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

arXiv: https://arxiv.org/abs/2410.07969 · HTML: https://mlsanity.com/paper/2410.07969/

## Key facts

- Cited by 8 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 10 Oct 2024.

## Built on by (most cited first, 8 of 8)

- [Automated Construction of Medical Indicator Knowledge Graphs Using Retrieval Augmented Large Language Models](https://mlsanity.com/paper/2511.13526/) (2025)
- [DeepEvidence: Empowering Biomedical Discovery with Deep Knowledge Graph Research](https://mlsanity.com/paper/2601.11560/) (2025)
- [Developing Large Language Models for Clinical Research Using One Million Clinical Trials](https://mlsanity.com/paper/2505.16097/) (2025)
- [Building evidence-based knowledge bases from full-text literature for disease-specific biomedical reasoning](https://mlsanity.com/paper/2603.28325/) (2026)
- [LogosKG: Hardware-Optimized Scalable and Interpretable Knowledge Graph Retrieval](https://mlsanity.com/paper/2604.18913/) (2026)
- [From Regulatory Approvals to Patents: Cross-Domain Linking for Cardiovascular Device Traceability](https://mlsanity.com/paper/2606.28353/) (2026)
- [ANCHOR-RE: An Agentic Neuro-Symbolic Framework for Grounded Biomedical Relation Extraction](https://mlsanity.com/paper/2608.03154/) (2026)
- [PriDyG: Privacy-preserving Dynamic Graph Inference with LLM-GNN Collaboration](https://mlsanity.com/paper/2608.04255/) (2026)

## Abstract (arXiv)

Papers, patents, and clinical trials are essential scientific resources in biomedicine, crucial for knowledge sharing and dissemination. However, these documents are often stored in disparate databases with varying management standards and data formats, making it challenging to form systematic and fine-grained connections among them. To address this issue, we construct 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 dispersed resources through 482 million biomedical entity linkages, 19 million citation linkages, and 7 million project linkages. The construction of PKG 2.0 wove together fine-grained biomedical entity extraction, high-performance author name disambiguation, multi-source citation integration, and high-quality project data from the NIH Exporter. Data validation demonstrates that PKG 2.0 excels in key tasks such as author disambiguation and biomedical entity recognition. This dataset provides valuable resources for biomedical researchers, bibliometric scholars, and those engaged in literature mining.