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

(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

Institutions

Publication Details

Journal
ALTEX
Published
2025-01-01
DOI
https://doi.org/10.14573/altex.2411161
Citations
2
Primary Topic
Computational Drug Discovery Methods
Type
article
Field-Weighted Citation Impact
3.01

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

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

Samuel J. Belfield, Eva Bay Wedebye, Sulev Sild, Anish Gomatam et al.
2 citations
ALTEX
Computational Drug Discovery Methods
3.01
article

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

Samuel J. Belfield, Eva Bay Wedebye, Sulev Sild, Anish Gomatam, James W. Firman, Aljŏs̆a Smajíć, Hassan Basiri, Swapnil Chavan, Uko Maran, Nikolai Georgiev Nikolov, Geven Piir, M Cronin, E. Vila, Judith C. Madden, Manuel Pastor, Nicoleta Sp̂înu, Steven J. Enoch, Palle Steen Helmke, Barry Hardy, Georgios Chrysochoou
article en
2 citations

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.

ALTEXVol. 42(4)
University of Vienna (AT), Universitat Pompeu Fabra (ES), RISE Research Institutes of Sweden (SE), University of Manchester (GB), Edelweiss Connect (Switzerland) (CH), University of Tartu (EE), Liverpool John Moores University (GB)
European Commission, Eesti Teadusagentuur, HORIZON EUROPE Framework Programme
Zero hunger
Openalex Percentile: Top 9%
Computational Drug Discovery Methods
3.01
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.