mlsanityData to 7 Oct 2026

Biomedical Knowledge Graph: A Survey of Domains, Tasks, and Real-World Applications

arXiv 2501.11632 ↗First posted 20 Jan 2025cs.CL cs.AI cs.CEcited by 6

Not on the map. Why?

Abstract (arXiv)

Biomedical knowledge graphs (BKGs) have emerged as powerful tools for organizing and leveraging the vast and complex data found across the biomedical field. Yet, current reviews of BKGs often limit their scope to specific domains or methods, overlooking the broader landscape and the rapid technological progress reshaping it. In this survey, we address this gap by offering a systematic review of BKGs from three core perspectives: domains, tasks, and applications. We begin by examining how BKGs are constructed from diverse data sources, including molecular interactions, pharmacological datasets, and clinical records. Next, we discuss the essential tasks enabled by BKGs, focusing on knowledge management, retrieval, reasoning, and interpretation. Finally, we highlight real-world applications in precision medicine, drug discovery, and scientific research, illustrating the translational impact of BKGs across multiple sectors. By synthesizing these perspectives into a unified framework, this survey not only clarifies the current state of BKG research but also establishes a foundation for future exploration, enabling both innovative methodological advances and practical implementations.

Key facts. Cited by 6 papers in the map (data through 7 Oct 2026). Builds on 46 of its 190 references that are in the map. First posted on arXiv 20 Jan 2025.

Builds on

46 of 190 references.

References · 46

  1. 2014Embedding Entities and Relations for Learning and Inference in Knowledge Basescited by 929
  2. 2016Complex Embeddings for Simple Link Predictioncited by 897
  3. 2019RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Spacecited by 893
  4. 2023Unifying Large Language Models and Knowledge Graphs: A Roadmapcited by 663
  5. 2020A Survey on Knowledge Graphs: Representation, Acquisition and Applicationscited by 643
  6. 2022Deep Bidirectional Language-Knowledge Graph Pretrainingcited by 156
  7. 2020When Radiology Report Generation Meets Knowledge Graphcited by 144
  8. 2020KG-BART: Knowledge Graph-Augmented BART for Generative Commonsense Reasoningcited by 106
  9. 2024Medical Graph RAG: Towards Safe Medical Large Language Model via Graph Retrieval-Augmented Generationcited by 89
  10. 2020Knowledge Graph Embedding for Link Prediction: A Comparative Analysiscited by 85
  11. 2021Can Language Models be Biomedical Knowledge Bases?cited by 83
  12. 2018GAMENet: Graph Augmented MEmory Networks for Recommending Medication Combinationcited by 79
34 more
  1. 2021Graph Representation Learning in Biomedicinecited by 79
  2. 2022Multi-Modal Knowledge Graph Construction and Application: A Surveycited by 74
  3. 2022OntoProtein: Protein Pretraining With Gene Ontology Embeddingcited by 70
  4. 2023Knowledge Graphs: Opportunities and Challengescited by 70
  5. 2024A Framework for Human Evaluation of Large Language Models in Healthcare Derived from Literature Reviewcited by 65
  6. 2023A Comprehensive Survey on Automatic Knowledge Graph Constructioncited by 63
  7. 2020Representation Learning of Histopathology Images using Graph Neural Networkscited by 40
  8. 2020Building a PubMed knowledge graphcited by 38
  9. 2024Knowledge Graph Large Language Model (KG-LLM) for Link Predictioncited by 36
  10. 2024Knowledge Graphs as Context Sources for LLM-Based Explanations of Learning Recommendationscited by 31
  11. 2020Drug Repurposing for COVID-19 via Knowledge Graph Completioncited by 30
  12. 2023Biomedical knowledge graph-optimized prompt generation for large language modelscited by 30
  13. 2019Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Networkcited by 29
  14. 2021Few-shot Knowledge Graph-to-Text Generation with Pretrained Language Modelscited by 29
  15. 2019OpenBioLink: A benchmarking framework for large-scale biomedical link predictioncited by 28
  16. 2020RECON: Relation Extraction using Knowledge Graph Context in a Graph Neural Networkcited by 28
  17. 2021Neural Multi-Hop Reasoning With Logical Rules on Biomedical Knowledge Graphscited by 25
  18. 2024RAG and RAU: A Survey on Retrieval-Augmented Language Model in Natural Language Processingcited by 25
  19. 2022GAP: A Graph-aware Language Model Framework for Knowledge Graph-to-Text Generationcited by 16
  20. 2024An Enhanced Prompt-Based LLM Reasoning Scheme via Knowledge Graph-Integrated Collaborationcited by 16
  21. 2021EventNarrative: A large-scale Event-centric Dataset for Knowledge Graph-to-Text Generationcited by 14
  22. 2024Cross-Data Knowledge Graph Construction for LLM-enabled Educational Question-Answering System: A Case Study at HCMUTcited by 14
  23. 2022A Review of Knowledge Graph Completioncited by 8
  24. 2021Explainable Biomedical Recommendations via Reinforcement Learning Reasoning on Knowledge Graphscited by 7
  25. 2022Mining On Alzheimer's Diseases Related Knowledge Graph to Identity Potential AD-related Semantic Triples for Drug Repurposingcited by 7
  26. 2023RNA-KG: An ontology-based knowledge graph for representing interactions involving RNA moleculescited by 5
  27. 2017Learning and inference in knowledge-based probabilistic model for medical diagnosiscited by 4
  28. 2023From Large Language Models to Knowledge Graphs for Biomarker Discovery in Cancercited by 4
  29. 2024Explainable Biomedical Hypothesis Generation via Retrieval Augmented Generation enabled Large Language Modelscited by 4
  30. 2021A Relational-learning Perspective to Multi-label Chest X-ray Classificationcited by 3
  31. 2023A Biomedical Knowledge Graph for Biomarker Discovery in Cancercited by 3
  32. 2022Multi-modal Protein Knowledge Graph Construction and Applicationscited by 2
  33. 2024GOProteinGNN: Leveraging Protein Knowledge Graphs for Protein Representation Learningcited by 2
  34. 2022Medical Knowledge Graph QA for Drug-Drug Interaction Prediction based on Multi-hop Machine Reading Comprehensioncited by 1

Built on by

Cited by year (2026 to 7 Oct)

Citing papers per year: 2025: 4; 2026: 2.

6 papers.

  1. 2025KARMA: Leveraging Multi-Agent LLMs for Automated Knowledge Graph Enrichmentcited by 26
  2. 2025MedKGent: A Large Language Model Agent Framework for Constructing Temporally Evolving Medical Knowledge Graphcited by 5
  3. 2025DoctorRAG: Medical RAG Fusing Knowledge with Patient Analogy through Textual Gradientscited by 4
  4. 2025ConTextual: Improving Clinical Text Summarization in LLMs with Context-preserving Token Filtering and Knowledge Graphscited by 3
  5. 2026VeriLLMed: Interactive Visual Debugging of Medical Large Language Models with Knowledge Graphscited by 0
  6. 2026EpiGraph: Building Generalists for Evidence-Intensive Epilepsy Reasoning in the Wildcited by 0