ELIXIR and Toxicology: a community in development
Jazyk angličtina Země Anglie, Velká Británie Médium electronic-ecollection
Typ dokumentu časopisecké články
Grantová podpora
Wellcome Trust - United Kingdom
001
World Health Organization - International
PubMed
37842337
PubMed Central
PMC10568213
DOI
10.12688/f1000research.74502.2
PII: ELIXIR-1129
Knihovny.cz E-zdroje
- Klíčová slova
- ELIXIR, FAIR, Toxicology, interoperability,
- MeSH
- biologické vědy * MeSH
- hodnocení rizik MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Evropa MeSH
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.
AIMMS Division of Molecular Toxicology Vrije Universiteit Amsterdam 1081 HZ The Netherlands
Bioinformatics and Biostatistics Hub Institut Pasteur Paris F 75015 France
Chemotargets SL Barcelona 08028 Spain
Data Readiness Group Department of Engineering Science University of Oxford Oxford UK
Data Sciences and Quantitative Biology Discovery Sciences AstraZeneca Cambridge UK
Department Biotechnology and Systems Biology National Institute of Biology Ljubljana 1000 Slovenia
Department of Bioinformatics BiGCaT Maastricht University Maastricht 6229 ER The Netherlands
Department of Computer Science Heriot Watt University Edinburgh UK
Department of Environment and Geography University of York UK York YO10 5NG UK
Department of Medical Biochemistry and Biophysics Karolinska Institute Stockholm 17177 Sweden
Department of Pharmaceutical Sciences University of Vienna Vienna 1090 Austria
Department of Physical Chemistry Palacky University Olomouc Olomouc 77146 Czech Republic
Department of Toxicogenomics Maastricht University Maastricht 6200 MD The Netherlands
Department of Toxicology Misvik Biology Turku 20520 Finland
ELIXIR Hub Wellcome Genome Campus Cambridge CB10 1SD UK
Environmental Institute Koš 97241 Slovakia
Faculty of Pharmacy Malaria Research and Training Center Bamako BP 1805 Mali
Forschungs und Beratungsinstitut Gefahrstoffe GmbH Freiburg im Breisgau 79106 Germany
Helmholtz Centre for Environmental Research UFZ Leipzig 04318 Germany
Ideaconsult Ltd Sofia Bulgaria
Institut d'Investigacio Sanitaria Pere Virgili Universitat Rovira i Virgili Tarragona 43007 Spain
Institut Français de Bioinformatique Evry F 91000 France
Institute of Biophysics and Biomedical Engineering Bulgarian Academy of Sciences Sofia 1113 Bulgaria
Institute of Chemistry University of Tartu Tartu 50411 Estonia
Institute of Environmental Medicine Karolinska Institute Stockholm 17177 Sweden
International Agency for Research on Cancer World Health Organisation Lyon 69372 France
Luxembourg Centre for Systems Biomedicine University of Luxembourg Belvaux 4367 Luxembourg
Maastricht Centre for Systems Biology Maastricht University Maastricht 6229 EN The Netherlands
MetaboHUB French metabolomics infrastructure in Metabolomics and Fluxomics Toulouse France
National Technical University of Athens Athens 15780 Greece
RECETOX Faculty of Science Masaryk University Brno Czech Republic
School of Biosciences University of Birmingham UK Birmingham B15 2TT UK
School of Science GSFC University Gujarat 391750 India
Scientific Network Management SL Barcelona 08015 Spain
Seven Past Nine Cerknica 1380 Slovenia
Toxalim Université de Toulouse Toulouse France
Zobrazit více v PubMed
