PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2024 Apr 4

PMID 38572754

Authors

Chih-Hsuan Wei

Alexis Allot

Po-Ting Lai

Robert Leaman

Shubo Tian

Ling Luo

Qiao Jin

Zhizheng Wang

Qingyu Chen

Zhiyong Lu

Affiliations

Soon will be listed here.

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.

Citing Articles

MedKG: enabling drug discovery through a unified biomedical knowledge graph.

Kumari M, Chauhan R, Garg P Mol Divers. 2025; .

PMID: 40085402 DOI: 10.1007/s11030-025-11164-z.

Pipeline to explore information on genome editing using large language models and genome editing meta-database.

Suzuki T, Bono H Database (Oxford). 2025; 2025.

PMID: 40056431 PMC: 11890094. DOI: 10.1093/database/baaf022.

A large language model framework for literature-based disease-gene association prediction.

Li P, Sun Y, Juan H, Chen C, Tsai H, Huang J Brief Bioinform. 2025; 26(1).

PMID: 39998433 PMC: 11851487. DOI: 10.1093/bib/bbaf070.

Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database.

Wiegers T, Davis A, Wiegers J, Sciaky D, Barkalow F, Wyatt B Database (Oxford). 2025; 2025.

PMID: 39982792 PMC: 11844237. DOI: 10.1093/database/baaf013.

Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data.

Poretsky E, Blake V, Andorf C, Sen T Database (Oxford). 2025; 2025.

PMID: 39963877 PMC: 11833239. DOI: 10.1093/database/baaf011.

References

Jiang J, Yuan J, Hu Z, Zhang Y, Zhang T, Xu M . Systematic illumination of druggable genes in cancer genomes. Cell Rep. 2022; 38(8):110400. PMC: 8919705. DOI: 10.1016/j.celrep.2022.110400. View

Islamaj R, Wei C, Cissel D, Miliaras N, Printseva O, Rodionov O . NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition. J Biomed Inform. 2021; 118:103779. PMC: 11037554. DOI: 10.1016/j.jbi.2021.103779. View

Rzhetsky A, Seringhaus M, Gerstein M . Seeking a new biology through text mining. Cell. 2008; 134(1):9-13. PMC: 2735884. DOI: 10.1016/j.cell.2008.06.029. View

Leaman R, Lu Z . TaggerOne: joint named entity recognition and normalization with semi-Markov Models. Bioinformatics. 2016; 32(18):2839-46. PMC: 5018376. DOI: 10.1093/bioinformatics/btw343. View

Jin Q, Leaman R, Lu Z . Retrieve, Summarize, and Verify: How Will ChatGPT Affect Information Seeking from the Medical Literature?. J Am Soc Nephrol. 2023; 34(8):1302-1304. PMC: 10400098. DOI: 10.1681/ASN.0000000000000166. View

Westergaard D, Staerfeldt H, Tonsberg C, Jensen L, Brunak S . A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PLoS Comput Biol. 2018; 14(2):e1005962. PMC: 5831415. DOI: 10.1371/journal.pcbi.1005962. View

Percha B, Altman R . A global network of biomedical relationships derived from text. Bioinformatics. 2018; 34(15):2614-2624. PMC: 6061699. DOI: 10.1093/bioinformatics/bty114. View

Xu J, Wu Y, Zhang Y, Wang J, Lee H, Xu H . CD-REST: a system for extracting chemical-induced disease relation in literature. Database (Oxford). 2016; 2016. PMC: 4808251. DOI: 10.1093/database/baw036. View

Wei C, Luo L, Islamaj R, Lai P, Lu Z . GNorm2: an improved gene name recognition and normalization system. Bioinformatics. 2023; 39(10). PMC: 10612401. DOI: 10.1093/bioinformatics/btad599. View

10.

Comeau D, Islamaj Dogan R, Ciccarese P, Cohen K, Krallinger M, Leitner F . BioC: a minimalist approach to interoperability for biomedical text processing. Database (Oxford). 2013; 2013:bat064. PMC: 3889917. DOI: 10.1093/database/bat064. View

11.

Pu Y, Beck D, Verspoor K . Graph embedding-based link prediction for literature-based discovery in Alzheimer's Disease. J Biomed Inform. 2023; 145:104464. DOI: 10.1016/j.jbi.2023.104464. View

12.

Legrand J, Gogdemir R, Bousquet C, Dalleau K, Devignes M, Digan W . PGxCorpus, a manually annotated corpus for pharmacogenomics. Sci Data. 2020; 7(1):3. PMC: 6940385. DOI: 10.1038/s41597-019-0342-9. View

13.

Mitsuhashi N, Toyo-Oka L, Katayama T, Kawashima M, Kawashima S, Miyazaki K . TogoVar: A comprehensive Japanese genetic variation database. Hum Genome Var. 2022; 9(1):44. PMC: 9744889. DOI: 10.1038/s41439-022-00222-9. View

14.

Li J, Sun Y, Johnson R, Sciaky D, Wei C, Leaman R . BioCreative V CDR task corpus: a resource for chemical disease relation extraction. Database (Oxford). 2016; 2016. PMC: 4860626. DOI: 10.1093/database/baw068. View

15.

Luo L, Lai P, Wei C, Arighi C, Lu Z . BioRED: a rich biomedical relation extraction dataset. Brief Bioinform. 2022; 23(5). PMC: 9487702. DOI: 10.1093/bib/bbac282. View

16.

Mayers M, Li T, Queralt-Rosinach N, Su A . Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network. BMC Bioinformatics. 2019; 20(1):653. PMC: 6907279. DOI: 10.1186/s12859-019-3297-0. View

17.

Lipscomb C . Medical Subject Headings (MeSH). Bull Med Libr Assoc. 2000; 88(3):265-6. PMC: 35238. View

18.

Lindberg D, Humphreys B . Rising expectations: access to biomedical information. Yearb Med Inform. 2008; :165-72. PMC: 2441483. View

19.

Kilicoglu H, Rosemblat G, Fiszman M, Shin D . Broad-coverage biomedical relation extraction with SemRep. BMC Bioinformatics. 2020; 21(1):188. PMC: 7222583. DOI: 10.1186/s12859-020-3517-7. View

20.

Islamaj Dogan R, Leaman R, Lu Z . NCBI disease corpus: a resource for disease name recognition and concept normalization. J Biomed Inform. 2014; 47:1-10. PMC: 3951655. DOI: 10.1016/j.jbi.2013.12.006. View