Uberon ROBOT plugin

Available commands

Currently, the Uberon ROBOT plugin provides the following commands:

• uberon:merge-species, to create composite cross-taxa ontologies;
• uberon:merge-equivalent-sets, to merge terms that are considered equivalent across several ontologies;
• uberon:create-species-subset, to create a subset of an ontology containing only terms that are valid for a specific taxon.

Use with ROBOT

To use the plugin with your local installation of ROBOT, download the plugin file uberon.jar and place it in ROBOT’s plugins directory (by default ~/.robot/plugins). You may then use any command provided by the plugin as any other ROBOT builtin commands.

Use with the ODK

To use the plugin in an ODK-managed ontology, add the following to your ODK configuration file (src/ontology/myontology-odk.yaml):

robot_plugins:
  plugins:
    - name: uberon
      mirror_from: https://github.com/obophenotype/uberon-robot-plugin/releases/download/uberon-robot-plugin-X.Y.Z/uberon.jar

where X.Y.Z is the version number of the Uberon ROBOT plugin.

Then, whenever you need the plugin in one of your custom Makefile rules, make the rule depend on the all_robot_plugins target, and invoke the command you need as part of a ROBOT pipeline by prefixing its name with uberon:. For example:

target.owl: source1.owl source2.owl | all_robot_plugins
	$(ROBOT) merge -i source1.owl -o source2.owl \
	         uberon:merge-species -t NCBITaxon:7227 -s 'D melanogaster' -o $@

Copying

The Uberon ROBOT plugin is distributed under the terms of a 3-clause BSD license. See the COPYING file in the source distribution.