The road from manual to automatic semantic indexing of biomedical literature: a 10 years journey

Abstract

Biomedical experts are facing challenges in keeping up with the vast amount of biomedical knowledge published daily. With millions of citations added to databases like MEDLINE/PubMed each year, efficiently accessing relevant information becomes crucial. Traditional term-based searches may lead to irrelevant or missed documents due to homonyms, synonyms, abbreviations, or term mismatch. To address this, semantic search approaches employing predefined concepts with associated synonyms and relations have been used to expand query terms and improve information retrieval. The National Library of Medicine (NLM) plays a significant role in this area, indexing citations in the MEDLINE database with topic descriptors from the Medical Subject Headings (MeSH) thesaurus, enabling advanced semantic search strategies to retrieve relevant citations, despite synonymy, and polysemy of biomedical terms. Over time, advancements in semantic indexing have been made, with Machine Learning facilitating the transition from manual to automatic semantic indexing in the biomedical literature. The paper highlights the journey of this transition, starting with manual semantic indexing and the initial efforts toward automatic indexing. The BioASQ challenge has served as a catalyst in revolutionizing the domain of semantic indexing, further pushing the boundaries of efficient knowledge retrieval in the biomedical field.