mlsanityData to 7 Oct 2026

BIOS: An Algorithmically Generated Biomedical Knowledge Graph

arXiv 2203.09975 ↗First posted 18 Mar 2022cs.CL cs.LGcited by 9

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Abstract (arXiv)

Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language processing, model development, and data exchange. For decades, these knowledge graphs have been developed via expert curation; however, this method can no longer keep up with today's AI development, and a transition to algorithmically generated BioMedKGs is necessary. In this work, we introduce the Biomedical Informatics Ontology System (BIOS), the first large-scale publicly available BioMedKG generated completely by machine learning algorithms. BIOS currently contains 4.1 million concepts, 7.4 million terms in two languages, and 7.3 million relation triplets. We present the methodology for developing BIOS, including the curation of raw biomedical terms, computational identification of synonymous terms and aggregation of these terms to create concept nodes, semantic type classification of the concepts, relation identification, and biomedical machine translation. We provide statistics on the current BIOS content and perform preliminary assessments of term quality, synonym grouping, and relation extraction. The results suggest that machine learning-based BioMedKG development is a viable alternative to traditional expert curation.

Key facts. Cited by 9 papers in the map (data through 7 Oct 2026). Builds on 24 of its 63 references that are in the map. First posted on arXiv 18 Mar 2022.

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24 of 63 references.

References · 24

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Cited by year

Citing papers per year: 2022: 1; 2023: 3; 2024: 2; 2025: 3.

9 papers.

  1. 2024Domain-Specific Retrieval-Augmented Generation Using Vector Stores, Knowledge Graphs, and Tensor Factorizationcited by 15
  2. 2022Automatic Biomedical Term Clustering by Learning Fine-grained Term Representationscited by 5
  3. 2023CARE-MI: Chinese Benchmark for Misinformation Evaluation in Maternity and Infant Carecited by 5
  4. 2025MedKGent: A Large Language Model Agent Framework for Constructing Temporally Evolving Medical Knowledge Graphcited by 5
  5. 2025CliniQ: A Multi-faceted Benchmark for Electronic Health Record Retrieval with Semantic Match Assessmentcited by 3
  6. 2023Exploring Partial Knowledge Base Inference in Biomedical Entity Linkingcited by 2
  7. 2023High-throughput Biomedical Relation Extraction for Semi-Structured Web Articles Empowered by Large Language Modelscited by 1
  8. 2024ISPO: An Integrated Ontology of Symptom Phenotypes for Semantic Integration of Traditional Chinese Medical Datacited by 1
  9. 2025DR.EHR: Dense Retrieval for Electronic Health Record with Knowledge Injection and Synthetic Datacited by 0