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Bubastis is an ontology Diff tool for detecting asserted logical differences between two ontologies, such as between versions.


Bubastis is available as a web application at

Alternatively, you can download Bubastis and use it as a Java library or as a command line executable.


Bubastis developed out of the need to track changes between versions of the Experimental Factor Ontology, but operates as a standalone Ontology Diff in it's own right. It will diff any ontology that can be parsed and loaded using the OWL API, including those in OBO format.

To use Bubastis, you simply need two ontology files to diff (usually different versions of the same ontology, but Bubastis will still produce a report between different ontologies). The documentation gives a quick overview and some examples.

In this example, we diff two versions of EFO - version 2.26 and version 2.27.

Simply paste the two URLs into the text boxes (the "oldest" version goes in the Ontology 1 box) and hit "Begin Ontology Diff". Bubastis Tool, front page

This produces a report showing the changes: blue text indicates the changed entity, with removals or deletions are in red, additions in green. Bubastic Tool, diff report


Below is a simple example of using Bubastis to diff two versions of the same ontology.


There are three diff options in Bubastis. You can toggle each item on and off to configure what information is shown in your diff report.

  • Modified classes
    • those with the same IRI between ontologies, but which have logically changed (e.g. axioms have been added that effect this class, or have had annotations added
  • Newly added classes
    • those in which the IRI for a class appears in the second ontology but not the first
  • Deleted classes
    • those in which the IRI for a class appears in the first ontology, but not the second

Data files

Input file format

Bubastis requires two input files in one of the following formats:

Output file format

Bubastis reports can be viewed as part of the web application, or exported as XML.

Issues and support

Issues and feature requests

To request a new feature or if you think you've found a bug, please use the Functional Genomics Production Team Ontology JIRA Tracker.


If you need help using this tool, please email


For more information or to get involved please email James Malone.


This tool was developed by James Malone.

This work was paid for by EMBL-EBI core funding.