README.md

DOI representing all stable versions, resolving to the latest:

DOI of the latest stable EDAM Bioimaging version alpha06:

Poster: EDAM Bioimaging 2024 (older, citable poster is at )

Twitter: @edamontology (follow; currently not attended)

EDAM Bioimaging

An ontology of bioimage informatics operations, types of data, data formats, and bioimaging topics

EDAM Bioimaging is an extension to the EDAM ontology (http://edamontology.org) for image analysis, bioimaging, AI/ML, bioimage informatics, mass spectrometry, and cytometry. It is being developed in on open between the ELIXIR Research Infrastructure consortium, and the bioimaging community (especially supporting were NEUBIAS and COMULIS COST Actions CA15124, CA17121, funded by the Horizon 2020 Framework Programme of the European Union), in close contact with the Euro-BioImaging Research Infrastructure consortium, the Global BioImaging network, and QUAREP-LiMi, the global grassroots organisation for standardisation in light microscopy.

Viewing

• Last stable version (now alpha06) at the NCBO BioPortal

• All versions at WebProtégé. Free registration at WebProtégé is required.

  • Live development version (now alpha07_dev)

  • Last stable version (now alpha06)

  • Frozen version alpha06

  • Frozen version alpha05

  • Frozen version alpha04

  • Frozen version alpha03

  • Frozen version alpha02

Visualization

• In WebVOWL: https://service.tib.eu/webvowl/#iri=https://edamontology.org/EDAM-bioimaging.owl

Download

Always the last stable version:

• In OWL format from http://edamontology.org/EDAM-bioimaging.owl

• In TSV format from http://edamontology.org/EDAM-bioimaging.tsv

• In CSV format from http://edamontology.org/EDAM-bioimaging.csv

Other versions, e.g. the current alpha06:

• In OWL format from http://edamontology.org/EDAM-bioimaging_alpha06.owl

• In TSV format from http://edamontology.org/EDAM-bioimaging_alpha06.tsv

• In CSV format from http://edamontology.org/EDAM-bioimaging_alpha06.csv

Contributing

This is an open community project (transparent and participatory), and thus contributions are very welcome!

The most accessible way of contributing is writing comments with suggestions or needs for clarification, and starting discussion threads. Multiple channels are avaialable:

Preferred:

• Add comments to the live development version of EDAM-bioimaging at WebProtégé. Free registration at WebProtégé is required. Select a concept and "Start new thread" in the "Comments" widget|window (not "Comments" tab, stay in the "Classes" tab). Contribute to already open threads ibid or in the "Comments" tab.

Other options:

• Submit or comment on an issue at GitHub
• Create a pull request to https://github.com/edamontology/edam-bioimaging
• Add a proposal or comment to EDAM-bioimaging at the NCBO BioPortal
  • to a selected concept in the "Classes" tab by clicking the small "Notes" tab on the right (still within the big "Classes" tab)
  • on the general level in the "Notes" tab. You can include new concept proposals here.
• Join the discussions at [email protected] (if member of, or invited to NeuBIAS on Glip). Mostly organisational stuff.
• Add comments to the stable versions of EDAM-bioimaging at WebProtégé, such as the last stable version and especially the frozen versions (alpha06, alpha05, alpha04, alpha03, alpha02) for more persistent comments. Note that comments to the live version are handled with the highest priority.

If you want to contribute in person, please join or organise a hackathon. Get in touch with [email protected] or [email protected] for planning. Usual hackathons for editing EDAM-bioimaging are the NEUBIAS Taggathons.

Editing

At this momentary early stage of the development, the content of EDAM-bioimaging is developed collaboratively at http://webprotege.stanford.edu/#projects/2ce704bf-83ed-4d2e-985f-84c4841fac71/edit/Classes. After one dev cycle, these developments are commited in a batch to git. Vice versa, commits from git are merged into WebProtégé.

N.B.: Due to this special setup, edit either:

• in only git or in only WebProtégé and merge afterwards
• or if needed in parallel, edit properties and root concepts only in git and other concepts only in WebProtégé. Merge afterwards.

N.B.: Be aware of how IDs of new concepts are assigned, and what it means for both merging into git and Comments in WebProtégé. See #7.

Citing

(Download BibTeX)

Before a full article is published, please cite the following when refering to EDAM Bioimaging in a scholarly publication:

• Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A. Kirschmann, Anatole Chessel, Leandro Scholz, Fabienne Rössler, Laura Nicolás Sáenz, Estibaliz Gómez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David Hörl, Lassi Paavolainen, Ivana Vrhovac Madunić, Dean Karaica, Arrate Muñoz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Hervé Ménager, Chong Zhang, Kota Miura, Julien Colombelli, and Perrine Paul-Gilloteaux. We are welcoming new contributors! (2020). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed]. F1000Research, 9(ELIXIR): 162. Poster. Open Access

The "mainline" EDAM ontology can be cited by:

• Jon Ison, Matúš Kalaš, Inge Jonassen, Dan Bolser, Mahmut Uludag, Hamish McWilliam, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics, 29(10): 1325-1332. PMID: 23479348 Open Access

EDAM Bioimaging releases are citable with DOIs too, for cases when that is needed. represents all releases and resolves to the DOI of the last stable release. For the DOI of a particular release of EDAM Bioimaging, please see /releases.