Bridging the Gap: Generating a Comprehensive Biomedical Knowledge Graph Question Answering Dataset

Research output: Contributions to collected editions/worksArticle in conference proceedingsResearchpeer-review

Authors

Despite the plethora of resources such as large-scale corpora and manually curated Knowledge Graphs (KGs), the ability to perform reasoning with natural language inputs over biomedical graphs remains challenging due to insufficient training data. We propose a novel method for automatically constructing a Biomedical Knowledge Graph Question Answering (BioKGQA) dataset sourced from PrimeKG, the largest precision medicine-oriented KG. In total, we create 85,368 question-answer pairs along with their respective SPARQL queries. Our approach generates a diverse array of contextually relevant questions covering a wide spectrum of biomedical concepts and levels of complexity. We evaluate our method based on automatic metrics alongside manual annotations. We establish novel standards tailored for KGQA systems to highlight the linguistic correctness and semantical faithfulness of the generated questions based on extracted KG facts. The compiled dataset – PrimeKGQA – serves as a valuable benchmarking resource for advancing knowledge-driven biomedical research and evaluating KGQA systems.
Original languageEnglish
Title of host publicationECAI 2024 : 27th European Conference on Artificial Intelligence, 19-24 October 2024, Santiago de Compostela, Spain; including 13th Conference on Prestigious Applications of Intelligent Systems (PAIS 2024), Proceedings
EditorsUlle Endriss, Francisco S. Melo, Kerstin Bach, Alberto José Bugarín Diz, Jose Maria Alonso-Moral, Senén Barro, Fredrik Heintz
Number of pages8
Place of PublicationAmsterdam
PublisherIOS Press BV
Publication date2024
Pages1198-1205
ISBN (electronic)978-1-64368-548-9
DOIs
Publication statusPublished - 2024
Event27th European Conference on Artificial Intelligence - ECAI 2024: "Celebrating the past. Inspiring the future" - University of Santiago de Compostela., Santiago de Compostela, Spain
Duration: 19.10.202424.10.2024
Conference number: 27
https://www.ecai2024.eu/

Bibliographical note

© 2024 The Authors.