mlsanityData to 14 Oct 2026

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

arXiv 2401.11048 ↗First posted 19 Jan 2024cs.CL q-bio.QMcited by 30

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Abstract (arXiv)

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.

Key facts. Cited by 30 papers in the map (data through 14 Oct 2026). Builds on 4 of its 38 references that are in the map. First posted on arXiv 19 Jan 2024.

Builds on

4 of 38 references.

References · 4

  1. 2022BioRED: A Rich Biomedical Relation Extraction Datasetcited by 85
  2. 2023PubMed and Beyond: Biomedical Literature Search in the Age of Artificial Intelligencecited by 16
  3. 2022tmVar 3.0: an improved variant concept recognition and normalization toolcited by 10
  4. 2023BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasetscited by 8

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2024: 7; 2025: 12; 2026: 11.

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  1. 2024Improving Scientific Hypothesis Generation with Knowledge Grounded Large Language Modelscited by 22
  2. 2025A Large-Language Model Framework for Relative Timeline Extraction from PubMed Case Reportscited by 10
  3. 2025Toward Reliable Scientific Hypothesis Generation: Evaluating Truthfulness and Hallucination in Large Language Modelscited by 9
  4. 2025Evolving Roles of LLMs in Scientific Innovation: Assistant, Collaborator, Scientist, and Evaluatorcited by 9
  5. 2025Hidden in the Haystack: Smaller Needles are More Difficult for LLMs to Findcited by 7
  6. 2025MedKGent: A Large Language Model Agent Framework for Constructing Temporally Evolving Medical Knowledge Graphcited by 5
  7. 2025BioVerge: A Comprehensive Benchmark and Study of Self-Evaluating Agents for Biomedical Hypothesis Generationcited by 4
  8. 2024Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Developmentcited by 3
  9. 2024CurateGPT: A flexible language-model assisted biocuration toolcited by 3
  10. 2024Leveraging Social Determinants of Health in Alzheimer's Research Using LLM-Augmented Literature Mining and Knowledge Graphscited by 2
  11. 2025Large Language Models for Zero-shot Inference of Causal Structures in Biologycited by 2
  12. 2025DeepEvidence: Empowering Biomedical Discovery with Deep Knowledge Graph Researchcited by 2
18 more
  1. 2025Can Frontier LLMs Replace Annotators in Biomedical Text Mining? Analyzing Challenges and Exploring Solutionscited by 1
  2. 2025Recent Advances and Future Directions in Literature-Based Discoverycited by 1
  3. 2025A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Designcited by 1
  4. 2026Toward Federated Large Language Models in Medicine: A Parameter-Efficient Framework for Privacy-Preserving, Multi-Institutional Adaptationcited by 1
  5. 2024EnzChemRED, a rich enzyme chemistry relation extraction datasetcited by 0
  6. 2024Hybrid X-Linker: Automated Data Generation and Extreme Multi-label Ranking for Biomedical Entity Linkingcited by 0
  7. 2024A Library Perspective on Supervised Text Processing in Digital Libraries: An Investigation in the Biomedical Domaincited by 0
  8. 2025MedSEBA: Synthesizing Evidence-Based Answers Grounded in Evolving Medical Literaturecited by 0
  9. 2026Knowledge Graph Extraction from Biomedical Literature for Alkaptonuria Rare Diseasecited by 0
  10. 2026Large Language Models Meet Biomedical Knowledge Graphs for Mechanistically Grounded Therapeutic Prioritizationcited by 0
  11. 2026Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scalecited by 0
  12. 2026What Do Biomedical NER and Entity Linking Benchmarks Measure? A Corpus-Centric Diagnostic Frameworkcited by 0
  13. 2026ANCHOR-RE: An Agentic Neuro-Symbolic Framework for Grounded Biomedical Relation Extractioncited by 0
  14. 2026Aligning Biomedical Texts and Knowledge Graphs: A Systematic Comparison of Lightweight Alignment Strategiescited by 0
  15. 2026Quantitative Evidence Mining for Plausibility-Aware Biomedical AI: A Narrative Review and Conceptual Frameworkcited by 0
  16. 2026Responsible Integration of AI in Cancer Genomics: Barriers, Risks, and Pathways to Trustworthy Clinical Translationcited by 0
  17. 2026BELXTR: Biomedical Entity Linking via Contextualized Token Retrievalcited by 0
  18. 2026CircuitATLAS: Agentic reasoning over a systems neuroscience knowledge graph for target discovery in circuitopathiescited by 0