is a Knowledge Graph.
Hetionet is an integrative network of biomedical knowledge assembled from 29 different databases of genes, compounds, diseases, and more. It combines over 50 years of biomedical information into a single resource.
Github: dhimmel
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| hetionet.neo4j | Hetionet v1.0 Neo4j Database | browser | Graphical Interface | http | Browser for complete Hetionet v1.0 gr... |
| hetionet.data.json | Hetionet v1.0 JSON | hetionet-v1.0.json.bz2 (131 B) | Graph | json | Hetionet v1.0 in JSON format |
| hetionet.data.neo4j | Hetionet v1.0 Neo4j | hetionet-v1.0.db.tar.bz2 (132 B) | Graph | neo4j | Hetionet v1.0 as a Neo4j database |
| hetionet.data.edges | Hetionet v1.0 edges (SIF) | hetionet-v1.0-edges.sif.gz (131 B) | Graph | sif | Hetionet v1.0 as SIF edges |
| hetionet.data.nodes | Hetionet v1.0 nodes (TSV) | hetionet-v1.0-nodes.tsv (417.1 KB) | Graph | tsv | Hetionet v1.0 as TSV nodes |
| hetionet.hetnetpy | hetnetpy | hetnetpy | Process | python | Python package for creating, querying... |
| hetionet.search | Hetnet Connectivity Search | search | Graphical Interface | http | Web application to search and explore... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| alzkb.browser | AlzKB Graph Database Browser | login | Graphical Interface | http | was influenced by | A browser interface for a knowledge g... |
| alzkb.data | AlzKB Data Release (Version 2.0.0) | v2.0.0 | Graph | mixed | was influenced by | Memgraph data release for AlzKB. |
| mechreponet.kg | MechRepoNet Knowledge Graph | publication | Product | mixed | had primary source | The MechRepoNet knowledge graph in it... |
| automat.hetio | hetio_automat | 85a5f53e63150e1e | Graph | kgx-jsonl | had primary source | Hetio Automat |
| drkg.graph | DRKG graph | drkg.tar.gz (206.6 MB) | Graph | mixed | had primary source | DRKG graph files, including a TSV of ... |
| kg4sl.synlethkg | SynLethKG Data Files | data | Graph | mixed | was influenced by | Data files for SynLethKG, the knowled... |
| pharmebinet.json | PharMeBINet JSON Release | content (3.4 GB) | Graph | json | was derived from | PharMeBINet V3 JSON release (Zenodo v... |
| pharmebinet.tsv | PharMeBINet TSV Release | content (3.5 GB) | Graph | tsv | was derived from | PharMeBINet V3 TSV release (Zenodo ve... |
| pharmebinet.graphml | PharMeBINet GraphML Release | content (3.8 GB) | Graph | mixed | was derived from | PharMeBINet V3 GraphML release (Zenod... |
| pharmebinet.neo4j | PharMeBINet Neo4j Database | content (7.7 GB) | Graph | neo4j | was derived from | PharMeBINet V3 Neo4j database release... |
| pharmebinet.neo4j.dump | PharMeBINet Neo4j Dump | content (7.5 GB) | Graph | neo4j | was derived from | PharMeBINet V3 Neo4j dump release (Ze... |
| automat.robokopkg | robokopkg | 4901b2bc764444ea | Graph | kgx-jsonl | had primary source | Robokop KG (Automat) |
Hetionet is a heterogeneous information network (hetnet) of biomedical knowledge. It integrates data from 29 public databases into a single network, containing 47,031 nodes of 11 types and 2,250,197 edges of 24 types. The network unifies information on genes, compounds, diseases, anatomy, biological processes, molecular functions, cellular components, pathways, pharmacologic classes, side effects, and symptoms.
Hetionet was originally developed as part of Project Rephetio, a study that utilized hetnets to predict new uses for existing drugs. The network has since been used for a variety of biomedical research purposes, including prioritizing disease-associated genes and providing insights into biological relationships.
The network is maintained by Daniel Himmelstein and collaborators in the Greene Lab at the University of Pennsylvania and the Baranzini Lab at the University of California, San Francisco. All data and software associated with Hetionet are open-source and freely available.
Created: June 24, 2025 | Last modified: September 23, 2026