Moving towards making (quantitative) structure-activity relationships ((Q)SARs) for toxicity-related endpoints findable, accessible, interoperable and reusable (FAIR).

Journal: ALTEX
Published Date:

Abstract

(Quantitative) structure-activity relationships ((Q)SARs) are widely used in chemical safety assessment to predict toxicological effects. Many thousands of (Q)SAR models have been developed and published, however, few are easily available to use. This investigation has applied previously developed Findability, Accessibility, Interoperability, and Reuse (FAIR) Principles for in silico models to six published, different, machine learning (ML) (Q)SARs for the same toxicity dataset (inhibition of growth to Tetrahymena pyriformis). The majority of principles were met, however, there are still gaps in making (Q)SARs FAIR. This study has enabled insights into, and recommendations for, the FAIRification of (Q)SARs including areas where more work and effort may be required. For instance, there is still a need for (Q)SARs to be associated with a unique identifier and full data / metadata for toxicological activity or endpoints, molecular properties and descriptors, as well as model description to be provided in a standardised manner. A number of solutions to the challenges were identified, such as building on the QSAR Model Reporting Format (QMRF) and the application of QSAR Assessment Framework (QAF). This study also demonstrated that resources such as the QSAR Databank (QsarDB, www.qsardb.org) are valuable in storing ML QSARs in a searchable database and also provide a Digital Object Identifier (DOI). Many activities related to FAIR are currently underway and (Q)SAR modellers should be encouraged to utilise these to move towards the easier access and use of models. Enabling FAIR computational toxicology models will support the overall progress towards animal free chemical safety assessment.

Authors

  • Samuel J Belfield
    School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK.
  • Homa Basiri
    School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK.
  • Swapnil Chavan
    Unit of Chemical and Pharmaceutical Toxicology, Research Institutes of Sweden (RISE), Södertalje, Sweden.
  • Georgios Chrysochoou
    School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK.
  • Steven J Enoch
    School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK.
  • James W Firman
    School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK.
  • Anish Gomatam
    Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, (NIPER Guwahati), Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India, Sila Katamur (Halugurisuk), Dist: Kamrup, P.O.: Changsari, Guwahati, Assam, 781101, India.
  • Barry Hardy
    Edelweiss Connect, Basel, Switzerland.
  • Palle S Helmke
    Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria.
  • Judith C Madden
    School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK.
  • Uko Maran
    Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia.
  • Eric March-Vila
    Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain.
  • Nikolai G Nikolov
    Technical University of Denmark, National Food Institute, Research Group for Chemical Risk Assessment and GMO, Lyngby, Denmark.
  • Manuel Pastor
    Research Programme on Biomedical Informatics (GRIB), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Hospital del Mar Medical Research Institute, Barcelona, Spain. Electronic address: manuel.pastor@upf.edu.
  • Geven Piir
    Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia.
  • Sulev Sild
    Institute of Chemistry, University of Tartu, Tartu, Estonia.
  • Aljoša Smajić
    Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
  • Nicoleta Spinu
    School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK. Electronic address: n.spinu@2017.ljmu.ac.uk.
  • Eva B Wedebye
    Technical University of Denmark, National Food Institute, Research Group for Chemical Risk Assessment and GMO, Lyngby, Denmark.
  • Mark T D Cronin
    School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom.

Keywords

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