Building an Adverse Outcome Pathway network for COVID-19 Article Swipe
Penny Nymark
,
Laure‐Alix Clerbaux
,
Maria João Amorim
,
Christos Andronis
,
F Bernardi
,
Gillina F. G. Bezemer
,
Sandra Coecke
,
Felicity N. E. Gavins
,
Daniel Jacobson
,
Eftychia Lekka
,
Luigi Margiotta‐Casaluci
,
Marvin Martens
,
Sally A. Mayasich
,
Holly M. Mortensen
,
Young Jun Kim
,
Magdalini Sachana
,
Shihori Tanabe
,
Vassilis Virvilis
,
Stephen W. Edwards
,
Sabina Halappanavar
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3389/fsysb.2024.1384481
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3389/fsysb.2024.1384481
The COVID-19 pandemic generated large amounts of data on the disease pathogenesis leading to a need for organizing the vast knowledge in a succinct manner. Between April 2020 and February 2023, the CIAO consortium exploited the Adverse Outcome Pathway (AOP) framework to comprehensively gather and systematically organize published scientific literature on COVID-19 pathology. The project considered 24 pathways relevant for COVID-19 by identifying essential key events (KEs) leading to 19 adverse outcomes observed in patients. While an individual AOP defines causally linked perturbed KEs towards an outcome, building an AOP network visually reflect the interrelatedness of the various pathways and outcomes. In this study, 17 of those COVID-19 AOPs were selected based on quality criteria to computationally derive an AOP network. This primary network highlighted the need to consider tissue specificity and helped to identify missing or redundant elements which were then manually implemented in the final network. Such a network enabled visualization of the complex interactions of the KEs leading to the various outcomes of the multifaceted COVID-19 and confirmed the central role of the inflammatory response in the disease. In addition, this study disclosed the importance of terminology harmonization and of tissue/organ specificity for network building. Furthermore the unequal completeness and quality of information contained in the AOPs highlighted the need for tighter implementation of the FAIR principles to improve AOP findability, accessibility, interoperability and re-usability. Finally, the study underlined that describing KEs specific to SARS-CoV-2 replication and discriminating physiological from pathological inflammation is necessary but requires adaptations to the framework. Hence, based on the challenges encountered, we proposed recommendations relevant for ongoing and future AOP-aligned consortia aiming to build computationally biologically meaningful AOP networks in the context of, but not limited to, viral diseases.
Related Topics
Concepts
Adverse Outcome Pathway
Interoperability
Computer science
Usability
Terminology
Coronavirus disease 2019 (COVID-19)
Outcome (game theory)
Harmonization
Visualization
Data science
Artificial intelligence
World Wide Web
Disease
Medicine
Computational biology
Infectious disease (medical specialty)
Biology
Pathology
Human–computer interaction
Physics
Acoustics
Philosophy
Mathematical economics
Mathematics
Linguistics
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fsysb.2024.1384481
- OA Status
- diamond
- Cited By
- 7
- References
- 30
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4399543803
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4399543803Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.3389/fsysb.2024.1384481Digital Object Identifier
- Title
-
Building an Adverse Outcome Pathway network for COVID-19Work title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-06-07Full publication date if available
- Authors
-
Penny Nymark, Laure‐Alix Clerbaux, Maria João Amorim, Christos Andronis, F Bernardi, Gillina F. G. Bezemer, Sandra Coecke, Felicity N. E. Gavins, Daniel Jacobson, Eftychia Lekka, Luigi Margiotta‐Casaluci, Marvin Martens, Sally A. Mayasich, Holly M. Mortensen, Young Jun Kim, Magdalini Sachana, Shihori Tanabe, Vassilis Virvilis, Stephen W. Edwards, Sabina HalappanavarList of authors in order
- Landing page
-
https://doi.org/10.3389/fsysb.2024.1384481Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
diamondOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.3389/fsysb.2024.1384481Direct OA link when available
- Concepts
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Adverse Outcome Pathway, Interoperability, Computer science, Usability, Terminology, Coronavirus disease 2019 (COVID-19), Outcome (game theory), Harmonization, Visualization, Data science, Artificial intelligence, World Wide Web, Disease, Medicine, Computational biology, Infectious disease (medical specialty), Biology, Pathology, Human–computer interaction, Physics, Acoustics, Philosophy, Mathematical economics, Mathematics, LinguisticsTop concepts (fields/topics) attached by OpenAlex
- Cited by
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7Total citation count in OpenAlex
- Citations by year (recent)
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2025: 7Per-year citation counts (last 5 years)
- References (count)
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30Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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