EDAM: the bioscientific data analysis ontology (update 2021)
Creators: name: Black, Melissa
name: Lamothe, Lucie
name: Hager Eldakroury
name: Kierkegaard, Mads
name: Ankita Priya
name: Machinda, Anne
name: Khanduja, Uttam Singh
name: Drashti Patoliya
name: Rashika Rathi
name: Tawah Peggy Che Nico
name: Umutesi, Gloria
name: Blankenburg, Claudia
name: Op, Anita
name: Chieke, Precious
name: Omodolapo Babatunde
name: Laurie, Steve
name: Neumann, Steffen
name: Schwämmle, Veit
name: Kuzmin, Ivan
name: Hunter, Chris
name: Karr, Jonathan
name: Ison, Jon
name: Gaignard, Alban
name: Brancotte, Bryan
name: Ménager, Hervé
name: Matúš Kalaš
Publisher: name: F1000 Research Limited
Year: 2022

description: <b>Homepage</b>: https://edamontology.org/<br> <b>Source Code</b>: https://github.com/edamontology/edamontology<br> <b>License</b>: CC BY-SA 4.0<br> <br> EDAM [1] is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life-cycle. Targetting usability by diverse end users, the structure of EDAM is relatively simple, divided into 4 main sections: <b><i>Topic</i></b> <b><i>Operation</i></b> <b><i>Data</i></b> (incl. <i>Identifier</i>) <i><b>Format</b></i> <br> EDAM is used in numerous resources, for example Bio.tools, Galaxy, Debian, or the ELIXIR Europe training portal TeSS. Thanks to the annotations with EDAM, <b>computational tools</b>, <b>workflows</b>, <b>standards</b>, <b>data</b>, and <b>learning materials</b> are easier to find, compare, choose, and integrate. EDAM contributes to <b>open science</b> by allowing semantic annotation of processed data, thus making the data more understandable, findable, and comparable. EDAM and its applications <b>lower the barrier</b> and effort for scientists and citizens alike, towards doing scientific research in a more <i>open</i>, <i>reliable</i>, and <i>inclusive</i> way.<br> <br> The main improvements in 2021 include: The addition of essential concepts of <i>data management</i> and <i>open science</i> Improved automated <b>validation</b> (CI) Improved contribution processes towards more <b>inclusion</b> and <b>engagement</b> with communities of scientific experts, software engineers, and volunteers Easier to <b>contribute</b>, and therefore new contributors and<br> new <b>collaborations</b>. And welcoming more! News from the applications: Galaxy can now visualise the tools panel sorted by EDAM. <br> The <b>EDAM community</b> brings together software engineers and science experts (academic, industrial, citizen), professionals and volunteers. It can be followed and contributed to via various channels. One option is GitHub, with dedicated repositories incl. edamontology and others. Other platforms for contributions to EDAM are especially the generic ontology browsers of the NCBO BioPortal (EDAM, EDAM Bioimaging [2]) and WebProtégé (EDAM, EDAM Bioimaging; free registration required also for viewing). The main communication channel is Gitter.<br> Along with the ontology, the community has developed a number of tools that enhance user experience with EDAM: <b>EDAM Browser</b> [3] is a lightweight and fast web-based ontology browser that provides a number of user-oriented features such as aggregated search across various EDAM-annotated resources (<i>e.g</i>. Bio.tools, TeSS), and <b>suggesting changes</b> to EDAM. <b>EDAMmap</b> is a tool for text mining EDAM concepts from articles. <b>EDAM Popovers</b> is a web-browser add-on<b>/</b>extension for showing details of EDAM concepts found in a website. Great <i>e.g.</i> for code and textual data on GitHub <sub><b>References:</b><br> [1] Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S. and Rice, P. (<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, 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, Perrine Paul-Gilloteaux, and welcoming new contributors! (<b>2020</b>)<i>.</i> 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):162 (Poster) DOI: 10.7490/f1000research.1117826.1 <i>Open access</i><br> [3] Brancotte, B., Blanchet, C. and Ménager, H. (<b>2018</b>). A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. <i>J. Open Source Softw.</i>, <b>3</b>(27): 698. DOI: 10.21105/joss.00698 <i>Open access</i><br> <br> <b>Acknowledgement:</b><br> EDAM maintainers and interns were supported by ELIXIR Europe, Norway, and France.<br> Dr. Melissa Black and Gloria Umutesi were awarded with complimentary registration at ISMB/ECCB 2021, funded by the BOSC 2021 sponsors.<br> The list of co-authors includes the substantial contributors to EDAM in 2020-2021 (version 1.26), without the contributors specific to EDAM Biomaging, EDAM Browser, or EDAMmap.</sub>