Systematic Organization of COVID-19 Data Supported by the Adverse Outcome Pathway Framework

Overview

Journal Front Public Health

Specialty Public Health

Date 2021 Jun 7

PMID 34095051

Citations 13

Authors

Penny Nymark

Magdalini Sachana

Sofia Batista Leite

Jukka Sund

Catharine E Krebs

Kristie Sullivan

Stephen Edwards

Laura Viviani

Catherine Willett

Brigitte Landesmann

Clemens Wittwehr

Affiliations

Soon will be listed here.

Abstract

Adverse Outcome Pathways (AOP) provide structured frameworks for the systematic organization of research data and knowledge. The AOP framework follows a set of key principles that allow for broad application across diverse disciplines related to human health, including toxicology, pharmacology, virology and medical research. The COVID-19 pandemic engages a great number of scientists world-wide and data is increasing with exponential speed. Diligent data management strategies are employed but approaches for systematically organizing the data-derived information and knowledge are lacking. We believe AOPs can play an important role in improving interpretation and efficient application of scientific understanding of COVID-19. Here, we outline a newly initiated effort, the CIAO project (https://www.ciao-covid.net/), to streamline collaboration between scientists across the world toward development of AOPs for COVID-19, and describe the overarching aims of the effort, as well as the expected outcomes and research support that they will provide.

Citing Articles

Expanding adverse outcome pathways towards one health models for nanosafety.

Saarimaki L, Del Giudice G, Greco D Front Toxicol. 2023; 5:1176745.

PMID: 37692900 PMC: 10485555. DOI: 10.3389/ftox.2023.1176745.

CIAO: a living experiment in interdisciplinary large-scale collaboration facilitated by the Adverse Outcome Pathway framework.

Carusi A, Filipovska J, Wittwehr C, Clerbaux L Front Public Health. 2023; 11:1212544.

PMID: 37637826 PMC: 10449328. DOI: 10.3389/fpubh.2023.1212544.

A curated gene and biological system annotation of adverse outcome pathways related to human health.

Saarimaki L, Fratello M, Pavel A, Korpilahde S, Leppanen J, Serra A Sci Data. 2023; 10(1):409.

PMID: 37355733 PMC: 10290716. DOI: 10.1038/s41597-023-02321-w.

Toxicogenomics Data for Chemical Safety Assessment and Development of New Approach Methodologies: An Adverse Outcome Pathway-Based Approach.

Saarimaki L, Morikka J, Pavel A, Korpilahde S, Del Giudice G, Federico A Adv Sci (Weinh). 2022; 10(2):e2203984.

PMID: 36479815 PMC: 9839874. DOI: 10.1002/advs.202203984.

The Adverse Outcome Pathway Framework Applied to Neurological Symptoms of COVID-19.

Hogberg H, Lam A, Ohayon E, Shahbaz M, Clerbaux L, Bal-Price A Cells. 2022; 11(21).

PMID: 36359807 PMC: 9658029. DOI: 10.3390/cells11213411.

References

Edwards S, Tan Y, Villeneuve D, Meek M, McQueen C . Adverse Outcome Pathways-Organizing Toxicological Information to Improve Decision Making. J Pharmacol Exp Ther. 2015; 356(1):170-81. DOI: 10.1124/jpet.115.228239. View

Villeneuve D, Landesmann B, Allavena P, Ashley N, Bal-Price A, Corsini E . Representing the Process of Inflammation as Key Events in Adverse Outcome Pathways. Toxicol Sci. 2018; 163(2):346-352. PMC: 6309953. DOI: 10.1093/toxsci/kfy047. View

Howard C, Huston P . The health effects of climate change: Know the risks and become part of the solutions. Can Commun Dis Rep. 2019; 45(5):114-118. PMC: 6587682. DOI: 10.14745/ccdr.v45i05a01. View

Keller K, Reangsing C, Schneider J . Clinical presentation and outcomes of hospitalized adults with COVID-19: A systematic review. J Adv Nurs. 2020; 76(12):3235-3257. DOI: 10.1111/jan.14558. View

Gijbels E, Vinken M . An Update on Adverse Outcome Pathways Leading to Liver Injury. Appl In Vitro Toxicol. 2019; 3(4):283-285. PMC: 6432878. DOI: 10.1089/aivt.2017.0027. View

