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Ontology of bioimage informatics operations, topics, types of data, and data formats. EDAM-Bioimaging is an extension of the EDAM ontology (edamontology.org) dedicated to bioimaging data analysis, and developed in an open collaboration including partners from NEUBIAS (neubias.org), COMULIS (comulis.eu), and ELIXIR (elixir-europe.org)..

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DOI representing all stable versions, resolving to the latest: 10.5281/zenodo.1149730

DOI of the latest stable EDAM-bioimaging version alpha06: 10.5281/zenodo.3695725

Poster: 10.7490/f1000research.1117826.1

Twitter: @edamontology (follow)

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, full-fledged reliable release.

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 bioimage analysis, bioimage informatics, and bioimaging. It is being developed in collaboration between the ELIXIR research infrastructure and the 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 (PP2) and the Global BioImaging network.

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Always the last stable version:

Other versions, e.g. the current alpha06:

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:

If you want to contribute in person, please join or organise a hackathon. Get in touch with wg4-edam_ontology@irbbarcelona.org.glip.com or matus.kalas@uib.no 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 https://github.com/edamontology/edam-bioimaging/issues/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. 10.7490/10.7490/f1000research.1117826.1 Open Access

The "mainline" EDAM ontology can be cited by:

EDAM-bioimaging releases are citable with DOIs too, for cases when that is needed. 10.5281/zenodo.1149730 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.

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Ontology of bioimage informatics operations, topics, types of data, and data formats. EDAM-Bioimaging is an extension of the EDAM ontology (edamontology.org) dedicated to bioimaging data analysis, and developed in an open collaboration including partners from NEUBIAS (neubias.org), COMULIS (comulis.eu), and ELIXIR (elixir-europe.org)..

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