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.
Last stable version (now alpha06) at the NCBO BioPortal
All versions at WebProtégé. Free registration at WebProtégé is required.
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
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:
- 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.
- 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
- Join the discussions at firstname.lastname@example.org (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@example.com or firstname.lastname@example.org for planning. Usual hackathons for editing EDAM-bioimaging are the NEUBIAS Taggathons.
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.
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.