publication . Article . Preprint . Other literature type . 2021

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

Penny Nymark; Magdalini Sachana; Sofia Batista-Leite; Jukka Sund; Catharine E Krebs; Kristie Sullivan; Stephen W. Edwards; Laura Viviani; Kate Willett; Brigitte Landesmann; ...
Open Access English
  • Published: 01 May 2021 Journal: Frontiers in Public Health, volume 9 (issn: 2296-2565, Copyright policy)
  • Publisher: Frontiers Media S.A.
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 e...
Subjects
free text keywords: adverse outcome pathways, COVID-19, systematic organization, interdisciplinarity, mechanisms, data integration, Public aspects of medicine, RA1-1270, allergology, Public Health, Environmental and Occupational Health, Public Health, Perspective, Medicine, business.industry, business, Coronavirus disease 2019 (COVID-19), Adverse Outcome Pathway, Intensive care medicine, medicine.medical_specialty
Communities
COVID-19
31 references, page 1 of 3

[1] Hutson M, Artificial-intelligence tools aim to tame the coronavirus literature. Nature (2020). doi:10.1038/d41586-020-01733-7 [OpenAIRE]

[2] Ankley GT, Bennett RS, Erickson RJ, Hoff DJ, Hornung MW, Johnson RD, Mount DR, Nichols JW, Russom CL, Schmieder PK, Serrrano JA, Tietge JE, and Villeneuve DL, Adverse outcome pathways: A conceptual framework to support ecotoxicology research and risk assessment. Environmental Toxicology and Chemistry 29 (2010) 730-741. doi:10.1002/etc.34

[5] Halappanavar S, van den Brule S, Nymark P, Gaté L, Seidel C, Valentino S, Zhernovkov V, Høgh Danielsen P, De Vizcaya A, Wolff H, Stöger T, Boyadziev A, Poulsen SS, Sørli JB, and Vogel U, 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 17 (2020) 16. doi:10.1186/s12989-020-00344-4

[6] Sachana M, and Leinala E, Approaching Chemical Safety Assessment Through Application of Integrated Approaches to Testing and Assessment: Combining Mechanistic Information Derived from Adverse Outcome Pathways and Alternative Methods. 3 (2017) 227-233. doi:10.1089/aivt.2017.0013

[7] Sakuratani Y, Horie M, and Leinala E, Integrated Approaches to Testing and Assessment: OECD Activities on the Development and Use of Adverse Outcome Pathways and Case Studies. 123 (2018) 20-28. doi:10.1111/bcpt.12955

[8] Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepelska M, Ottinger MA, Vergauwen L, and Whelan M, Adverse outcome pathway (AOP) development I: strategies and principles. Toxicological Sciences 142 (2014) 312-20. doi:10.1093/toxsci/kfu199

[9] Garvin MR, Alvarez C, Miller JI, Prates ET, Walker AM, Amos BK, Mast AE, Justice A, Aronow B, and Jacobson D, A mechanistic model and therapeutic interventions for COVID19 involving a RAS-mediated bradykinin storm. eLife 9 (2020) e59177. doi:10.7554/eLife.59177

[10] Jaiswal J, LoSchiavo C, and Perlman DC, Disinformation, Misinformation and InequalityDriven Mistrust in the Time of COVID-19: Lessons Unlearned from AIDS Denialism. AIDS Behav 24 (2020) 2776-2780. doi:10.1007/s10461-020-02925-y [OpenAIRE]

[11] Kim Y, Nymark P, Lee Y, Wittwehr C, and Landesmann B, Application of Adverse Outcome Pathway Framework to COVID-19. Journal (2020). Available at: https://www.iscb.org/cms_addon/conferences/ismb2020/posters.php?track=COVID19&session=B#search

[12] Nymark P, Rieswijk L, Ehrhart F, Jeliazkova N, Tsiliki G, Sarimveis H, Evelo CT, Hongisto V, Kohonen P, Willighagen E, and Grafström RC, A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions. Toxicological sciences : an official journal of the Society of Toxicology 162 (2018) 264-275. doi:10.1093/toxsci/kfx252

[13] Vinken M, A putative AOP for pneumonia related to COVID-19. Arch Toxicol 94 (2020) 3343- 3345. doi:10.1007/s00204-020-02860-w [OpenAIRE]

[14] Keller KG, Reangsing C, and Schneider JK, Clinical presentation and outcomes of hospitalized adults with COVID-19: A systematic review. J Adv Nurs. 00 (2020) 1- 23. doi:10.1111/jan.14558

[16] Gagliardi MC, Tieri P, Ortona E, and Ruggieri A, ACE2 expression and sex disparity in COVID-19. Cell Death Discovery 6 (2020) 37. doi:10.1038/s41420-020-0276-1 [OpenAIRE]

[17] George PM, Wells AU, and Jenkins RG, Pulmonary fibrosis and COVID-19: the potential role for antifibrotic therapy. The Lancet Respiratory Medicine 8 (2020) 807-815. doi:10.1016/S2213-2600(20)30225-3

