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ROBOT is an OBO Tool

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.

Convert

Official documentation

Convert an ontology between different formats: owl, ttl, omn, obo.

The input and output format is determined by the file extension.

robot convert --input ontology.ttl --output ontology.owl

Extract terms form one ontology onto another

Official documentation

robot extract --method BOT --input source_onto.owl --term-file terms.txt --output destination_onto.owl

--method defines the method for importing the terms, which can be:

  • BOT or BOTTOM: takes a view from the BOTTOM of the class-hierarchy upwards. Importing the term request and super-classes and the inter-relations.
  • TOP: takes a view from the TOP of the class-hierarchy downwards
  • SMART: terms ... and the inter-relations between them (not necessarily sub- and super-classes)

--term-file is a file containing the IRIs of the terms to be imported from the source ontology to the destination ontology

Example --term-file file:

http://purl.obolibrary.org/obo/IAO_0000004 # has measurement value
http://purl.obolibrary.org/obo/IAO_0000404 # has x coordinate value