FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology

• Published in: Bioinformatics (Oxford, England) Vol. 40; no. 7
• Main Authors: Groza, Tudor, Gration, Dylan, Baynam, Gareth, Robinson, Peter N
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2024
• Subjects: Algorithms; Biological Ontologies; Humans; Natural Language Processing; Original Paper; Phenotype; Software
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btae406

Human Phenotype Ontology (HPO)-based phenotype concept recognition (CR) underpins a faster and more effective mechanism to create patient phenotype profiles or to document novel phenotype-centred knowledge statements. While the increasing adoption of large language models (LLMs) for natural language understanding has led to several LLM-based solutions, we argue that their intrinsic resource-intensive nature is not suitable for realistic management of the phenotype CR lifecycle. Consequently, we propose to go back to the basics and adopt a dictionary-based approach that enables both an immediate refresh of the ontological concepts as well as efficient re-analysis of past data. We developed a dictionary-based approach using a pre-built large collection of clusters of morphologically equivalent tokens-to address lexical variability and a more effective CR step by reducing the entity boundary detection strictly to candidates consisting of tokens belonging to ontology concepts. Our method achieves state-of-the-art results (0.76 F1 on the GSC+ corpus) and a processing efficiency of 10 000 publication abstracts in 5 s. FastHPOCR is available as a Python package installable via pip. The source code is available at https://github.com/tudorgroza/fast_hpo_cr. A Java implementation of FastHPOCR will be made available as part of the Fenominal Java library available at https://github.com/monarch-initiative/fenominal. The up-to-date GCS-2024 corpus is available at https://github.com/tudorgroza/code-for-papers/tree/main/gsc-2024.