PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge

Author:

Wei Chih-Hsuan1ORCID,Allot Alexis1ORCID,Lai Po-Ting1ORCID,Leaman Robert1ORCID,Tian Shubo1ORCID,Luo Ling1ORCID,Jin Qiao1ORCID,Wang Zhizheng1ORCID,Chen Qingyu1ORCID,Lu Zhiyong1ORCID

Affiliation:

1. National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , Bethesda, MD  20894 , USA

Abstract

Abstract PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly. PubTator 3.0's online interface and API utilize these precomputed entity relations and synonyms to provide advanced search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results. We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive set of features and tools that allow researchers to navigate the ever-expanding wealth of biomedical literature, expediting research and unlocking valuable insights for scientific discovery.

Funder

National Institutes of Health

Publisher

Oxford University Press (OUP)

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