Uberon ROBOT plugin

This project is intended to provide some extra ROBOT commands to be used in portions of the Uberon pipeline.

Mostly, the goal is to be able to replace the use of OWLTools by ROBOT commands only, so that building Uberon no longer requires constantly switching between ROBOT and OWLTools.

Provided commands

merge-species

This command provides the same feature as OWLTools’ --merge-species-ontology command, used in Uberon to build the “composite” cross-species products (such as composite-metazoan).

The syntax is similar to that of the original OWLTools command:

robot merge-species -i <FILE> -t <TAXON> -s <SUFFIX> -o <FILE>

except that the -q, --include-property option must be repeated for each property to include (that is, use -q RO:0002202 -q RO:0002496 instead of -q RO:0002202 RO:0002496).

The command offers additional features that were not available in the original OWLTools command. They are all disabled by default, use the following options to enable them:

• -d: delete class declaration axioms for classes that have been merged;
• -x: translate more class types of class expression than just ObjectSomeValuesFrom (ObjectIntersectionOf, ObjectUnionOf, ObjectComplementOf, and Object(Exact|Min|Max)Cardinality expressions are supported);
• -g: translate general class axioms that refer to a class that has been merged;
• -G: delete (instead of translating) general class axioms that refer to a class that has been merged.

merge-equivalent-sets

This command provides the same feature as OWLTools’ --merge-equivalence-sets command, also used in Uberon to build the composite ontologies.

The command accepts the same options as the original OWLTools command. However, scores assigned to each prefix should be specified as prefix=score pairs. That is, use -s UBERON=10 -s CL=9 instead of -s UBERON 10 -s CL 9.

create-species-subset

This command is intended to replace OWLTools’ --make-species-subset command. Given a a NCBITaxon ID (specified with option -t, --taxon), the command will create a subset containing only the classes that do not violate known taxon constraints in that taxon.

By default, the subset is evaluated from the top of the ontology (owl:Thing). Use the --root option to evaluate from a specific class; all classes above the root will not be included in the subset. The option may be repeated to evaluate the subset from more than one root class.

The default behavior of the command is to remove all classes that are found not to belong in the subset from the output ontology. Alternatively, to merely tag the classes as belonging to the subset without actively remove them, use both the --no-remove option to keep the classes in the ontology and the --subset-name option to specify the subset IRI to tag the classes with.

Building and using

Build with Maven by running:

mvn clean package

This will produce two Jar files in the target directory.

The uberon.jar file is the plugin itself, to be used with a version of ROBOT that supports plugins. If you have such a version, place this file in your plugins directory (by default ~/.robot/plugins), then call the commands by prefixing them with the basename of the Jar file in the plugins directory.

For example, if you placed the plugin at ~/.robot/plugins/uberon.jar, you may call the merge-species command as follows:

robot uberon:merge-species ...

The uberon-robot-standalone-X.Y.Z.jar file is a standalone version of ROBOT that includes the commands provided by this plugin as is they were built-in commands. It is intended to be used until a plugin-enabled version of ROBOT becomes available.

Using 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

Since the Uberon ROBOT plugin is, at least for now, made of commands that are merely a port of the original OWLTools versions, the plugin is distributed under the same terms as OWLTools (3-clause BSD license). See the COPYING file in the source distribution.