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

Human Phenotype Ontology 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.

Citation:
Groza T, Gration D, Baynam G, Robinson PN. FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology. Bioinformatics. 2024;40(7).

Keywords:
Algorithms; biological ontologies; phenotype

Abstract:
Human Phenotype Ontology 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.