Crosswell LC, Thornton JM: ELIXIR: a distributed infrastructure for European biological data. Trends Biotechnol. may 2012;30(5):241–242. 10.1016/j.tibtech.2012.02.002 PubMed DOI
Kortenkamp A: Low dose mixture effects of endocrine disrupters and their implications for regulatory thresholds in chemical risk assessment. Curr. Opin. Pharmacol. 2014;19:105–111. 10.1016/j.coph.2014.08.006 PubMed DOI
Escher BI, Stapleton HM, Schymanski EL: Tracking complex mixtures of chemicals in our changing environment. Science. 2020;367(6476):388–392. 10.1126/science.aay6636 PubMed DOI PMC
Tropsha A: Best practices for QSAR model development, validation, and exploitation. Molecular Informatics. 2010;29(6-7):476–488. 10.1002/minf.201000061 PubMed DOI
Patlewicz G, Ball N, Booth ED, et al. : Use of category approaches, read-across and (q)sar: General considerations. Regul. Toxicol. Pharmacol. 2013;67(1):1–12. 10.1016/j.yrtph.2013.06.002 PubMed DOI
Wilkinson MD, Dumontier M, Aalbersberg IJJ, et al. : Comment: The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. mar 2016;3(1):160018–9. 10.1038/sdata.2016.18 PubMed DOI PMC
Jacobsen A, Miranda Azevedo R, Juty N, et al. : FAIR Principles: Interpretations and Implementation Considerations. Data intelligence. 2020;2(4):10–29. 10.1162/dint_r_00024 DOI
Courtot M, Cherubin L, Faulconbridge A, et al. : BioSamples database: an updated sample metadata hub. Nucleic Acids Res. 11 2018;47(D1):D1172–D1178. 10.1093/nar/gky1061 PubMed DOI PMC
Sarkans U, Füllgrabe A, Ali A, et al. : From ArrayExpress to BioStudies. Nucleic Acids Res. 11 2020;49(D1):D1502–D1506. 10.1093/nar/gkaa1062 PubMed DOI PMC
The FAIRsharing Community Sansone S-A, McQuilton P, et al. : FAIRsharing as a community approach to standards, repositories and policies. Nat. Biotechnol. April 2019;37(4):358–367. 10.1038/s41587-019-0080-8 PubMed DOI PMC
The FAIRsharing Team: FAIRsharing Website. 2020. Reference Source
Wang Z, Walker GW, Muir DCG, et al. : Toward a global understanding of chemical pollution: A first comprehensive analysis of national and regional chemical inventories. Environ. Sci. Technol. 2020;54(5):2575–2584. 10.1021/acs.est.9b06379 PubMed DOI
Gocht T, Berggren E, Ahr HJ, et al. : The SEURAT-1 approach towards animal free human safety assessment. ALTEX. 2015;32(1):9–24. 10.14573/altex.1408041 PubMed DOI
Daneshian M, Kamp H, Hengstler J, et al. : Highlight report: Launch of a large integrated European in vitro toxicology project: EU-ToxRisk. Arch. Toxicol. may 2016;90(5):1021–1024. 10.1007/s00204-016-1698-7 PubMed DOI PMC
Sanz F, Pognan F, Steger-Hartmann T, et al. : Legacy data sharing to improve drug safety assessment: The eTOX project. Nat. Rev. Drug Discov. nov 2017;16(12):811–812. 10.1038/nrd.2017.177 PubMed DOI
Pognan F, Steger-Hartmann T, Díaz C, et al. : The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives. Pharmaceuticals. 2021;14(3). 10.3390/ph14030237 PubMed DOI PMC
The Eurion Consortium: Eurion Project Website. 2021. Reference Source
Jeliazkova N, Koch V, Li Q, et al. : Linking LRI AMBIT chemoinformatic system with the IUCLID substance database to support read-across of substance endpoint data and category formation. Toxicol. Lett. 2016;258:S114–S115. 10.1016/j.toxlet.2016.06.1469 DOI
EU-US Roadmap – Nanoinformatics 2030 – EU NanoSafety Cluster:2020. Reference Source
