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[Preprint]. 2025 Mar 24:2025.03.21.644517.
doi: 10.1101/2025.03.21.644517.

FAIRification of computational models in biology

Irina Balaur  1 , David P Nickerson  2 , Danielle Welter  1   3 , Judith A H Wodke  4 , Francois Ancien  1 , Tom Gebhardt  4 , Valentin Grouès  1 , Henning Hermjakob  5 , Matthias König  6 , Nicole Radde  7 , Adrien Rougny  1 , Reinhard Schneider  1 , Rahuman S Malik-Sheriff  5 , Kirubel Biruk Shiferaw  4 , Melanie Stefan  8 , Venkata Satagopam  1 , Dagmar Waltemath  4
Affiliations

FAIRification of computational models in biology

Irina Balaur et al. bioRxiv. .

Abstract

Computational models are essential for studying complex systems which, particularly in clinical settings, need to be quality-approved and transparent. To enhance the communication of a model's features and capabilities, we propose an adaptation of the Findability, Accessibility, Interoperability and Reusability (FAIR) indicators published by the Research Data Alliance to assess models encoded in domain-specific standards, such as those established by COMBINE. The assessments guide FAIRification and add value to models.

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Figures

Figure 1:
Figure 1:
Workflow of the FAIR COMBINE Archive Indicators project: an iterative and integrative community-level process to adapt the RDA FAIR indicators to the specificities of COMBINE models and archives. We extended the FAIRplus template of RDA FAIR indicators and performed FAIR assessment for 5 types of COMBINE models and archives from major model repositories (BioModels and PMR) at different curation stages.
Figure 2:
Figure 2:
Example: FAIR assessment results for one of the model types considered during the workshops and hackathons - https://models.physiomeproject.org/e/48/elowitz_leibler_2000.cellml. Results are shown for the resource itself (Model or Archive) and the metadata component (namely Model metadata or Archive metadata), for each FAIR indicator. The result illustration is made using the FAIR-Viz tool. Legend: Findability (blue), Accessibility (orange), Interoperability (green), Reusability (red).
See this image and copyright information in PMC

References

    1. Le Novère N. Quantitative and logic modelling of molecular and gene networks. Nat Rev Genet 16, 146–158 (2015). - PMC - PubMed
    1. CMES | Data-Driven Healthcare: The Role of Computational Methods in Medical Innovation. https://www.techscience.com/CMES/v142n1/58985.
    1. Tiwari K. et al. Reproducibility in systems biology modelling. Mol Syst Biol 17, e9982 (2021). - PMC - PubMed
    1. König M. et al. Challenges and opportunities for system biology standards and tools in medical research.
    1. Tatka L. T., Smith L. P., Hellerstein J. L. & Sauro H. M. Adapting modeling and simulation credibility standards to computational systems biology. Journal of Translational Medicine 21, 501 (2023). - PMC - PubMed

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