PharmKG
PharmKG is a multi-relational, attributed biomedical knowledge graph benchmark that integrates curated databases and literature-derived relationships to link genes, drugs (chemicals), and diseases. It contains ~500,000 typed relations across ~7,600–8,000 disambiguated entities (29 relation types), with domain-specific features for entities from multi-omics sources (e.g., gene expression, chemical structure, disease embeddings). It provides baselines for knowledge graph embedding and a neural network-based method, and supports downstream tasks such as drug repurposing and target identification.
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{"activity_status": "active", "category": "KnowledgeGraph", "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "github", "value": "MindRank-Biotech"}, {"contact_type": "url", "value": "https://github.com/MindRank-Biotech/PharmKG"}], "label": "MindRank Biotech"}], "creation_date": "2025-08-12T00:00:00Z", "description": "PharmKG is a multi-relational, attributed biomedical knowledge graph benchmark that integrates curated databases and literature-derived relationships to link genes, drugs (chemicals), and diseases. It contains ~500,000 typed relations across ~7,600\u20138,000 disambiguated entities (29 relation types), with domain-specific features for entities from multi-omics sources (e.g., gene expression, chemical structure, disease embeddings). It provides baselines for knowledge graph embedding and a neural network-based method, and supports downstream tasks such as drug repurposing and target identification.", "domains": ["biomedical", "drug discovery", "pharmacology"], "evaluation_page": "resource/pharmkg/pharmkg_eval.html", "homepage_url": "https://github.com/MindRank-Biotech/PharmKG", "id": "pharmkg", "last_modified_date": "2026-06-22T00:00:00Z", "layout": "resource_detail", "license": {"id": "https://creativecommons.org/licenses/by/4.0/", "label": "CC BY 4.0", "logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png"}, "name": "PharmKG", "products": [{"category": "GraphProduct", "description": "Cleaned benchmark graph (PharmKG-8k) with typed relations between genes, chemicals, and diseases", "edge_count": 500958, "format": "mixed", "id": "pharmkg.graph", "name": "PharmKG graph", "node_count": 7603, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "biogps"}, {"relation_type": "prov:hadPrimarySource", "source": "connectivitymap"}, {"relation_type": "prov:hadPrimarySource", "source": "drugbank"}, {"relation_type": "prov:hadPrimarySource", "source": "gnbr"}, {"relation_type": "prov:hadPrimarySource", "source": "humannet"}, {"relation_type": "prov:hadPrimarySource", "source": "mesh"}, {"relation_type": "prov:hadPrimarySource", "source": "ncbigene"}, {"relation_type": "prov:hadPrimarySource", "source": "omim"}, {"relation_type": "prov:hadPrimarySource", "source": "pharmgkb"}, {"relation_type": "prov:hadPrimarySource", "source": "pharmkg"}, {"relation_type": "prov:hadPrimarySource", "source": "pubchem"}, {"relation_type": "prov:hadPrimarySource", "source": "sider"}, {"relation_type": "prov:hadPrimarySource", "source": "ttd"}], "product_url": "https://zenodo.org/record/4077338"}], "publications": [{"authors": ["Shuangjia Zheng", "Jiahua Rao", "Ying Song", "Jixian Zhang", "Xianglu Xiao", "Evandro Fei Fang", "Yuedong Yang", "Zhangming Niu"], "doi": "10.1093/bib/bbaa344", "id": "doi:10.1093/bib/bbaa344", "journal": "Briefings in Bioinformatics", "title": "PharmKG: a dedicated knowledge graph benchmark for biomedical data mining", "year": "2021"}], "repository": "https://github.com/MindRank-Biotech/PharmKG", "taxon": ["NCBITaxon:9606"]}