Karcher S, Willighagen EL, Rumble J, et al. : Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. NanoImpact. jan 2018;9:85–101. 10.1016/j.impact.2017.11.002 PubMed DOI PMC
Kohonen P, Parkkinen JA, Willighagen EL, et al. : A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury. Nat. Commun. 8, jul 2017. 10.1038/ncomms15932 PubMed DOI PMC
Luechtefeld T, Maertens A, Russo DP, et al. : Global analysis of publicly available safety data for 9,801 substances registered under REACH from 2008-2014. ALTEX. 2016;33(2):95–109. 10.14573/altex.1510052 PubMed DOI PMC
Ganter B, Snyder RD, Halbert DN, et al. : Toxicogenomics in drug discovery and development: mechanistic analysis of compound/class-dependent effects using the drugmatrix ® database. Pharmacogenomics. 2006;7(7):1025–1044. 10.2217/14622416.7.7.1025 PubMed DOI
Richard AM, Judson RS, Houck KA, et al. : Toxcast chemical landscape: Paving the road to 21st century toxicology. Chem. Res. Toxicol. 2016;29(8):1225–1251. 10.1021/acs.chemrestox.6b00135 PubMed DOI
Igarashi Y, Nakatsu N, Yamashita T, et al. : Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res. 10 2014;43(D1):D921–D927. 10.1093/nar/gku955 PubMed DOI PMC
Hendrickx DM, Aerts HJWL, Caiment F, et al. : diXa: a data infrastructure for chemical safety assessment. Bioinformatics. 2015;31(9):1505–1507. 10.1093/bioinformatics/btu827 PubMed DOI PMC
Čihák R: Reach - an overview. Interdiscip. Toxicol. 01 Jun. 2009;2(2):42–44. 10.2478/v10102-009-0007-1 PubMed DOI PMC
Cases M, Briggs K, Steger-Hartmann T, et al. : The eTOX data-sharing project to advance in Silico drug-induced toxicity prediction. Int. J. Mol. Sci. nov 2014;15(11):21136–21154. 10.3390/ijms151121136 PubMed DOI PMC
OECD: eChemPortal. 2020. Reference Source
ECHA: IUCLID. 2020. Reference Source
OECD: QSAR Toolbox. 2020. Reference Source
Leist M, Ghallab A, Graepel R, et al. : Adverse outcome pathways: opportunities, limitations and open questions. Arch. Toxicol. nov 2017;91(11):3477–3505. 10.1007/s00204-017-2045-3 PubMed DOI
Nymark P, Rieswijk L, Ehrhart F, et al. : A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions. Toxicol. Sci. 2018;162(1):264–275. 10.1093/toxsci/kfx252 PubMed DOI
Ring CL, Arnot JA, Bennett DH, et al. : Consensus modeling of median chemical intake for the u.s. population based on predictions of exposure pathways. Environ. Sci. Technol. 2019;53(2):719–732. 10.1021/acs.est.8b04056 PubMed DOI PMC
Wambaugh JF, Wang A, Dionisio KL, et al. : High throughput heuristics for prioritizing human exposure to environmental chemicals. Environ. Sci. Technol. 2014;48(21):12760–12767. 10.1021/es503583j PubMed DOI
Wild CP: Complementing the genome with an “exposome”: The outstanding challenge of environmental exposure measurement in molecular epidemiology. Cancer Epidemiology and Prevention Biomarkers. 2005;14(8):1847–1850. 10.1158/1055-9965.EPI-05-0456 PubMed DOI
Escher BI, Hackermüller J, Polte T, et al. : From the exposome to mechanistic understanding of chemical-induced adverse effects. Environ. Int. 2017;99:97–106. 10.1016/j.envint.2016.11.029 PubMed DOI PMC
Vermeulen R, Schymanski EL, Barabási A-L, et al. : The exposome and health: Where chemistry meets biology. Science. 2020;367(6476):392–396. 10.1126/science.aay3164 PubMed DOI PMC
Barouki R, Audouze K, Coumoul X, et al. : Integration of the human exposome with the human genome to advance medicine. Biochimie. 2018;152:155–158. 10.1016/j.biochi.2018.06.023 PubMed DOI
