Article (Scientific journals)
Natural language processing in toxicology: Delineating adverse outcome pathways and guiding the application of new approach methodologies.
Corradi, Marie P F; de Haan, Alyanne M; Staumont, Bernard et al.
2022In Biomaterials and Biosystems, 7, p. 100061
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Keywords :
AOP, Adverse Outcome Pathway; NAM, New Approach Methodology; NLP, Natural Language Processing; Toxicology; Biochemistry; Biotechnology; Biomedical Engineering
Abstract :
[en] Adverse Outcome Pathways (AOPs) are conceptual frameworks that tie an initial perturbation (molecular initiating event) to a phenotypic toxicological manifestation (adverse outcome), through a series of steps (key events). They provide therefore a standardized way to map and organize toxicological mechanistic information. As such, AOPs inform on key events underlying toxicity, thus supporting the development of New Approach Methodologies (NAMs), which aim to reduce the use of animal testing for toxicology purposes. However, the establishment of a novel AOP relies on the gathering of multiple streams of evidence and information, from available literature to knowledge databases. Often, this information is in the form of free text, also called unstructured text, which is not immediately digestible by a computer. This information is thus both tedious and increasingly time-consuming to process manually with the growing volume of data available. The advancement of machine learning provides alternative solutions to this challenge. To extract and organize information from relevant sources, it seems valuable to employ deep learning Natural Language Processing techniques. We review here some of the recent progress in the NLP field, and show how these techniques have already demonstrated value in the biomedical and toxicology areas. We also propose an approach to efficiently and reliably extract and combine relevant toxicological information from text. This data can be used to map underlying mechanisms that lead to toxicological effects and start building quantitative models, in particular AOPs, ultimately allowing animal-free human-based hazard and risk assessment.
Disciplines :
Biotechnology
Engineering, computing & technology: Multidisciplinary, general & others
Author, co-author :
Corradi, Marie P F ;  Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht, Heidelberglaan 7, Utrecht 3584 CS, the Netherlands
de Haan, Alyanne M;  Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht, Heidelberglaan 7, Utrecht 3584 CS, the Netherlands
Staumont, Bernard ;  Université de Liège - ULiège > Département d'aérospatiale et mécanique > Génie biomécanique
Piersma, Aldert H;  Centre for Health Protection of the Dutch National Institute for Public Health and the Environment (RIVM), Heidelberglaan 8, Utrecht 3584 CS, the Netherlands
Geris, Liesbet  ;  Université de Liège - ULiège > Département d'aérospatiale et mécanique > Génie biomécanique
Pieters, Raymond H H;  Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht, Heidelberglaan 7, Utrecht 3584 CS, the Netherlands
Krul, Cyrille A M;  Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht, Heidelberglaan 7, Utrecht 3584 CS, the Netherlands
Teunis, Marc A T;  Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht, Heidelberglaan 7, Utrecht 3584 CS, the Netherlands
Language :
English
Title :
Natural language processing in toxicology: Delineating adverse outcome pathways and guiding the application of new approach methodologies.
Publication date :
August 2022
Journal title :
Biomaterials and Biosystems
eISSN :
2666-5344
Publisher :
Elsevier Ltd, England
Volume :
7
Pages :
100061
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 11 May 2023

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