The SPOKE network captures the essential structure of biomedicine and human health for discovery.


Scalable Precision Medicine Oriented Knowledge Engine. A database of databases.





The true nature of biology and the complex interactions present in human health, disease, and medical treatment are best represented as pathways, or node-arc graphs, in which “nodes” model the layers that make up a human (genetics, epigenomics, proteins, tissues, organs, clinical phenotypes, environment, lifestyle, etc.), and “arcs” represent the various types of relationships amongst them. SPOKE offers a graph-theoretic database that will allow researchers to explore these interconnected pathways, enabling new discoveries.

SPOKE affords a wide variety of applications: suggesting testable hypotheses and new conceptual syntheses for researchers, implicating mechanisms of disease for researchers and clinicians, and enabling more precise diagnoses and treatments for individual patients. 

SPOKE pulls data out of silos, connecting the wealth of information that already exists from basic molecular research, clinical insights, environmental data and others.  Current data includes 19 databases such as LINCS, GWAS Catalog, ChemBL, DrugBank, SIDER and iRefIndex. The clinical insight sources include UCSF’s large data store of de-identified patient clinical data.  SPOKE continuously acquires new data – from laboratory experiments and clinical trials to electronic health records and pedometer readings – to better inform our collective understanding of health.

Information Commons

The UCSF Information Commons provides a shared repository of data, tools and models for today’s demands of integrative research and precision medicine. SPOKE operates as a layer on top of the Information Commons, both drawing from, and adding to it.

Neighborhood Explorer is HERE!

The Neighborhood Explorer allows searching SPOKE for a node of interest, such as a specific drug compound, gene, or protein, and seeing what other nodes are in its immediate connectivity neighborhood, such as related diseases, side effects, pathways, and other compounds, genes, or proteins.