EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (2019 update)
Creators: name: Matúš Kalaš
name: Plantard, Laure
name: Nataša Sladoje
name: Lindblad, Joakim
name: Kirschmann, Moritz Alexander
name: Jones, Martin
name: Chessel, Anatole
name: Scholz, Leandro Aluisio
name: Rössler, Fabienne
name: Dufour, Alexandre
name: Bogovic, John
name: Zhang, Chong
name: Waithe, Dominic
name: Sampaio, Paula
name: Paavolainen, Lassi
name: Hörl, David
name: Munck, Sebastian
name: Golani, Ofra
name: Moore, Josh
name: Gaignard, Alban
name: Levet, Florian
name: Participants In The NEUBIAS Taggathons
name: Paul-Gilloteaux, Perrine
name: Ison, Jon
name: Team, The EDAM Dev
name: Miura, Kota
name: Colombelli, Julien
name: And Welcoming New Contributors
Publisher: name: F1000 Research Limited
Year: 2019

description: EDAM is a well-established ontology of operations, topics, types of data, and data formats that are used in bioinformatics and its neighbouring fields [1,2,3] . EDAM-bioimaging is an extension of EDAM dedicated to bioimage analysis, bioimage informatics, and bioimaging. It is developed in collaboration between the NEUBIAS and ELIXIR Europe|ELIXIR-EXCELERATE projects, in contact with Euro-BioImaging and Global BioImaging.<br><br>EDAM-bioimaging contains an inter-related hierarchy of concepts including bioimage analysis and related operations, bioimaging topics and technologies, and bioimage data and their formats. The modelled concepts enable interoperable descriptions of software, publications, data, and workflows, fostering reliable and transparent, "reproducible" bioimage analysis.<br><br>EDAM-bioimaging is under active development, with a few alpha releases publicly available. It is used in BISE|biii.eu, the bioimaging tools and resources information portal, and emerging also in descriptions of Debian Med packages available in Debian and Bio-Linux. Development of EDAM-bioimaging has been carried out in a successful open community manner, in a fruitful collaboration between numerous bioimaging experts and ontology developers. The last stable release at the time of poster submission is version <i>alpha05</i> [4], and the live development version can be viewed and commented on WebProtégé (free registration required). New contributors are warmly welcome!<br><br>[1] Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S. and Rice, P. (2013). EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. <i>Bioinformatics</i>, 29(10): 1325-1332. DOI: 10.1093/bioinformatics/btt113 <i>Open Access</i><br>[2] Kalaš, M., Ménager, H., Schwämmle, V., Ison, J. and EDAM Contributors (2017)<i>.</i> EDAM – the ontology of bioinformatics operations, types of data, topics, and data formats (2017 update) [version 1; not peer reviewed]. <i>F1000Research</i>, 6(ISCB Comm J):1181 (Poster) DOI: 10.7490/f1000research.1114459.1 <i>Open Access</i><br>[3] Kalaš, M., Ménager, H., Ison, J. and Willighagen, E. (2018). edamontology/edamontology: EDAM 1.21 (Version 1.21). <i>Zenodo</i>. DOI: 10.5281/zenodo.1325952<i> Open Access</i><br>[4] Matúš Kalaš, Nataša Sladoje, Laure Plantard, Martin Jones, Leandro Aluisio Scholz, Joakim Lindblad, and contributors (2019). edamontology/edam-bioimaging: alpha05 (Version alpha05). <i>Zenodo</i>. DOI:  10.5281/zenodo.2557012 <i>Open Access</i>