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, developed in collaboration between partners from NEUBIAS Cost Action (Horizon 2020 CA15124) and ELIXIR-EXCELERATE WP1 (Horizon 2020 676559), in contact with partners from Euro-BioImaging PP2.
Last stable version (now alpha05) 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 alpha05:
In OWL format from http://edamontology.org/EDAM-bioimaging_alpha05.owl
In TSV format from http://edamontology.org/EDAM-bioimaging_alpha05.tsv
In CSV format from http://edamontology.org/EDAM-bioimaging_alpha05.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
- 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 (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, Moritz Alexander Kirschmann, Joakim Lindblad, Anatole Chessel, Nataša Sladoje-Matić, Leandro A. Scholz, Chong Zhang, Fabienne Rössler, Alexandre Dufour, John A. Bogovic, Martin Jones, Josh Moore, Alban Gaignard, Lassi Paavolainen, David Hörl, Ofra Golani, Participants in the NEUBIAS Taggathons, Perrine Paul-Gilloteaux, the EDAM dev team, Kota Miura, Julien Colombelli, and welcoming contributors (2018). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats [version 1; not peer reviewed]. F1000Research, 7(ELIXIR): 180. Poster. Open Access
- Matúš Kalaš, Laure Plantard, Nataša Sladoje, Joakim Lindblad, Moritz Alexander Kirschmann, Martin Jones, Anatole Chessel, Leandro Aluisio Scholz, Fabienne Rössler, Alexandre Dufour, John Bogovic, Chong Zhang, Dominic Waithe, Paula Sampaio, Lassi Paavolainen, David Hörl, Sebastian Munck, Ofra Golani, Josh Moore, Alban Gaignard, Florian Levet, participants in the NEUBIAS Taggathons, Perrine Paul-Gilloteaux, Jon Ison, the EDAM dev team, Kota Miura, Julien Colombelli, and welcoming new contributors (2019). EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (2019 update) [version 1; not peer reviewed]. F1000Research, 8(ELIXIR): 158. 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.