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The command-line tool is packaged a Java JAR file and can be run via the robot shell script. Before getting started, make sure you have Java 11 or later installed. Check by entering java -version on the command line.

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Where D:/ontology is the directory that contains the ontology or ontologies you want to work on (there is no equivalent for $PWD on Windows when running a command on the command line directly).

R.C. Jackson, J.P. Balhoff, E. Douglass, N.L. Harris, C.J. Mungall, and J.A. Overton. ROBOT: A tool for automating ontology workflows. BMC Bioinformatics, vol. 20, July 2019.

ROBOT is a tool for working with Open Biomedical Ontologies. It can be used as a command-line tool or as a library for any language on the Java Virtual Machine.

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- - - - - - - - - - view on github getting started common errors chaining commands global options makefile plugins - - - - - - - - - - annotate collapse convert diff expand explain export export-prefixes extract filter materialize measure merge mirror python query reason reduce relax remove rename repair report template unmerge validate-profile verify - - - - - - - - - - ROBOT is licensed under the BSD 3-Clause License. Theme by orderedlist

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ROBOT is written in Java, and can be used from any language that runs on the Java Virtual Machine. It’s available on Maven Central and javadoc.io. The code is divided into two parts:

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The robot-core library provides a number of Operation classes for working with ontologies. The IOHelper class contains convenient methods for loading and saving ontologies, and for loading sets of term IRIs. Here’s an example of extracting a “core” subset from an ontology:

Click on the command names in the sidebar for documentation and examples, and visit our JavaDocs for robot-core and robot-command for technical details.