BioRED: a rich biomedical relation extraction dataset

• Published in: Briefings in bioinformatics Vol. 23; no. 5
• Main Authors: Luo, Ling, Lai, Po-Ting, Wei, Chih-Hsuan, Arighi, Cecilia N, Lu, Zhiyong
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 20.09.2022; Oxford Publishing Limited (England)
• Subjects: Algorithms; Annotations; Automation; Availability; Benchmarks; Coders; Data Mining; Datasets; Protein interaction; Proteins; PubMed; Review; named entity recognition; biomedical dataset; relation extraction; biomedical natural language processing
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbac282

Abstract Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for biomedical RE only focus on relations of a single type (e.g. protein–protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then, we present a first-of-its-kind biomedical relation extraction dataset (BioRED) with multiple entity types (e.g. gene/protein, disease, chemical) and relation pairs (e.g. gene–disease; chemical–chemical) at the document level, on a set of 600 PubMed abstracts. Furthermore, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including Bidirectional Encoder Representations from Transformers (BERT)-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a rich dataset can successfully facilitate the development of more accurate, efficient and robust RE systems for biomedicine. Availability: The BioRED dataset and annotation guidelines are freely available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.