EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats (update 2019)
Résumé
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.
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.
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 alpha05 [4], and the live development version can be viewed and commented on WebProtégé (free registration required). New contributors are warmly welcome!
[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. Bioinformatics, 29(10): 1325-1332. DOI: 10.1093/bioinformatics/btt113 Open Access
[2] Kalaš, M., Ménager, H., Schwämmle, V., Ison, J. and EDAM Contributors (2017). EDAM – the ontology of bioinformatics operations, types of data, topics, and data formats (2017 update) [version 1; not peer reviewed]. F1000Research, 6(ISCB Comm J):1181 (Poster) DOI: 10.7490/f1000research.1114459.1 Open Access
[3] Kalaš, M., Ménager, H., Ison, J. and Willighagen, E. (2018). edamontology/edamontology: EDAM 1.21 (Version 1.21). Zenodo. DOI: 10.5281/zenodo.1325952 Open Access
[4] Matúš Kalaš, Nataša Sladoje, Laure Plantard, Martin Jones, Leandro Aluisio Scholz, Joakim Lindblad, and contributors (2019). edamontology/edam-bioimaging: alpha05 (Version alpha05). Zenodo. DOI: 10.5281/zenodo.2557012 Open Access