Journal articles

ELIXIR and Toxicology: a community in development

Marvin Martens ^{1, *} Rob Stierum ² Emma Schymanski ³ Chris Evelo ^{1, 4} Reza Aalizadeh ⁵ Hristo Aladjov ⁶ Kasia Arturi ⁷ Karine Audouze ⁸ Pavel Babica ⁹ Karel Berka ¹⁰ Jos Bessems ¹¹ Ludek Blaha ⁹ Evan Bolton ¹² Montserrat Cases ¹³ Dimitrios Damalas ⁵ Kirtan Dave ¹⁴ Marco Dilger ¹⁵ Thomas Exner ¹⁶ Daan Geerke ¹⁷ Roland Grafström ^{18, 19} Alasdair Gray ²⁰ John Hancock ²¹ Henner Hollert ²² Nina Jeliazkova ²³ Danyel Jennen ²⁴ Fabien Jourdan ^{25, 26} Pascal Kahlem Jana Klanova ⁹ Jos Kleinjans ²⁴ Todor Kondic ³ Boï Kone ²⁷ Iseult Lynch ²⁸ Uko Maran ²⁹ Sergio Martinez Cuesta ³⁰ Hervé Ménager ^{31, 32} Steffen Neumann ³³ Penny Nymark ¹⁸ Herbert Oberacher ³⁴ Noelia Ramirez ³⁵ Sylvie Remy ¹¹ Philippe Rocca-Serra ³⁶ Reza Salek ³⁷ Brett Sallach ³⁸ Susanna-Assunta Sansone ³⁶ Ferran Sanz ³⁹ Haralambos Sarimveis ⁴⁰ Sirarat Sarntivijai ²¹ Tobias Schulze ⁴¹ Jaroslav Slobodnik ⁴² Ola Spjuth ⁴³ Jonathan Tedds ²¹ Nikolaos Thomaidis ⁵ Ralf Weber ²⁸ Gerard van Westen ⁴⁴ Craig Wheelock ¹⁸ Antony Williams ⁴⁵ Hilda Witters ¹¹ Barbara Zdrazil ⁴⁶ Anže Županič ⁴⁷ Egon Willighagen ^{24, *}

* Corresponding author

1 BiGCaT - Department of Bioinformatics, Maastricht University Medical Center

2 TNO - The Netherlands Organisation for Applied Scientific Research

3 LCSB - Luxembourg Centre For Systems Biomedicine

4 MaCSBio - Maastricht Centre for Systems Biology, Maastricht University Medical Center

5 NKUA - National and Kapodistrian University of Athens

6 BAS - Bulgarian Academy of Sciences

7 Swiss Federal Institute of Aquatic Science & Technology (EAWA)

8 T3S - UMR_S 1124 - Toxicité environnementale, cibles thérapeutiques, signalisation cellulaire

9 RECETOX / MUNI - Research Centre for Toxic Compounds in the Environment [Brno]

10 Palacky University Olomouc

11 VITO - Flemish Institute for Technological Research

12 NCBI - National Center for Biotechnology Information

13 Chemotargets SL

14 GSFC University

15 Forschungs- und Beratungsinstitut Gefahrstoffe GmbH (FoBiG)

16 Seven Past Nine

17 VU - Vrije Universiteit Amsterdam [Amsterdam]

18 Karolinska Institutet [Stockholm]

19 Misvik Biology

20 HWU - Heriot-Watt University [Edinburgh]

21 ELIXIR Hub [Cambridge]

22 Goethe-University Frankfurt am Main

23 Ideaconsult

24 Maastricht University [Maastricht]

25 ToxAlim - ToxAlim

26 MetaToul-MetaboHUB

27 FMPOS - Faculté de Médecine, de pharmacie et d’Odonto-Stomatologie [Bamako, Mali]

28 University of Birmingham [Birmingham]

29 University of Tartu

30 AstraZeneca [Cambridge, UK]

31 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB

32 IFB-CORE - Institut Français de Bioinformatique

33 IPB - Leibniz Institute of Plant Biochemistry

34 IMU - Innsbruck Medical University [Austria]

35 Universitat Rovira i Virgili

36 University of Oxford [Oxford]

37 CIRC - IARC - Centre International de Recherche contre le Cancer - International Agency for Research on Cancer

38 University of York [York, UK]

39 UPF - Universitat Pompeu Fabra [Barcelona]

40 NTUA - National Technical University of Athens [Athens]

41 UFZ - Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research

42 Environmental Institute Kos

43 Uppsala University

44 Leiden Academic Center for Drug Research

45 United States Environmental Protection Agency [Cincinnati]

46 University of Vienna [Vienna]

47 NIB - National Institute of Biology [Ljubljana]

Abstract : Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.

Keywords : Toxicology ELIXIR interoperability FAIR

Document type :

Journal articles

Domain :

Computer Science [cs] / Bioinformatics [q-bio.QM]

Life Sciences [q-bio] / Toxicology

Complete list of metadata

https://hal-pasteur.archives-ouvertes.fr/pasteur-03680151
Contributor : Hervé Ménager Connect in order to contact the contributor
Submitted on : Friday, May 27, 2022 - 3:13:28 PM
Last modification on : Tuesday, June 7, 2022 - 12:57:23 PM

Vignette du document

f61cccea-d930-4df8-b15d-88449b...

Publication funded by an institution