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The EDAM Framework and Control Room. The EDAM Framework and Control Room: Facing the data deluge, one concept at a time
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Edité par CCSD -
International audience. EDAM is an ontology aimed at standardising terms and definitions for the analysis and management of data in life sciences. Those terms, or concepts, are organised into 4 sub-ontologies: topics, operations, data types and formats. The ontology allows the annotation of digital resources and thus facilitates their findability and reusability, contributing to the FAIRification of tools and other resources in biosciences and beyond. EDAM is used in key resources such as Galaxy, the ELIXIR bio.tools [1] and TeSS catalogues [2], or Bioschemas [3]. Several tools have been developed in order to facilitate the development and usage of EDAM, including the EDAM Browser [4] and Caséologue [5]. However, as new topics or experimental techniques emerge continuously, developing and maintaining the quality of the EDAM ontology and its associated tools, as well as its scientific accuracy and relevance, proves to be a challenge. In order to facilitate and accelerate the development of EDAM, we created the EDAM Control Room, a web tool that allows a wide range of users to contribute to the ontology without the need for advanced skills in programming or ontology edition. The control room allows to i) visualise the contents of the ontology and compare its versions, ii) orientate potential contributors by highlighting tasks catering to their skills or availability (eg high-priority, quick-to-solve, domain specific), and iii) facilitate the use of GitHub to gather expert knowledge and credit contributions.We developed the EDAM Control Room, which allows a wider community of people to contribute to the project in a semi-guided fashion. We hope to facilitate spontaneous contributions, as well as provide a ready-to-use platform to be used in contexts such as hackathons, where volunteers of any scientific background could contribute punctually without the need for heavy supervision. By promoting the use of the EDAM Control Room, we are also hoping to reduce the amount of downstream validation and manual curation needed for the release of future EDAM updates.ReferencesIson J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, et al. The bio.tools registry of software tools and data resources for the life sciences. Genome Biology. 2019 Aug 12;20(1):164. Beard N, Bacall F, Nenadic A, Thurston M, Goble CA, Sansone SA, et al. TeSS: a platform for discovering life-science training opportunities. Bioinformatics. 2020 May 15;36(10):3290–1. 1.Gray AJG, Goble C, Jimenez RC. Bioschemas: From Potato Salad to Protein Annotation. In International Semantic Web Conference (Posters, Demos & Industry Tracks). 2017.Brancotte B, Blanchet C, Ménager H. A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. Journal of Open Source Software. 2018 Jul 22;3(27):698. Lamothe L, Gaignard A, Kierkegaard M, Eldakroury H, Black M, Brancotte B, et al. EDAM, life sciences ontology for data analysis and management. Zenodo. 2022 Jun 28.
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