The Biological Imaging Methods Ontology (FBbi) is an ontology for the description of sample preparation, visualisation, and imaging methods used in biomedical research.
This GitHub repository is used to maintain and update the source files for the ontology.
- You may browse terms, definitions and relations in FBbi in the EBI's Ontology Lookup Service. You can click on the term in the tree to explore the hierarchy.
- You may request new terms or ask questions in the GitHub tracker or, if easier, using the
ontologytag on image.sc; - You can see metadata about FBbi and its maintenance status in the OBO Foundry website.
The ontology was originally developed by FlyBase until circa 2005. The latest version edited by FlyBase is available on https://s3ftp.flybase.org/releases/FB2025_02/precomputed_files/ontologies/image.obo.gz.
It was later extended and used by several groups beyond FlyBase, including:
- Chris Woodcock and the Cell Image Library;
- Willy Wong and the Center for Research in Biological Systems (version available on GitHub);
- David Osumi-Sutherland as part of the PhenoImageShare project (version available on Github).
From 2026 onwards, the ontology is maintained by a joint effort under the umbrella of the FoundingGIDE project.
The ontology is known to be used by:
- FlyBase;
- Virtual Fly Brain;
- the Cell Image Library;
- the Human Cell Atlas;
- the FoundingGIDE project.
- A brief introduction to ontologies in general and to the Biological Imaging Methods Ontology in particular was given to the Euro-Bioimaging Image Data Community Days 2026. The slides of that presentation are available here.
The latest version of the ontology can always be found at: http://purl.obolibrary.org/obo/fbbi.owl.
Editors of this ontology should use the edit version, src/ontology/fbbi-edit.owl
Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.
This ontology is maintained using the Ontology Development Kit.