ELIXIR and Toxicology: a community in development

F1000Research, vol. 10, pp. 1129

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.

Authors 60

1. Marvin Martens

   Maastricht University

   Affiliation as printed

   Department of Bioinformatics - BiGCaT Maastricht 6229 ER Maastricht University

   Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands

2. Rob H. Stierum

   Netherlands Organisation for Applied Scientific Research

   Affiliation as printed

   Risk Analysis for Products In Development (RAPID) Utrecht 3584 CB Netherlands Organisation for applied scientific research TNO

   Risk Analysis for Products In Development (RAPID), Netherlands Organisation for applied scientific research TNO, Utrecht, 3584 CB, The Netherlands

3. Emma Schymanski

   University of Luxembourg · Luxembourg Centre for Systems Biomedicine

   Affiliation as printed

   Luxembourg Centre for Systems Biomedicine (LCSB) Belvaux 4367 University of Luxembourg

   Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg

4. Chris T. Evelo

   Maastricht University Medical Centre · Maastricht University

   Affiliation as printed

   Department of Bioinformatics - BiGCaT Maastricht 6229 ER Maastricht University

   Maastricht Centre for Systems Biology (MaCSBio) Maastricht 6229 EN Maastricht University

   Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands

   Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 EN, The Netherlands

5. Reza Aalizadeh

   National and Kapodistrian University of Athens

   Affiliation as printed

   Laboratory of Analytical Chemistry, Department of Chemistry Athens 15771 National and Kapodistrian University of Athens

   Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece

6. Hristo Aladjov

   Bulgarian Academy of Sciences · Institute of Biophysics and Biomedical Engineering · Institute of Biophysics

   Affiliation as printed

   Institute of Biophysics and Biomedical Engineering Sofia 1113 Bulgarian Academy of Sciences

   Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria

7. Katarzyna Arturi

   Swiss Federal Institute of Aquatic Science and Technology

   Affiliation as printed

   Department Environmental Chemistry Dübendorf 8600 Swiss Federal Institute of Aquatic Science and Technology

   Department Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, 8600, Switzerland

8. Karine Audouze

   Inserm · Université Paris Cité · Health and Functional Exposomics · Délégation Paris 6

   Affiliation as printed

   Paris F-75006 Université de Paris

   Université de Paris, T3S, Inserm UMR-S1124, Paris, F-75006, France

9. Pavel Babica

   Masaryk University · RECETOX

   Affiliation as printed

   RECETOX, Faculty of Science Brno Masaryk University

   RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic

10. Karel Berka

    Palacký University Olomouc

    Affiliation as printed

    Department of Physical Chemistry Olomouc 77146 Palacky University Olomouc

    Department of Physical Chemistry, Palacky University Olomouc, Olomouc, 77146, Czech Republic

11. Jos G.M. Bessems

    Flemish Institute for Technological Research

    Affiliation as printed

    Health Unit Mol 2400 Health

    Health Unit, Flemish Institute for Technological Research (VITO), Mol, 2400, Belgium

12. Luděk Bláha

    Masaryk University · RECETOX

    Affiliation as printed

    RECETOX, Faculty of Science Brno Masaryk University

    RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic

13. Evan Bolton

    National Institutes of Health · National Center for Biotechnology Information

    Affiliation as printed

    National Center for Biotechnology Information Bethesda MD 20894 National Library of Medicine, National Institutes of Health

    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

14. Montserrat Cases
    Affiliation as printed

    Barcelona 08028 Chemotargets SL

    Chemotargets SL, Barcelona, 08028, Spain

15. Dimitrios Ε. Damalas

    National and Kapodistrian University of Athens

    Affiliation as printed

    Laboratory of Analytical Chemistry, Department of Chemistry Athens 15771 National and Kapodistrian University of Athens

    Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece

16. Kirtan Dave

    Gujarat University · National Forensic Sciences University

    Affiliation as printed

    School of Science Gujarat 391750 GSFC University

    School of Science, GSFC University, Gujarat, 391750, India

17. Marco Dilger

    Landesamt für Geologie, Rohstoffe und Bergbau

    Affiliation as printed

    Freiburg im Breisgau 79106 Forschungs- und Beratungsinstitut Gefahrstoffe (FoBiG) GmbH

    Forschungs- und Beratungsinstitut Gefahrstoffe (FoBiG) GmbH, Freiburg im Breisgau, 79106, Germany

18. Thomas E. Exner

    Seven Past Nine

    Affiliation as printed

    Cerknica 1380 Seven Past Nine

    Seven Past Nine, Cerknica, 1380, Slovenia

19. Daan P. Geerke

    Vrije Universiteit Amsterdam

    Affiliation as printed

    AIMMS Division of Molecular Toxicology Amsterdam 1081 HZ Vrije Universiteit

    AIMMS Division of Molecular Toxicology, Vrije Universiteit, Amsterdam, 1081 HZ, The Netherlands

