Lifestyle factors in the biomedical literature: An ontology and comprehensive resources for named entity recognition

Abstract

MotivationDespite lifestyle factors (LSFs) being increasingly acknowledged in shaping individual health trajectories, particularly in chronic diseases, they have still not been systematically described in the biomedical literature. This is in part because no named entity recognition (NER) system exists, which can comprehensively detect all types of LSFs in text. The task is challenging due to their inherent diversity, lack of a comprehensive LSF classification for dictionary-based NER, and lack of a corpus for deep learning-based NER. ResultsWe present a novel Lifestyle Factor Ontology (LSFO), which we used to develop a dictionarybased system for recognition and normalization of LSFs. Additionally, we introduce a manually annotated corpus for LSFs (LSF200) suitable for training and evaluation of NER systems, and use it to train a transformer-based system. Evaluating the performance of both NER systems on the corpus revealed an F-score of 64% for the dictionary-based system and 76% for the transformer-based system. Largescale application of these systems on PubMed abstracts and PMC Open Access articles identified over 300 million mentions of LSF in the biomedical literature. AvailabilityLSFO, the annotated LSF200 corpus, and the detected LSFs in PubMed and PMC-OA articles using both NER systems, are available under open licenses via the following GitHub repository: https://github.com/EsmaeilNourani/LSFO-expansion. This repository contains links to two associated GitHub repositories and a Zenodo project related to the study. LSFO is also available at BioPortal: https://bioportal.bioontology.org/ontologies/LSFO. Contactkaterina.nastou@cpr.ku.dk, soren.brunak@cpr.ku.dk, lars.juhl.jensen@cpr.ku.dk Supplementary informationSupplementary data are available at Bioinformatics online.