AOP-helpFinder 2.0: Integration of an event-event searches module

Jaylet, Thomas; Coustillet, Thibaut; Jornod, Florence; Margaritte‐Jeannin, Patricia; Audouze, Karine

doi:10.1016/j.envint.2023.108017

Cited by 13 publications

(4 citation statements)

References 33 publications

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“…Finally, we relied on artificial intelligence (AI) based tool, AOP-helpFinder (Jaylet et al, 2023; Jornod et al, 2022) (https://aop-helpfinder.u-paris-sciences.fr/), and Abstract Sifter (Baker et al, 2017) (https://comptox.epa.gov/dashboard/chemical/pubmed-abstract-sifter/) to screen published literature and manually identified novel associations between the B[a]P-induced toxicities and the remaining 30 KEs in the directed AOP network (Supplementary Table S13). Additionally, we compiled auxiliary evidence for the 36 KEs that were associated with B[a]P-induced toxicity through our systematic data integrative approach.…”

Section: Resultsmentioning

confidence: 99%

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Sahoo,

Chivukula,

Madgaonkar

et al. 2024

Preprint

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Plastics are widespread pollutants found in atmospheric, terrestrial and aquatic ecosystems due to their extensive usage and environmental persistence. Plastic additives, that are utilized to achieve specific functionality in plastics, leach into the environment upon plastic degradation and pose considerable risk to ecological and human health. Limited knowledge concerning the presence of plastic additives throughout the plastic life cycle has hindered their effective regulation, thereby posing risks to product safety. In this study, we leveraged the adverse outcome pathway (AOP) framework to understand the mechanisms underlying plastic additives-induced toxicities. We first identified an exhaustive list of 6470 plastic additives from chemicals documented to be found in plastics. Next, we leveraged heterogenous toxicogenomics and biological endpoints data from five exposome-relevant resources, and identified associations between 1287 plastic additives and 322 complete and high quality AOPs within AOP-Wiki. Based on these plastic additive-AOP associations, we constructed a stressor-centric AOP network, wherein the stressors are categorized into 10 priority use sectors and AOPs are linked to 27 disease categories. We visualized the plastic additives-AOP network for each of the 1287 plastic additives and made them available in a dedicated website: https://cb.imsc.res.in/saopadditives/. Finally, we showed the utility of the constructed plastic additives-AOP network by identifying 28 highly relevant AOPs associated with benzo[a]pyrene, and thereafter, explored the associated toxicity pathways leading to respiratory and gastrointestinal system diseases in humans and developmental disorders in aquatic species. Overall, the constructed plastic additives-AOP network will enable regulatory risk assessment of plastic additives, thereby contributing towards a toxic-free circular economy for plastics.

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Section: Resultsmentioning

confidence: 99%

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Sahoo,

Chivukula,

Madgaonkar

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…Subsequently, to assess the rationality of associations between the remaining 30 KEs in LCC and inorganic cadmium, we relied on the toxicity data in published literature. We leveraged an artificial intelligence (AI) based tool, AOP-helpFinder [74,75] (https://aop-helpfinder.u-paris-sciences.fr/) to screen existing literature and identify associations of KEs with inorganic cadmium. In addition, we relied on Abstract Sifter [76] (https://comptox.epa.gov/dashboard/chemical/pubmed-abstract-sifter/) to filter published literature from PubMed (https://pubmed.ncbi.nlm.nih.gov/) that are relevant for cadmium-induced toxicity.…”

Section: Resultsmentioning

confidence: 99%

An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity

Sahoo,

Chivukula,

Ramesh

et al. 2023

Preprint

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Cadmium is a prominent toxic heavy metal that contaminates both terrestrial and aquatic environments. Owing to its high biological half-life and low excretion rates, cadmium causes a variety of adverse biological outcomes. Adverse outcome pathway (AOP) networks were envisioned to systematically capture toxicological information to enable risk assessment and chemical regulation. Here, we leveraged AOP-Wiki and integrated heterogeneous data from four other exposome-relevant resources to build the first AOP network relevant for inorganic cadmium-induced toxicity. From AOP-Wiki, we filtered 309 high confidence AOPs, identified 312 key events (KEs) associated with inorganic cadmium, and thereafter, curated 30 cadmium relevant AOPs (cadmium-AOPs), using a data-centric approach. By constructing the undirected AOP network, we identified a large connected component of 18 cadmium-AOPs. Further, we analyzed the directed network of 59 KEs and 82 key event relationships (KERs) in the largest component using graph-theoretic approaches. Subsequently, we mined published literature using artificial intelligence-based tools to provide auxiliary evidence of cadmium association for all KEs in the largest component. Finally, we performed case studies to verify the rationality of cadmium-induced toxicity in humans and aquatic species. Overall, cadmium-AOP network constructed in this study will aid ongoing research in systems toxicology and chemical exposome.

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“…Subsequently, to assess the rationality of associations between the remaining 30 KEs in LCC and inorganic cadmium, we relied on the toxicity data in published literature. We leveraged an artificial intelligence (AI) based tool, AOP-helpFinder [74,75] (https://aophelpfinder.u-paris-sciences.fr/) to screen existing literature and identify associations of KEs with inorganic cadmium. In addition, we relied on Abstract Sifter [76] (https://comptox.epa.gov/dashboard/chemical/pubmed-abstract-sifter/) to filter published literature from PubMed (https://pubmed.ncbi.nlm.nih.gov/) that are relevant for cadmiuminduced toxicity.…”

Section: Auxiliary Evidence For Cadmium-induced Toxicity Pathways In ...mentioning

confidence: 99%

An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity

Sahoo,

Chivukula,

Ramesh

et al. 2024

Science of The Total Environment

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AOP-helpFinder 2.0: Integration of an event-event searches module

Cited by 13 publications

References 33 publications

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

Leveraging integrative toxicogenomic approach towards development of stressor-centric adverse outcome pathway networks for plastic additives

An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity

An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity

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