BioMedGraphica

BioMedGraphica is an all-in-one platform for biomedical data integration and knowledge graph generation. It harmonizes fragmented biomedical datasets into a unified, graph AI-ready resource that facilitates precision medicine, therapeutic target discovery, and integrative biomedical AI research.

Developed using data from 43 biomedical databases, BioMedGraphica integrates:

• 11 entity types
• 30 relation types
• Over 2.3 million entities and 27 million relations

✨ Highlights

• Multi-omics integration: Genomic, transcriptomic, proteomic, metabolomic, microbiomic, exposomic
• Graph AI-ready: Outputs subgraphs ready for GNNs and ML models
• Soft matching: Uses BioBERT for fuzzy entity resolution (disease, phenotype, drug, exposure)
• GUI software: Provides Windows-based interface for end-to-end pipeline
• Connected graph variant: Isolated nodes removed for efficient downstream training

📊 Dataset Statistics

Metric	Count
Total Entities	2,306,921
Total Relations	27,232,091
Connected Entities	834,809
Connected Relations	27,087,971
Entity Types	11
Relation Types	30

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🧬 Entity Types

Entity Type	Count	Percentage (%)	Connected Count	Connected (%)
Promoter	230,358	9.99	86,238	10.33
Gene	230,358	9.99	86,238	10.33
Transcript	412,326	17.87	412,039	49.36
Protein	173,978	7.54	121,419	14.54
Pathway	6,793	0.29	1,930	0.23
Metabolite	218,335	9.46	62,364	7.47
Microbiota	621,882	26.96	1,119	0.13
Exposure	1,159	0.05	1,037	0.12
Phenotype	19,532	0.85	19,078	2.29
Disease	118,814	5.15	22,429	2.69
Drug	273,386	11.85	20,918	2.51
Total	2,306,921	100	834,809	100

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🔗 Relation Types

Relation Type	Count	Percentage (%)
Promoter-Gene	230,358	0.85
Gene-Transcript	427,810	1.57
Transcript-Protein	152,585	0.56
Protein-Protein	16,484,820	60.53
Protein-Pathway	152,912	0.56
Protein-Phenotype	478,279	1.76
Protein-Disease	143,394	0.53
Pathway-Protein	176,133	0.65
Pathway-Drug	1,795	0.01
Pathway-Exposure	301,448	1.11
Metabolite-Protein	2,804,430	10.30
Metabolite-Pathway	12,198	0.04
Metabolite-Metabolite	931	0.003
Metabolite-Disease	24,970	0.09
Microbiota-Disease	22,371	0.08
Microbiota-Drug	866	0.003
Exposure-Gene	28,982	0.11
Exposure-Pathway	301,448	1.11
Exposure-Disease	979,780	3.60
Phenotype-Phenotype	23,427	0.09
Phenotype-Disease	181,192	0.67
Disease-Phenotype	181,192	0.67
Disease-Disease	12,006	0.04
Drug-Protein	84,859	0.31
Drug-Pathway	3,065	0.01
Drug-Metabolite	3,589	0.01
Drug-Microbiota	866	0.003
Drug-Phenotype	93,826	0.34
Drug-Disease	39,977	0.15
Drug-Drug	3,882,582	14.26
Total	27,232,091	100

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📦 Access and Downloads

• Knowledge Graph Dataset: Hugging Face
• Software & Tutorials: GitHub

🧪 Validation

• Hard matching for structured identifiers (e.g. Ensembl, HGNC)
• BioBERT-based soft matching for flexible terms (e.g., diseases, phenotypes, drugs)
• Case study and benchmarking with Synapse dataset

📚 Citation

@article{zhang2024biomedgraphica,
title={BioMedGraphica: An All-in-One Platform for Biomedical Prior Knowledge and Omic Signaling Graph Generation},
author={Zhang, Heming and Liang, Shunning and Xu, Tim and Li, Wenyu and Huang, Di and Dong, Yuhan and Li, Guangfu and Miller, J Philip and Goedegebuure, S Peter and Sardiello, Marco and others},
journal={bioRxiv},
year={2024}
}