Authors
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, Sebastien Munck, Ofra Golani, Josh Moore, Alban Gaignard, Florian Levet, Jon Ison, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux
Publication date
2020/6/10
Conference
ELIXIR All Hands 2020
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] . EDAM-bioimaging is an extension of EDAM dedicated to bioimage analysis, bioimage informatics, and bioimaging. It is being developed in collaboration between the ELIXIR research infrastructure and the NEUBIAS and COMULIS COST Actions, in close contact with the Euro-BioImaging research infrastructure and the Global BioImaging network. 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, workflows, and training materials, fostering open science and "reproducible" bioimage analysis. New developments in EDAM-bioimaging at the time of publication [3] include among others: A concise but relatively comprehensive ontology of Machine learning, Artificial intelligence, and Clustering (to the level relevant in particular in bioimaging, biosciences, and also scientific data analysis in general) Added and refined topics and synonyms within Sample preparation and Tomography, and finalised coverage of imaging techniques (all of these to the high-level extent that influences choices of downstream analysis, i.e. the scope of EDAM) EDAM-bioimaging continues being under active development, with a growing and diversifying community of contributors. It is used in BIII.eu, the registry of bioimage analysis tools, workflows, and training materials, and emerging also in …
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