20. Roland Grafström

    Karolinska Institutet

    Affiliation as printed

    Department of Toxicology Turku 20520 Misvik Biology

    Institute of Environmental Medicine Stockholm 17177 Karolinska Institute

    Department of Toxicology, Misvik Biology, Turku, 20520, Finland

    Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden

21. Alasdair J. G. Gray

    Heriot-Watt University · Heriot-Watt University Malaysia

    Affiliation as printed

    Department of Computer Science Edinburgh Heriot-Watt University

    Department of Computer Science, Heriot-Watt University, Edinburgh, UK

22. John M. Hancock

    ELIXIR

    Affiliation as printed

    ELIXIR Hub Cambridge CB10 1SD Wellcome Genome Campus

    ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK

23. Henner Hollert

    Goethe University Frankfurt · Goethe-Institute United Kingdom

    Affiliation as printed

    Department Evolutionary Ecology & Environmental Toxicology (E3T) Frankfurt D-60438 Goethe-University

    Department Evolutionary Ecology & Environmental Toxicology (E3T), Goethe-University, Frankfurt, D-60438, Germany

24. Nina Jeliazkova

    IDEAconsult

    Affiliation as printed

    Sofia Ideaconsult Ltd

    Ideaconsult Ltd., Sofia, Bulgaria

25. Danyel G. J. Jennen

    Maastricht University

    Affiliation as printed

    Department of Toxicogenomics Maastricht 6200 MD Maastricht University

    Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands

26. Fabien Jourdan

    Université Toulouse III - Paul Sabatier · École Nationale Vétérinaire de Toulouse · Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Toxicologie Alimentaire · MetaboHUB · Université de Toulouse

    Affiliation as printed

    MetaboHUB Toulouse French metabolomics infrastructure in Metabolomics and Fluxomics

    Toxalim (Research Centre in Food Toxicology) Toulouse Université de Toulouse

    MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France

    Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France

27. Pascal Kahlem
    Affiliation as printed

    Barcelona 08015 Scientific Network Management SL

    Scientific Network Management SL, Barcelona, 08015, Spain

28. Jana Klánová

    Masaryk University · RECETOX

    Affiliation as printed

    RECETOX, Faculty of Science Brno Masaryk University

    RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic

29. Jos C. S. Kleinjans

    Maastricht University

    Affiliation as printed

    Department of Toxicogenomics Maastricht 6200 MD Maastricht University

    Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands

30. Todor Kondić

    University of Luxembourg · Luxembourg Centre for Systems Biomedicine

    Affiliation as printed

    Luxembourg Centre for Systems Biomedicine (LCSB) Belvaux 4367 University of Luxembourg

    Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg

31. Boī Koné

    University of Bamako · Malaria Research and Training Center

    Affiliation as printed

    Faculty of Pharmacy Bamako BP:1805 Malaria Research and Training Center

    Faculty of Pharmacy, Malaria Research and Training Center, Bamako, BP:1805, Mali

32. Iseult Lynch

    University of Birmingham

    Affiliation as printed

    School of Geography, Earth and Environmental Sciences Birmingham B15 2TT University of Birmingham, UK

    School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

33. Uko Maran

    University of Tartu

    Affiliation as printed

    Department of Chemistry Tartu 50411 University of Tartu

    Department of Chemistry, University of Tartu, Tartu, 50411, Estonia

34. Sergio Martínez Cuesta

    AstraZeneca (United Kingdom) · AstraZeneca (Australia)

    Affiliation as printed

    Data Sciences and Quantitative Biology, Discovery Sciences Cambridge AstraZeneca

    Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, UK

35. Hervé Ménager

    Institut Pasteur · Université Paris Cité · Institut Français de Bioinformatique

    Affiliation as printed

    Bioinformatics and Biostatistics Hub Paris F-75015 Institut Pasteur

    Evry F-91000 Institut Français de Bioinformatique

    Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, Paris, F-75015, France

    Institut Français de Bioinformatique, Evry, F-91000, France

36. Steffen Neumann

    Leibniz Institute of Plant Biochemistry

    Affiliation as printed

    Research group Bioinformatics and Scientific Data Halle 06120 Leibniz Institute of Plant Biochemistry

    Research group Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany

37. Penny E. H. Nymark

    Karolinska Institutet

    Affiliation as printed

    Institute of Environmental Medicine Stockholm 17177 Karolinska Institute

    Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden

38. Herbert Oberacher

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Institute of Legal Medicine and Core Facility Metabolomics Innsbruck A-6020 Medical University of Innsbruck

    Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, A-6020, Austria

39. Noelia Ramírez

    Institut de Recerca Biomèdica Catalunya Sud · Universitat Rovira i Virgili

    Affiliation as printed

    Tarragona 43007 Institut d'Investigacio Sanitaria Pere Virgili-Universitat Rovira i Virgili

