1. Enabling the SSSOM commands in ROBOT

ROBOT >= 1.9.5 has built-in support for pluggable commands. To enable the commands provided by this project in ROBOT, place the sssom-robot-plugin-X.Y.Z.jar file in a directory where ROBOT searches for plugins:

• the ~/.robot/plugins directory in your home directory;
• the directory specified by the ROBOT_PLUGINS_DIRECTORY environment variable;
• the directory specified by the robot.pluginsdir Java system property.

It is recommended to rename the archive file to a simple, mono-word name, such as sssom.jar. The commands provided by the plugins will then be available from the command line under the name sssom:COMMAND_NAME, such as sssom:xref-extract.

If for some reasons the use of a plugin is not possible or not wanted, building SSSOM-Java with the standard Maven goal package will also produce a Jar file named sssom-robot-standalone-X.Y.Z.jar. That file will contain a full distribution of the latest version of ROBOT (1.9.5) in which the commands below will be available as built-in comands (in addition to all the standard commands).

Note that in the standalone version, the inject and rename commands are renamed to sssom-inject and sssom-rename, for clarity (and to avoid a clash with the standard rename command).

2. Available commands

Currently, this project provides three commands:

• xref-extract to extract mappings from cross-reference annotations in an ontology;
• inject to inject SSSOM-derived axioms into an ontology;
• rename to rename entities in an ontology, using a mapping set as data source.