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Large Language Models in Bio-Ontology Research: A Review.

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  • 1Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182, USA.

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Large language models (LLMs) offer automated solutions for developing biomedical ontologies, improving knowledge structuring and data analysis in life sciences. This review explores LLM applications, challenges, and future trends in bio-ontology research.

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Area of Science:

  • Life Sciences
  • Bioinformatics
  • Artificial Intelligence

Background:

  • Biomedical ontologies are essential for organizing life science knowledge and enabling integrated analyses.
  • Traditional ontology development is time-consuming and requires significant expert input.
  • Advancements in artificial intelligence, specifically large language models (LLMs), present opportunities to streamline ontology research.

Purpose of the Study:

  • To review recent studies on the application of LLM-assisted techniques in biomedical ontology development.
  • To synthesize findings on LLM use in ontology creation, mapping, integration, and semantic search.
  • To identify and discuss challenges and future directions in LLM-based bio-ontology research.

Main Methods:

  • Literature review of recent studies focusing on LLM applications in biomedical ontologies.
  • Synthesis of findings related to LLM-assisted ontology creation, mapping, integration, and semantic search.
  • Analysis of challenges including bias, reliability, and ethical considerations.

Main Results:

  • LLMs show significant potential to automate and enhance various stages of biomedical ontology development.
  • LLM applications span ontology creation, data mapping, integration, and semantic search functionalities.
  • Key challenges include managing LLM bias, ensuring reliability, and addressing ethical implications.

Conclusions:

  • LLMs are poised to transform the development, maintenance, and utilization of biomedical ontologies.
  • Addressing challenges is crucial for the responsible and effective integration of LLMs in bio-ontology.
  • Future research should focus on emerging trends to further advance LLM-driven bio-ontology.