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Reply to: Prospects and challenges for FAIR toxicogenomics data

Nature Nanotechnology volume 17, pages 19–20 (2022)Cite this article

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The Original Article was published on 23 December 2021

A discussion about the present status and challenges for the FAIRification of data in toxicogenomics.

replying to L. A. Saarimäki et al. Nature Nanotechnology [MATTERS ARISING https://doi.org/10.1038/s41565-021-01049-1] (2021)

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References

  1. Jeliazkova, N. et al. Towards FAIR nanosafety data. Nat. Nanotechnol. 16, 644–654 (2021).

    Article  CAS  Google Scholar 

  2. Saarimäki, L., Melagraki, G., Afantitis, A., Lynch, I. & Greco, D. Prospects and challenges for FAIR toxicogenomics data. Nat. Nanotechnol. https://doi.org/10.1038/s41565-021-01049-1 (2021).

  3. Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 3, 160018 (2016).

    Article  Google Scholar 

  4. Berrios, D. C., Beheshti, A. & Costes, S. V. FAIRness and usability for open-access omics data systems. AMIA Annu. Symp. Proc 2018, 232–241 (2018).

    Google Scholar 

  5. Chervitz, S. A. et al. Data standards for omics data: the basis of data sharing and reuse. Methods Mol. Biol. 719, 31–69 (2011).

    Article  CAS  Google Scholar 

  6. Kohonen, P. et al. A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury. Nat. Commun. 8, 15932 (2017).

    Article  CAS  Google Scholar 

  7. Liu, Z., Huang, R., Roberts, R. & Tong, W. Toxicogenomics: a 2020 vision. Trends Pharmacol. Sci. 40, 92–103 (2019).

    Article  CAS  Google Scholar 

  8. Federico, A. et al. Transcriptomics in toxicogenomics, part II: preprocessing and differential expression analysis for high quality data. Nanomaterials 10, 903 (2020).

    Article  CAS  Google Scholar 

  9. Kinaret, P. A. S. et al. Transcriptomics in toxicogenomics, part I: experimental design, technologies, publicly available data, and regulatory aspects. Nanomaterials 10, 750 (2020).

    Article  CAS  Google Scholar 

  10. Serra, A. et al. Transcriptomics in toxicogenomics, part III: data modelling for risk assessment. Nanomaterials 10, 708 (2020).

    Article  CAS  Google Scholar 

  11. Saarimäki, L. A. et al. Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials. Sci. Data 8, 49 (2021).

    Article  Google Scholar 

  12. Harrill, J. A. et al. Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology. Regul. Toxicol. Pharm. 125, 105020 (2021).

    Article  Google Scholar 

  13. Nymark, P. et al. Toward rigorous materials production: new approach methodologies have extensive potential to improve current safety assessment practices. Small 16, 1904749 (2020).

    Article  CAS  Google Scholar 

  14. Soeteman-Hernandez, L. G. et al. Safe innovation approach: towards an agile system for dealing with innovations. Mater. Today Commun. 20, 100548 (2019).

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden

    Roland Grafström, Pekka Kohonen & Penny Nymark

  2. Division of Toxicology, Misvik Biology, Turku, Finland

    Roland Grafström & Pekka Kohonen

  3. German Federal Institute for Risk Assessment, Berlin, Germany

    Andrea Haase

  4. Ideaconsult Ltd, Sofia, Bulgaria

    Nina Jeliazkova

Authors
  1. Roland Grafström
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  2. Andrea Haase
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  3. Pekka Kohonen
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  4. Nina Jeliazkova
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  5. Penny Nymark
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Contributions

R.G. wrote the manuscript. A.H., P.K. and N.J. contributed and reviewed the final manuscript. P.N. conceptualized and wrote the manuscript.

Corresponding author

Correspondence to Penny Nymark.

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The authors declare no competing interests.

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Grafström, R., Haase, A., Kohonen, P. et al. Reply to: Prospects and challenges for FAIR toxicogenomics data. Nat. Nanotechnol. 17, 19–20 (2022). https://doi.org/10.1038/s41565-021-01050-8

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