OBO Tutorial Code

The src directory contains Java code to support the tutorial. If you download a release version of the tutorial, you can just run the bin/obo-tutorial.jar file like this:

cd examples
java -jar ../bin/obo-tutorial.jar

This command will print more information about using the tool, and the tutorial includes several examples. Here's a summary of all the build steps in the tutorial:

cd examples
java -jar ../bin/obo-tutorial.jar map terms.csv data-before.csv data-after.csv
java -jar ../bin/obo-tutorial.jar extract \
  uberon.owl \
  uberon-terms.txt \
  uberon-module.owl \
  "https://github.com/jamesaoverton/obo-tutorial/raw/master/examples/uberon-module.owl"
java -jar ../bin/obo-tutorial.jar convert prefixes.ttl data-after.csv data-raw.ttl
java -jar ../bin/obo-tutorial.jar model data-raw.ttl application.owl model.rq data-after.ttl
java -jar ../bin/obo-tutorial.jar merge \
  data-after.ttl \
  obo-tutorial.owl \
  "https://github.com/jamesaoverton/obo-tutorial/raw/master/examples/obo-tutorial.owl"

Requirements

To run this code you will need a Java Runtime Environment. You probably already have one installed on your computer, but if not you can get it here:

http://www.oracle.com/technetwork/es/java/javase/downloads/index.html

Building

To build this code you need Java plus Apache Ant and Apache Ivy. Please follow their respective installation instructions. Then:

1. change to the code directory: cd code
2. download required libraries: ant deps
3. build and package the code: ant package

The result is the bin/obo-tutorial.jar file, including all dependencies.

See the build.xml and ivy.xml configuration files for build details.