrator and then to use maven to build the project. In the following, we show a command that will display a help message–if you see this, then you have successfully built the program.
$ git clone https://github.com/TheJacksonLaboratory/PDXintegrator
$ cd PDXintegrator
$ mvn package
$ java -jar target/PdxIntegrator.jar
[ERROR] no command
Program: PdxIntegrator (Common Knowledge Graph PdxModel for PDXNet)
Version: 0.0.2
usage: java -jar PdxIntegrator.jar command [-c <arg>] [-d <arg>] [-o <arg>]
Available commands:
download
java -jar PdxIntegrator.jar download [-d directory]: Download NCI files to directory at -d (default="data").
simulate
java -jar PdxIntegrator.jar simulate [-d directory]: Requires NCI files in directory at -d (default="data").
map
java -jar PdxIntegrator.jar map [-d directory]: todo.
Setting up drugbank¶
Before running the simulation
command, the Drugbank XML file needs to be downloaded and processed. See drugbank.
Running the simulation command¶
Currently, we are building out a complete RDF model for the PDX Minimal Information standard
(https://www.ncbi.nlm.nih.gov/pubmed/29092942). Our strategy for development is to generate
random PDX cases, write the corresponding RDF code to file (with the simulate
command). Then, to test
the query-ability of the model, we ingest the RDF file and query it using SPARQL queries (with the query
command). This is inteded to allow collaborators to view the model and make suggestions for improvement.
The end game would be to develop this code to allow ETL of PDX data into this model. The following sections
show how to set up and run the simulation