Jaiswal J, LoSchiavo C, Perlman D . Disinformation, Misinformation and Inequality-Driven Mistrust in the Time of COVID-19: Lessons Unlearned from AIDS Denialism. AIDS Behav. 2020; 24(10):2776-2780. PMC: 7241063. DOI: 10.1007/s10461-020-02925-y. View

Halappanavar S, van den Brule S, Nymark P, Gate L, Seidel C, Valentino S . Adverse outcome pathways as a tool for the design of testing strategies to support the safety assessment of emerging advanced materials at the nanoscale. Part Fibre Toxicol. 2020; 17(1):16. PMC: 7249325. DOI: 10.1186/s12989-020-00344-4. View

Villeneuve D, Crump D, Garcia-Reyero N, Hecker M, Hutchinson T, LaLone C . Adverse outcome pathway (AOP) development I: strategies and principles. Toxicol Sci. 2014; 142(2):312-20. PMC: 4318923. DOI: 10.1093/toxsci/kfu199. View

Bal-Price A, Lein P, Keil K, Sethi S, Shafer T, Barenys M . Developing and applying the adverse outcome pathway concept for understanding and predicting neurotoxicity. Neurotoxicology. 2016; 59:240-255. PMC: 5114159. DOI: 10.1016/j.neuro.2016.05.010. View

10.

Busquet F, Hartung T, Pallocca G, Rovida C, Leist M . Harnessing the power of novel animal-free test methods for the development of COVID-19 drugs and vaccines. Arch Toxicol. 2020; 94(6):2263-2272. PMC: 7245508. DOI: 10.1007/s00204-020-02787-2. View

11.

Delrue N, Sachana M, Sakuratani Y, Gourmelon A, Leinala E, Diderich R . The adverse outcome pathway concept: A basis for developing regulatory decision-making tools. Altern Lab Anim. 2016; 44(5):417-429. DOI: 10.1177/026119291604400504. View

12.

Vinken M . A putative AOP for pneumonia related to COVID-19. Arch Toxicol. 2020; 94(9):3343-3345. PMC: 7369467. DOI: 10.1007/s00204-020-02860-w. View

13.

Scully E, Haverfield J, Ursin R, Tannenbaum C, Klein S . Considering how biological sex impacts immune responses and COVID-19 outcomes. Nat Rev Immunol. 2020; 20(7):442-447. PMC: 7288618. DOI: 10.1038/s41577-020-0348-8. View

14.

Grafstrom R, Nymark P, Hongisto V, Spjuth O, Ceder R, Willighagen E . Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures. Altern Lab Anim. 2015; 43(5):325-32. DOI: 10.1177/026119291504300506. View

15.

Carusi A, Davies M, De Grandis G, Escher B, Hodges G, Leung K . Harvesting the promise of AOPs: An assessment and recommendations. Sci Total Environ. 2018; 628-629:1542-1556. PMC: 5888775. DOI: 10.1016/j.scitotenv.2018.02.015. View

16.

Langley G, Adcock I, Busquet F, Crofton K, Csernok E, Giese C . Towards a 21st-century roadmap for biomedical research and drug discovery: consensus report and recommendations. Drug Discov Today. 2016; 22(2):327-339. DOI: 10.1016/j.drudis.2016.10.011. View

17.

Gagliardi M, Tieri P, Ortona E, Ruggieri A . ACE2 expression and sex disparity in COVID-19. Cell Death Discov. 2020; 6:37. PMC: 7248455. DOI: 10.1038/s41420-020-0276-1. View

18.

George P, Wells A, Gisli Jenkins R . Pulmonary fibrosis and COVID-19: the potential role for antifibrotic therapy. Lancet Respir Med. 2020; 8(8):807-815. PMC: 7228727. DOI: 10.1016/S2213-2600(20)30225-3. View

19.

Nymark P, Rieswijk L, Ehrhart F, Jeliazkova N, Tsiliki G, Sarimveis H . A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions. Toxicol Sci. 2017; 162(1):264-275. DOI: 10.1093/toxsci/kfx252. View

20.

Ankley G, Bennett R, Erickson R, Hoff D, Hornung M, Johnson R . Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment. Environ Toxicol Chem. 2010; 29(3):730-41. DOI: 10.1002/etc.34. View