FAIRification of nanosafety data to improve applicability of (Q)SAR approaches: A case study on in vitro Comet assay genotoxicity data

Cecilia Bossa; Cristina Andreoli; Martine Bakker; Flavia Barone; Isabella De Angelis; Nina Jeliazkova; Penny Nymark; Chiara Laura Battistelli

doi:10.1016/j.comtox.2021.100190

FAIRification of nanosafety data to improve applicability of (Q)SAR approaches: A case study on in vitro Comet assay genotoxicity data

Comput Toxicol. 2021 Nov:20:100190. doi: 10.1016/j.comtox.2021.100190.

Authors

Cecilia Bossa¹, Cristina Andreoli¹, Martine Bakker², Flavia Barone¹, Isabella De Angelis¹, Nina Jeliazkova³, Penny Nymark⁴, Chiara Laura Battistelli¹

Affiliations

¹ Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy.
² Centre for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
³ Ideaconsult Ltd., Sofia, Bulgaria.
⁴ Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.

Abstract

(Quantitative) structure-activity relationship ([Q]SAR) methodologies are widely applied to predict the (eco)toxicological effects of chemicals, and their use is envisaged in different regulatory frameworks for filling data gaps of untested substances. However, their application to the risk assessment of nanomaterials is still limited, also due to the scarcity of large and curated experimental datasets. Despite a great amount of nanosafety data having been produced over the last decade in international collaborative initiatives, their interpretation, integration and reuse has been hampered by several obstacles, such as poorly described (meta)data, non-standard terminology, lack of harmonized reporting formats and criteria. Recently, the FAIR (Findable, Accessible, Interoperable, and Reusable) principles have been established to guide the scientific community in good data management and stewardship. The EU H2020 Gov4Nano project, together with other international projects and initiatives, is addressing the challenge of improving nanosafety data FAIRness, for maximizing their availability, understanding, exchange and ultimately their reuse. These efforts are largely supported by the creation of a common Nanosafety Data Interface, which connects a row of project-specific databases applying the eNanoMapper data model. A wide variety of experimental data relating to characterization and effects of nanomaterials are stored in the database; however, the methods, protocols and parameters driving their generation are not fully mature. This article reports the progress of an ongoing case study in the Gov4nano project on the reuse of in vitro Comet genotoxicity data, focusing on the issues and challenges encountered in their FAIRification through the eNanoMapper data model. The case study is part of an iterative process in which the FAIRification of data supports the understanding of the phenomena underlying their generation and, ultimately, improves their reusability.

Keywords: (Q)SAR approaches; (Q)SAR, (Quantitative) structure-activity relationship; AOP, Adverse Outcome Pathway; ECHA, European Chemicals Agency; FAIR principles; FAIR, Findable, Accessible, Interoperable, and Reusable; Fpg, Formamido pyrimidine glycosilase; Genotoxicity; IATA, Integrated Approaches to Testing and Assessment; ISA–Tab, Investigation/Study/Assay Tab-delimited; JRC, Joint Research Centre; MIRCA, Minimum Information for Reporting Comet Assay; NMBP, Horizon 2020 Advisory Group for Nanotechnologies, Advanced Materials, Biotechnology and Advanced Manufacturing and Processing; NMBP-13-2018 projects, Gov4Nano, NANORIGO and RiskGONE; NMs, nanomaterials; Nano-EHS, Nano Environment, Health and Safety; Nanomaterials; Nanosafety data; OECD, Organisation for Economic Co-operation and Development; OTM, Olive tail moment; REACH, Registration, Evaluation Authorisation and Restriction of Chemicals; SCGE, Single Cell Gel Electrophoresis; SOPs, Standard Operating Procedures; in vitro Comet assay.