# EDAM, the life-science ontology for data analysis and management

Lucie Lamothe, Alban Gaignard, Mads Kierkegaard, Hager Eldakroury, Melissa Black, Bryan Brancotte, Jon Ison, Veit Schwämmle, Matúš Kalaš, Hervé Ménager

► To cite this version:

Lucie Lamothe, Alban Gaignard, Mads Kierkegaard, Hager Eldakroury, Melissa Black, et al. EDAM, the life-science ontology for data analysis and management. JOBIM, Jul 2022. Rennes, France. 10.5281/zenodo.6769072. hal-03702557

HAL Id: hal-03702557

https://hal.science/hal-03702557

Submitted on 23 Jun 2022

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Distributed under a Creative Commons Attribution 4.0 International License
# EDAM, life sciences ontology for data analysis and management

Lucie Lamothe<fnref n="1" />, Alban Gaignard<fnref n="2" />, Mads Kierkegaard<fnref n="3" />, Hager Eldakroury<fnref n="4" />, Melissa Black<fnref n="5" />, Bryan Brancotte<fnref n="6" />, Jon Ison<fnref n="1" />, Veit Schwämmle<fnref n="3" />, Matúš Kalaš<fnref n="7" />, Hervé Ménager<fnref n="1" />,<fnref n="6" />, and the EDAM community

EDAM is an ontology of **data analysis** and **data management**, within and beyond life sciences. It comprises concepts related to data analysis, modelling, optimisation, and data life cycle. EDAM is a human and machine-actionable **controlled vocabulary**, used to annotate data, tools, workflows and training materials, so that they can be more easily found, reused, and combined.

EDAM is developed in a **participatory** and **transparent** fashion, within a broad and growing **community of contributors** from both inside and outside of ELIXIR.

Community extensions of EDAM are:

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**EDAM Bioimaging** (including machine learning)

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**EDAM Geo** for interdisciplinary applications, such as **global** and **planetary health**

The community-driven development comes with a set of **challenges**.

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Design by Alban Sauvalle, IFB-core, ELIXIR France. Using icons from Flaticon.com

To help the community use and contribute to EDAM, a set of tools are provided:

## EDAM Browser

A web interface that lets users **explore EDAM** and its usage graphically. It also allows contributors to **submit a suggestion** to the GitHub repository using a graphical user interface.

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## EDAM validation

The quality-control tooling includes standard tools such as **ELK** and **ROBOT**, plus a custom validator working on both the syntactic and semantic levels. The validation tools are run by **continuous integration (CI)** workflows, using GitHub Actions. Additional tests are available for **curation**.

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edamontology

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@edamontology

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INSTITUT FRANÇAIS DE BIOINFORMATIQUE

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Inserm

INRAO

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<footnote n="1">¹CNRS, Institut Français de Bioinformatique, IFB-core, **France** (J.I. at the time of contribution)</footnote>

<footnote n="2">²Nantes Université, CNRS, INSERM, L'institut du thorax, **France**</footnote>

<footnote n="3">³University of Southern Denmark, Ødense, **Denmark**</footnote>

<footnote n="4">⁴Outreachy intern (EDAM), Cairo, **Egypt** (at the time of contribution)</footnote>

<footnote n="5">⁵Outreachy intern (EDAM), São Paulo, **Brazil** (at the time of contribution)</footnote>

<footnote n="6">⁶Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, **France**</footnote>

<footnote n="7">⁷University of Bergen, **Norway**</footnote>