EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020)
Creators: name: Matúš Kalaš
name: Ménager, Hervé
name: Gaignard, Alban
name: Schwämmle, Veit
name: Ison, Jon
name: Contributors, The EDAM
Publisher: name: F1000 Research Limited
Year: 2020

description: <b>Project website:</b> http://edamontology.org<br><b>Source code:</b> https://github.com/edamontology/edamontology<br><b>License:</b> CC BY-SA 4.0<br><br>EDAM is an ontology of well-established, familiar concepts that are prevalent within bioinformatics, and bioscientific data analysis in general [1,2]. The scope of EDAM includes types of data and data identifiers, data formats, operations, and topics. EDAM has a relatively simple structure, and comprises a set of concepts with terms, synonyms, definitions, relations, links, and some additional information (especially for data formats).<br><br>EDAM is developed in a participatory and transparent fashion, within a growing international community of contributors. The development of EDAM is coordinated with the development and curation of tools registries (<i>e.g.</i> bio.tools and BIII.eu); registries of training materials (<i>e.g. </i>TeSS); with packaging of open-source bioinformatics software (especially Debian Med [3]); the Common Workflow Language [4]; and other related communities and initiatives. These include the developers’ community of Galaxy [5], and collaborations with specialised networks of experts, such as within the development of EDAM-bioimaging [6]. EDAM-bioimaging is an extension of EDAM towards bioimage informatics and machine learning, where a broad group of experts in bioimaging, image analysis, and deep learning has been contributing to the common effort. The comprehensive but concise inclusion of machine learning topics is one of the new additions in 2020.The latest release of EDAM at the time of publication was version 1.24 [7], and EDAM-bioimaging version <i>alpha06</i> [8].<br><br>In summary, EDAM functions as common controlled vocabulary when publishing, sharing, and integrating information about bioinformatics tools, workflows, training materials, and other resources. In addition, EDAM is also useful when choosing terminology, for data provenance, and in text mining (<i>e.g.</i> EDAMmap).<br><br><sub>Slightly shorter versions of this abstract were reviewed by members of the corresponding committees of the listed conferences.<br><br>[1] Jon Ison, Matúš Kalaš, Inge Jonassen, Dan Bolser, Mahmut Uludag, Hamish McWilliam, James Malone, Rodrigo Lopez, Steve Pettifer, Peter Rice. <b>(2013)</b>. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. <i>Bioinformatics</i>, <b>29</b>(10): 1325-1332. DOI: 10.1093/bioinformatics/btt113 <i>Open access</i><br>[2] Matúš Kalaš, Hervé Ménager, Jon Ison, Egon Willighagen, Björn Grüning <b>(2017-2020)</b>. edamontology/edamontology (All versions). <i>Zenodo</i>. DOI: 10.5281/zenodo.822690 <i>Open access</i><br>[3] Steffen Möller, Stuart W. Prescott, Lars Wirzenius, Petter Reinholdtsen, Brad Chapman, Pjotr Prins, Stian Soiland-Reyes, Fabian Klötzl, Andrea Bagnacani, Matúš Kalaš, Andreas Tille, Michael R. Crusoe <b>(2017)</b>. Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis. <i>Data Sci. Eng.</i>, <b>2</b>:<b> </b>232–244. DOI: 10.1007/s41019-017-0050-4 <i>Open access</i><br>[4] Peter Amstutz, Michael R. Crusoe, Nebojša Tijanić (editors), Brad Chapman, John Chilton, Michael Heuer, Andrey Kartashov, Dan Leehr, Hervé Ménager, Maya Nedeljkovich, Matt Scales, Stian Soiland-Reyes, Luka Stojanovic <b>(2016)</b>. Common Workflow Language, v1.0. Specification, <i>Common Workflow Language working group</i>. https://w3id.org/cwl/v1.0/ DOI: 10.6084/m9.figshare.3115156.v2 <i>Open access</i><br>[5] Hervé Ménager, Jon Ison, Matúš Kalaš, Veit Schwämmle, EDAM contributors <b>(2017)</b>. The EDAM ontology and its integration into Galaxy [version 1; not peer reviewed]. <i>F1000Research</i>, <b>6</b>(Galaxy):1032 (Poster). DOI: 10.7490/f1000research.1114336.1 <i>Open access</i><br>[6] 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! <b>(2020)</b>. EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) [version 1; not peer reviewed]. <i>F1000Research</i>, <b>9</b>(ELIXIR,NEUBIAS):162 (Poster). DOI: 10.7490/f1000research.1117826.1 <i>Open access</i><br>[7] Matúš Kalaš, Hervé Ménager, Jon Ison, Egon Willighagen, Björn Grüning <b>(2020)</b>. edamontology/edamontology: EDAM 1.24 (Version 1.24). <i>Zenodo</i>. DOI: 10.5281/zenodo.3608238 <i>Open access</i><br>[8] Joakim Lindblad, Laure Plantard, Martin Jones, Nataša Sladoje, Marie-Charlotte Domart, Matthia Karreman, </sub> <sub>Estibaliz Gómez de Mariscal, Laura Nicolás Sáenz, Christos Kyprianou, María Arrate Muñoz-Barrutia, Raf Van de Plas, Xavier Heiligenstein, Ivana Vrhovac Madunić, Dean Karaica, Daniel Sage, Robert Haase, and all contributors to the previous versions, Matúš Kalaš <b>(2020)</b>. edamontology/edam-bioimaging: alpha06 (Version alpha06). <i>Zenodo</i>. DOI: 10.5281/zenodo.3695725 <i>Open access</i></sub>