# Biological Imaging Methods Ontology

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. 

## Quick actions

* You may browse terms, definitions and relations in FBbi in the [EBI's Ontology Lookup Service](https://www.ebi.ac.uk/ols4/ontologies/fbbi/). You can click on the term in the tree to explore the hierarchy.

<img width="1137" height="917" alt="grafik" src="https://github.com/user-attachments/assets/793604fe-0125-4cfe-bc8e-4f15f9066210" />


* You may request new terms or ask questions in the [GitHub tracker](https://github.com/foundingGIDE/fbbi/issues) or, if easier, using the [`ontology` tag on image.sc](https://forum.image.sc/t/a-new-version-of-the-biological-imaging-methods-ontology-fbbi-is-available/119993);
* You can see metadata about FBbi and its maintenance status in the [OBO Foundry website](https://obofoundry.org/ontology/fbbi.html).

## History
The ontology was originally developed by [FlyBase](https://flybase.org/)
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](http://www.cellimagelibrary.org/);
* Willy Wong and the Center for Research in Biological Systems (version
  [available on GitHub](https://github.com/CRBS/Biological_Imaging_Methods_Ontology));
* David Osumi-Sutherland as part of the PhenoImageShare project (version
  [available on Github](https://github.com/Imaging-semantics/fbbi)).

From 2026 onwards, the ontology is maintained by a joint effort under the
umbrella of the [FoundingGIDE](https://founding-gide.eurobioimaging.eu) project.

## Known users
The ontology is known to be used by:

* [FlyBase](https://flybase.org/);
* [Virtual Fly Brain](https://wwwvirtualflybrain.org/);
* the [Cell Image Library](https://www.cellimagelibrary.org/);
* the [Human Cell Atlas](https://www.humancellatlas.org/);
* the [FoundingGIDE project](https://founding-gide.eurobioimaging.eu).

## Further documentation

* 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](https://www.eurobioimaging.eu/events/image-data-community-days-2026/).
The slides of that presentation are available
[here](https://github.com/foundingGIDE/fbbi/releases/download/v2026-03-30/Image.Data.Community.Days.2026.pdf).

## Versions

### Stable release versions
The latest version of the ontology can always be found at:
<http://purl.obolibrary.org/obo/fbbi.owl>.

### Editors' version
Editors of this ontology should use the edit version, [src/ontology/fbbi-edit.owl](src/ontology/fbbi-edit.owl)

## Contact
Please use this GitHub repository's [Issue tracker](https://github.com/foundingGIDE/fbbi/issues)
to request new terms/classes or report errors or specific concerns
related to the ontology.

## Acknowledgements
This ontology is maintained using the [Ontology Development Kit](https://github.com/INCATools/ontology-development-kit).