Audouze K, Sarigiannis D, Alonso-Magdalena P, et al. : Integrative strategy of testing systems for identification of endocrine disruptors inducing metabolic disorders—an introduction to the oberon project. Int. J. Mol. Sci. 2020;21(8). 10.3390/ijms21082988 PubMed DOI PMC
Kohonen P, Benfenati E, Bower D, et al. : The ToxBank data warehouse: Supporting the replacement of in vivo repeated dose systemic toxicity testing. Mol. Inform. jan 2013;32(1):47–63. 10.1002/minf.201200114 PubMed DOI
Jeliazkova N, Chomenidis C, Doganis P, et al. : The eNanoMapper database for nanomaterial safety information. Beilstein J. Nanotechnol. 2015;6(1):1609–1634. 10.3762/bjnano.6.165 PubMed DOI PMC
H2020 Green Deal Call LC-GD-8-1-2020: Innovative, systemic zero-pollution solutions to protect health, environment and natural resources from persistent and mobile chemicals. 2020. Reference Source
H2020 Green Deal Call LC-GD-8-2-2020: Fostering regulatory science to address combined exposures to industrial chemicals and pharmaceuticals: from science to evidence-based policies. 2020. Reference Source
Ganzleben C, Antignac J-P, Barouki R, et al. : Human biomonitoring as a tool to support chemicals regulation in the european union. Int. J. Hyg. Environ. Health. 2017;220(2, Part A):94–97. Special Issue: Human Biomonitoring 2016. 10.1016/j.ijheh.2017.01.007 PubMed DOI
Dulio V, Bavel B, Brorström-Lundén E, et al. : Emerging pollutants in the EU: 10 years of NORMAN in support of environmental policies and regulations. Environ. Sci. Eur. 5, December 2018;30(1):5–4715. 10.1186/s12302-018-0135-3 PubMed DOI PMC
Dulio V, Koschorreck J, Bavel B, et al. : The NORMAN Association and the European Partnership for Chemicals Risk Assessment (PARC): let’s cooperate!. Environ. Sci. Eur. December 2020;32(1):100. 10.1186/s12302-020-00375-w DOI
Ammar A, Bonaretti S, Winckers L, et al. : A semi-automated workflow for fair maturity indicators in the life sciences. Nanomaterials. 2020;10(10):1–14. 10.3390/nano10102068 PubMed DOI PMC
Rijswijk M, Beirnaert C, Caron C, et al. : The future of metabolomics in ELIXIR [version 2; peer review: 3 approved]. F1000Research. 2017;6(1649). 10.12688/f1000research.12342.2 PubMed DOI PMC
Beard N, Bacall F, Nenadic A, et al. : TeSS: a platform for discovering life-science training opportunities. Bioinformatics. 02 2020;36(10):3290–3291. 10.1093/bioinformatics/btaa047 PubMed DOI PMC
Afgan E, Baker D, Batut B, et al. : The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. jul 2018;46(W1):W537–W544. 10.1093/nar/gky379 PubMed DOI PMC
Ison J, Ienasescu H, Chmura P, et al. : The bio.tools registry of software tools and data resources for the life sciences. Genome Biol. 2019;20(1):164. 10.1186/s13059-019-1772-6 PubMed DOI PMC
Williams AJ, Harland L, Groth P, et al. : Open PHACTS: semantic interoperability for drug discovery. Drug Discov. Today. 2012;17(21):1188–1198. 10.1016/j.drudis.2012.05.016 PubMed DOI
Ferreira S, Fisher C, Furlong LI, et al. : Quantitative systems toxicology modeling to address key safety questions in drug development: A focus of the transqst consortium. Chem. Res. Toxicol. 2020;33(1):7–9. 10.1021/acs.chemrestox.9b00499 PubMed DOI
