LexExp: a system for automatically expanding concept lexicons for noisy biomedical texts

• Type of Material: Article
• Authors: Md. Abeed Sarker, Emory University
• Language: English
• Date: 2021-08-15
• Publisher: OXFORD UNIV PRESS
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2020. Published by Oxford University Press.
• License: Creative Commons Attribution-NonCommercial 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1093/bioinformatics/btaa995
• Title of Journal or Parent Work: BIOINFORMATICS
• Volume: 37
• Issue: 16
• Start Page: 2499
• End Page: 2501
• Grant/Funding Information: Research reported in this publication was supported by the National Institute on Drug Abuse (NIDA) of the National Institutes of Health (NIH) under award No. R01DA046619. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
• Keywords: Life Sciences & Biomedicine; Physical Sciences; CORPUS; Science & Technology; Statistics & Probability; Mathematics; Computer Science, Interdisciplinary Applications; KNOWLEDGE; Biotechnology & Applied Microbiology; Technology; Computer Science; Mathematical & Computational Biology; Biochemistry & Molecular Biology; Biochemical Research Methods
• Research Categories: Biology, Molecular; Chemistry, Biochemistry; Engineering, Biomedical

Abstract

SUMMARY: LexExp is an open-source, data-centric lexicon expansion system that generates spelling variants of lexical expressions in a lexicon using a phrase embedding model, lexical similarity-based natural language processing methods and a set of tunable threshold decay functions. The system is customizable, can be optimized for recall or precision and can generate variants for multi-word expressions. AVAILABILITY AND IMPLEMENTATION: Code available at: https://bitbucket.org/asarker/lexexp; data and resources available at: https://sarkerlab.org/lexexp.