    Institut d'Investigacio Sanitaria Pere Virgili-Universitat Rovira i Virgili, Tarragona, 43007, Spain

40. Sylvie Rémy

    Flemish Institute for Technological Research

    Affiliation as printed

    Health Unit Mol 2400 Health

    Health Unit, Flemish Institute for Technological Research (VITO), Mol, 2400, Belgium

41. Philippe Rocca‐Serra

    University of Oxford · Science Oxford

    Affiliation as printed

    Data Readiness Group, Department of Engineering Science Oxford University of Oxford

    Data Readiness Group, Department of Engineering Science, University of Oxford, Oxford, UK

42. Reza M. Salek

    Centre international de recherche sur le cancer

    Affiliation as printed

    International Agency for Research on Cancer Lyon 69372 World Health Organisation

    International Agency for Research on Cancer, World Health Organisation, Lyon, 69372, France

43. Brett Sallach

    Stockholm Environment Institute · University of York

    Affiliation as printed

    Department of Environment and Geography York YO10 5NG University of York, UK

    Department of Environment and Geography, University of York, UK, York, YO10 5NG, UK

44. Susanna‐Assunta Sansone

    University of Oxford · Science Oxford

    Affiliation as printed

    Data Readiness Group, Department of Engineering Science Oxford University of Oxford

    Data Readiness Group, Department of Engineering Science, University of Oxford, Oxford, UK

45. Ferrán Sanz

    Universitat Pompeu Fabra · Hospital Del Mar · Municipal Institute for Medical Research · Hospital del Mar Research Institute

    Affiliation as printed

    Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences Barcelona 08003 Pompeu Fabra University

    Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, 08003, Spain

46. Haralambos Sarimveis

    National Technical University of Athens

    Affiliation as printed

    Athens 15780 National Technical University of Athens

    National Technical University of Athens, Athens, 15780, Greece

47. Sirarat Sarntivijai

    ELIXIR

    Affiliation as printed

    ELIXIR Hub Cambridge CB10 1SD Wellcome Genome Campus

    ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK

48. Tobias Schulze

    Helmholtz Centre for Environmental Research

    Affiliation as printed

    Leipzig 04318 Helmholtz Centre for Environmental Research - UFZ

    Helmholtz Centre for Environmental Research - UFZ, Leipzig, 04318, Germany

49. Jaroslav Slobodnı́k

    Environmental Institute

    Affiliation as printed

    Koš 97241 Environmental Institute

    Environmental Institute, Koš, 97241, Slovakia

50. Ola Spjuth

    Uppsala University · Science for Life Laboratory

    Affiliation as printed

    Department of Pharmaceutical Biosciences and Science for Life Laboratory Uppsala SE-75124 Uppsala University

    Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, SE-75124, Sweden

51. Jonathan A. Tedds

    ELIXIR

    Affiliation as printed

    ELIXIR Hub Cambridge CB10 1SD Wellcome Genome Campus

    ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK

52. Νikolaos S. Τhomaidis

    National and Kapodistrian University of Athens

    Affiliation as printed

    Laboratory of Analytical Chemistry, Department of Chemistry Athens 15771 National and Kapodistrian University of Athens

    Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece

53. Ralf J. M. Weber

    University of Birmingham

    Affiliation as printed

    School of Biosciences Birmingham B15 2TT University of Birmingham, UK

    School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

54. Gerard J. P. van Westen Aachen Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research

    Leiden University · Centre for Human Drug Research

    Affiliation as printed

    Division of Drug Discovery and Safety Leiden 2333 CC Leiden Academic Center for Drug Research

    Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research, Leiden, 2333 CC, The Netherlands

55. Craig E. Wheelock

    Karolinska University Hospital · Karolinska Institutet

    Affiliation as printed

    Department of Medical Biochemistry and Biophysics Stockholm 17177 Karolinska Institute

    Department of Respiratory Medicine and Allergy Stockholm SE-141-86 Karolinska University Hospital

    Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden

    Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm SE-141-86, Sweden

56. Antony John Williams

    Environmental Protection Agency · Research Triangle Park Foundation

    Affiliation as printed

    Center for Computational Toxicology and Exposure Research Triangle Park NC 27711 United States Environmental Protection Agency

    Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA

57. Hilda E. Witters

    Flemish Institute for Technological Research

    Affiliation as printed

    Health Unit Mol 2400 Health

    Health Unit, Flemish Institute for Technological Research (VITO), Mol, 2400, Belgium

58. Barbara Zdrazil

    University of Vienna

    Affiliation as printed

    Department of Pharmaceutical Sciences Vienna 1090 University of Vienna

    Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria

59. Anže Županič

    National Institute of Biology

    Affiliation as printed

    Department Biotechnology and Systems Biology Ljubljana 1000 National Institute of Biology

    Department Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia

60. Egon Willighagen

    Maastricht University

    Affiliation as printed

    Department of Bioinformatics - BiGCaT Maastricht 6229 ER Maastricht University

    Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands