To compare two text files and check for differences, you can use the Unix diff command on Linux or Mac OS X:
or on Windows the FC command:
Any number of graphical diff tools are also available, for example FileMerge is part of Apple’s free XCode tools.
Although OWL ontology files are text, it’s possible to have two identical ontologies saved to two files with very different structure. ROBOT provides a diff command that compares two ontologies while ignoring these differences:
robot diff --left edit.owl --right release.owl
If --output is provided then a report will be written with any differences between the two ontologies:
robot diff --left edit.owl \
--right release.owl \
--output results/release-diff.txt
If your left and right ontologies have different catalog files (perhaps pointing to different import files), you can load them with their correct catalog files using --left-catalog and --right-catalog:
robot diff --left imports.owl \
--left-catalog catalog.xml \
--right imports-right.owl \
--right-catalog catalog-right.xml \
--output results/catalog-diff.txt
See release-diff.txt for an example.
The default “plain” output is in OWL Functional syntax with IRIs. You can include entity labels with --labels true. In addition, Markdown and HTML diff formats (based on Manchester syntax) are available. You can select the desired format using the --format (or -f) option, with possible values plain, pretty (text with labels and CURIEs), html, or markdown.
You can also compare ontologies by IRI with --left-iri and --right-iri. You may want to compare a local file to a release, in which case:
robot diff --left edit.owl \
--right-iri http://purl.obolibrary.org/obo/release.owl
You may specify the input with either --left/--right or --left-iri/--right-iri, but you may not use both option methods for one side.
Both --left and --right input ontologies are required.
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