Natural language processing in toxicology: Delineating adverse outcome pathways and guiding the application of new approach methodologies

Authors Marie P.F. Corradi , Alyanne M. de Haan , Bernard Staumont , Aldert H. Piersma , Liesbet Geris , Raymond H.H. Pieters , Cyrille A.M. Krul , Marc A.T. Teunis
Published in Biomaterials and Biosystems
Publication date 2022
Research groups Innovative Testing in Life Sciences and Chemistry
Type Article

Summary

Adverse Outcome Pathways (AOPs) are conceptual frameworks that tie an initial perturbation (molecular initiat- ing 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 infor- mation, 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 advance- ment 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.

On this publication contributed

  • Raymond Pieters | Professor | Research group Innovative Testing in Life Sciences & Chemistry
    Raymond H.H. Pieters
    • Professor
    • Research groups: Innovative Testing in Life Sciences and Chemistry
  • Cyrille Krul
    Cyrille A.M. Krul
    • Professor
    • Research groups: Innovative Testing in Life Sciences and Chemistry
  • Marc Teunis | Researcher | Research group Innovative Testing in Life Sciences and Chemistry
    Marc A.T. Teunis
    • Researcher
    • Research groups: Innovative Testing in Life Sciences and Chemistry

Language English
Published in Biomaterials and Biosystems
Key words natural language processing, adverse outcome pathways, new approach methodologies, toxicology
Digital Object Identifier 10.1016/j.bbiosy.2022.100061

Innovative Testing in Life Sciences and Chemistry