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)

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 MetaboHUB-MetaToul
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 = Medizinische Universität Innsbruck
35 Universitat Rovira i Virgili
36 University of 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]

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

Domains: Computer Science [cs]; Bioinformatics [q-bio.QM]; Life Sciences [q-bio]; Toxicology

Marvin Martens, Rob Stierum, Emma Schymanski, Chris Evelo, Reza Aalizadeh, et al.. ELIXIR and Toxicology: a community in development. F1000Research, 2021, 10, pp.1129. ⟨10.12688/f1000research.74502.1⟩. ⟨pasteur-03680151⟩