PubMed knowledge graph 2.0: Connecting papers, patents, and clinical trials in biomedical science

However, these documents are often stored in disparate databases with varying management standards and data formats, making it challenging to form systematic, fine-grained connections among them. To address this issue, we introduce PKG 2.0, a comprehensive knowledge graph dataset encompassing over 36 million papers, 1.3 million patents, and 0.48 million clinical trials in the biomedical field.

PKG 2.0 integrates these previously dispersed resources through various links, including biomedical entities, author networks, citation relationships, and research projects.For more details, please refer to our paper or dataset homepage:Paper: Xu, J., Yu, C., Xu, J. et al. PubMed knowledge graph 2.0: Connecting papers, patents, and clinical trials in biomedical science. Sci Data ​​12​​, 1018 (2025). doi.org/10.1038/s41597-025-05343-8Homepage: https://pubmedkg.github.io/Updates:[Jul 20, 2025] The PKG dataset has been updated to PKG24S4 based on the PubMed 2025 Baseline.