[18] Scully EP, Haverfield J, Ursin RL, Tannenbaum C, and Klein SL, Considering how biological sex impacts immune responses and COVID-19 outcomes. Nature Reviews Immunology 20 (2020) 442-447. doi:10.1038/s41577-020-0348-8 [OpenAIRE]

31 references, page 1 of 3
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 e...
Subjects
free text keywords: adverse outcome pathways, COVID-19, systematic organization, interdisciplinarity, mechanisms, data integration, Public aspects of medicine, RA1-1270, allergology, Public Health, Environmental and Occupational Health, Public Health, Perspective, Medicine, business.industry, business, Coronavirus disease 2019 (COVID-19), Adverse Outcome Pathway, Intensive care medicine, medicine.medical_specialty
Communities
COVID-19
31 references, page 1 of 3

[1] Hutson M, Artificial-intelligence tools aim to tame the coronavirus literature. Nature (2020). doi:10.1038/d41586-020-01733-7 [OpenAIRE]

[2] Ankley GT, Bennett RS, Erickson RJ, Hoff DJ, Hornung MW, Johnson RD, Mount DR, Nichols JW, Russom CL, Schmieder PK, Serrrano JA, Tietge JE, and Villeneuve DL, Adverse outcome pathways: A conceptual framework to support ecotoxicology research and risk assessment. Environmental Toxicology and Chemistry 29 (2010) 730-741. doi:10.1002/etc.34

[5] Halappanavar S, van den Brule S, Nymark P, Gaté L, Seidel C, Valentino S, Zhernovkov V, Høgh Danielsen P, De Vizcaya A, Wolff H, Stöger T, Boyadziev A, Poulsen SS, Sørli JB, and Vogel U, 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 17 (2020) 16. doi:10.1186/s12989-020-00344-4

[6] Sachana M, and Leinala E, Approaching Chemical Safety Assessment Through Application of Integrated Approaches to Testing and Assessment: Combining Mechanistic Information Derived from Adverse Outcome Pathways and Alternative Methods. 3 (2017) 227-233. doi:10.1089/aivt.2017.0013

[7] Sakuratani Y, Horie M, and Leinala E, Integrated Approaches to Testing and Assessment: OECD Activities on the Development and Use of Adverse Outcome Pathways and Case Studies. 123 (2018) 20-28. doi:10.1111/bcpt.12955

[8] Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepelska M, Ottinger MA, Vergauwen L, and Whelan M, Adverse outcome pathway (AOP) development I: strategies and principles. Toxicological Sciences 142 (2014) 312-20. doi:10.1093/toxsci/kfu199

[9] Garvin MR, Alvarez C, Miller JI, Prates ET, Walker AM, Amos BK, Mast AE, Justice A, Aronow B, and Jacobson D, A mechanistic model and therapeutic interventions for COVID19 involving a RAS-mediated bradykinin storm. eLife 9 (2020) e59177. doi:10.7554/eLife.59177

[10] Jaiswal J, LoSchiavo C, and Perlman DC, Disinformation, Misinformation and InequalityDriven Mistrust in the Time of COVID-19: Lessons Unlearned from AIDS Denialism. AIDS Behav 24 (2020) 2776-2780. doi:10.1007/s10461-020-02925-y [OpenAIRE]

[11] Kim Y, Nymark P, Lee Y, Wittwehr C, and Landesmann B, Application of Adverse Outcome Pathway Framework to COVID-19. Journal (2020). Available at: https://www.iscb.org/cms_addon/conferences/ismb2020/posters.php?track=COVID19&session=B#search

[12] Nymark P, Rieswijk L, Ehrhart F, Jeliazkova N, Tsiliki G, Sarimveis H, Evelo CT, Hongisto V, Kohonen P, Willighagen E, and Grafström RC, A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions. Toxicological sciences : an official journal of the Society of Toxicology 162 (2018) 264-275. doi:10.1093/toxsci/kfx252

[13] Vinken M, A putative AOP for pneumonia related to COVID-19. Arch Toxicol 94 (2020) 3343- 3345. doi:10.1007/s00204-020-02860-w [OpenAIRE]

[14] Keller KG, Reangsing C, and Schneider JK, Clinical presentation and outcomes of hospitalized adults with COVID-19: A systematic review. J Adv Nurs. 00 (2020) 1- 23. doi:10.1111/jan.14558

[16] Gagliardi MC, Tieri P, Ortona E, and Ruggieri A, ACE2 expression and sex disparity in COVID-19. Cell Death Discovery 6 (2020) 37. doi:10.1038/s41420-020-0276-1 [OpenAIRE]

[17] George PM, Wells AU, and Jenkins RG, Pulmonary fibrosis and COVID-19: the potential role for antifibrotic therapy. The Lancet Respiratory Medicine 8 (2020) 807-815. doi:10.1016/S2213-2600(20)30225-3

[18] Scully EP, Haverfield J, Ursin RL, Tannenbaum C, and Klein SL, Considering how biological sex impacts immune responses and COVID-19 outcomes. Nature Reviews Immunology 20 (2020) 442-447. doi:10.1038/s41577-020-0348-8 [OpenAIRE]

31 references, page 1 of 3
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