Vocabulary Matters: An Annotation Pipeline and Four Deep Learning Algorithms for Enzyme Named Entity Recognition

• Published in: Journal of proteome research Vol. 23; no. 6; pp. 1915 - 1925
• Main Authors: Wang, Meiqi, Vijayaraghavan, Avish, Beck, Tim, Posma, Joram M.
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 07.06.2024
• Subjects: Algorithms; architecture; Data Mining - methods; Deep Learning; Enzymes; Humans; languages; Molecular Sequence Annotation - methods; Natural Language Processing; pipelines; processing technology; proteome; deep learning; biomedical natural language processing; named entity recognition
• ISSN: 1535-3893; 1535-3907; 1535-3907
• DOI: 10.1021/acs.jproteome.3c00367

Enzymes are indispensable in many biological processes, and with biomedical literature growing exponentially, effective literature review becomes increasingly challenging. Natural language processing methods offer solutions to streamline this process. This study aims to develop an annotated enzyme corpus for training and evaluating enzyme named entity recognition (NER) models. A novel pipeline, combining dictionary matching and rule-based keyword searching, automatically annotated enzyme entities in >4800 full-text publications. Four deep learning NER models were created with different vocabularies (BioBERT/SciBERT) and architectures (BiLSTM/transformer) and evaluated on 526 manually annotated full-text publications. The annotation pipeline achieved an F1-score of 0.86 (precision = 1.00, recall = 0.76), surpassed by fine-tuned transformers for F1-score (BioBERT: 0.89, SciBERT: 0.88) and recall (0.86) with BiLSTM models having higher precision (0.94) than transformers (0.92). The annotation pipeline runs in seconds on standard laptops with almost perfect precision, but was outperformed by fine-tuned transformers in terms of F1-score and recall, demonstrating generalizability beyond the training data. In comparison, SciBERT-based models exhibited higher precision, and BioBERT-based models exhibited higher recall, highlighting the importance of vocabulary and architecture. These models, representing the first enzyme NER algorithms, enable more effective enzyme text mining and information extraction. Codes for automated annotation and model generation are available from https://github.com/omicsNLP/enzymeNER and https://zenodo.org/doi/10.5281/zenodo.10581586.