Leveraging Large Language Models for Biomedical Knowledge Graph Construction and Querying: An Advanced NLP Approach

Jadhav, Suramya and Perumal, Suki and Tadavi, Yasmin and Dash, Bikshita and Parthiban, Srinivasan (2025) Leveraging Large Language Models for Biomedical Knowledge Graph Construction and Querying: An Advanced NLP Approach. COMPANION PROCEEDINGS OF THE ACM WEB CONFERENCE 2025, WWW COMPANION 2025. pp. 2560-2566.

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Abstract

This paper introduces a novel methodology for constructing a comprehensive biomedical knowledge graph by applying advanced Natural Language Processing (NLP) techniques. By leveraging Large Language Models (LLMs) and a multifaceted prompt engineering approach, we effectively perform Named Entity Recognition (NER) and Relation Extraction (RE) on biomedical literature, targeting entities such as diseases, drugs, proteins, procedures, and symptoms. Our methodology incorporates eight distinct prompt engineering strategies for NER and a standardized approach for RE, facilitating the extraction of intricate inter-entity relationships. The resulting knowledge graph amalgamates diverse data sources into a unified framework, enabling efficient querying, visualization, and analysis of biomedical information. Furthermore, we present an innovative query processing pipeline that integrates GPT-3.5 turbo with the knowledge graph, allowing users to interact with the graph through natural language. This integrated system empowers the discovery of novel correlations, accelerating scientific research and fostering interdisciplinary collaboration. This represents a substantial contribution to the field of biomedical knowledge graph construction, offering a robust platform for accelerating scientific discovery and informing clinical decision-making.

Item Type: Article
Uncontrolled Keywords: Named Entity Recognition, Relationship Extraction, Large Language Models, Prompt Engineering, Knowledge Graphs, Query rocessing
Subjects: Computer Science > Artificial Intelligence
Computer Science > Computer Science
Divisions: Engineering and Technology > Aarupadai Veedu Institute of Technology, Chennai, India > Computer Science and Engineering
Engineering and Technology > Aarupadai Veedu Institute of Technology, Chennai, India > Artificial Intelligence and Data Science
Depositing User: Unnamed user with email techsupport@mosys.org
Last Modified: 06 Feb 2026 07:12
URI: https://ir.vmrfdu.edu.in/id/eprint/7057

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