Jeliazkova N, Jeliazkov V: AMBIT RESTful web services: An implementation of the OpenTox application programming interface. J. Cheminformatics. 2011;3(1). 10.1186/1758-2946-3-18 PubMed DOI PMC
Hastings J, Jeliazkova N, Owen G, et al. : eNanoMapper: Harnessing ontologies to enable data integration for nanomaterial risk assessment. J. Biomed. Semant. mar 2015;6(1):10. 10.1186/s13326-015-0005-5 PubMed DOI PMC
Burgoon LD: The AOPOntology: A semantic artificial intelligence tool for predictive toxicology. Appl. In Vitro Toxicol. sep 2017;3(3):278–281. 10.1089/aivt.2017.0012 DOI
Stierum R, Aarts J, Boorsma A, et al. : Assuring safety without animal testing concept (ASAT). Integration of human disease data with in vitro data to improve toxicology testing. Toxicol. Lett. 2014;229:S4. 10.1016/j.toxlet.2014.06.041 DOI
Hendrickx DM, Boyles RR, Kleinjans JCS, et al. : Workshop report: Identifying opportunities for global integration of toxicogenomics databases, 26–27 June 2013, Research Triangle Park, NC, USA. Arch. Toxicol. nov 2014;88(12):2323–2332. 10.1007/s00204-014-1387-3 PubMed DOI PMC
Williams AJ, Grulke CM, Edwards J, et al. : The CompTox Chemistry Dashboard: A community data resource for environmental chemistry. J. Cheminformatics. nov 2017;9(1):61. 10.1186/s13321-017-0247-6. PubMed DOI PMC
Kim S, Chen J, Cheng T, et al. : PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 2019;47(D1):D1102–D1109. 10.1093/nar/gky1033 PubMed DOI PMC
Schymanski EL, Bolton EE: FAIR chemical structures in the Journal of Cheminformatics. J. Cheminform. 2021;13(1):50. 10.1186/s13321-021-00520-4 PubMed DOI PMC
Sinclair G, Thillainadarajah I, Meyer B, et al. : Wikipedia on the CompTox Chemicals Dashboard: Connecting Resources to Enrich Public Chemical Data. J. Chem. Inf. Model. 2022;62(20):4888–4905. 10.1021/acs.jcim.2c00886 PubMed DOI PMC
Gruening B, Sallou O, Moreno P, et al. : Recommendations for the packaging and containerizing of bioinformatics software [version 1; peer review: 2 approved with reservations]. F1000Research. 2018;7(742). 10.12688/f1000research.15140.1 PubMed DOI PMC
Athar A, Füllgrabe A, George N, et al. : ArrayExpress update – from bulk to single-cell expression data. Nucleic Acids Res. 2019;47(D1):D711–D715. 10.1093/nar/gky964 PubMed DOI PMC
Sansone S-A, Rocca-Serra P, Field D, et al. : Toward interoperable bioscience data. Nat. Genet. Jan 2012;44(2):121–126. 10.1038/ng.1054 PubMed DOI PMC
Ruusmann V, Sild S, Maran U: QSAR DataBank - an approach for the digital organization and archiving of QSAR model information. J. Cheminformatics. 25, 2014;6(1). 10.1186/1758-2946-6-25 PubMed DOI PMC
Ison J, Kalaš M, Jonassen I, et al. : EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinformatics. 03 2013;29(10):1325–1332. 10.1093/bioinformatics/btt113 PubMed DOI PMC
The RE3 Team: Registry of Research Data Repositories Website. 2020. Reference Source
Vitali F, Lombardo R, Rivero D, et al. : ONS: an ontology for a standardized description of interventions and observational studies in nutrition. Genes Nutr. 12, 2018;13(1):12. 10.1186/s12263-018-0601-y PubMed DOI PMC
Amstutz P, Crusoe MR, Nebojša TN, et al. : Common Workflow Language, v1.0. Specification, Common Workflow Language working group. 2016. Reference Source
: Systems toxicology: from basic research to risk assessment. Chem Res Toxicol .2014;27(3) : 10.1021/tx400410s 314-29 10.1021/tx400410s PubMed DOI PMC