SPOKE Nodes and Edges

SPOKE (Scalable Precision Medicine Knowledge Engine) is a very large network containing multiple types of biological data. Pooling such diverse data into a single knowledge environment allows identifying new connections, with implications for biomedical applications like personalized medicine: suggesting which drugs may be effective for a specific patient. An earlier version of the network was used to suggest new uses for existing drugs (Himmelstein et al., 2017).

SPOKE is a heterogeneous network, meaning that different nodes (points) within the network can represent different types of data. The edges between pairs of nodes represent known connections. Paths that follow a series of edges may connect nodes not previously known to be related.

Node and edge types and their data sources are given below. Except as noted, data are updated weekly on a rotating basis (different types on different days).
   = updated currently    = in progress    = present but static

See also: source licenses, edge directionality

Node Types

Edge Types

Technical Notes

MeSH term co-occurrence. The following were calculated for each pair of Medical Subject Headings (MeSH) terms:

Disease-localizes-Anatomy and Disease-presents-Symptom calculations used only papers in which the disease term was major and the other term (anatomy or symptom) was used directly (no “explosion” via the MeSH tree). Disease and anatomy MeSH terms were taken from Disease Ontology and Uberon, respectively.

References

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Gordon DE, Jang GM, [...] Shoichet BK, Krogan NJ. Nature. 2020 Apr 30.
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. Himmelstein DS, Lizee A, Hessler C, Brueggeman L, Chen SL, Hadley D, Green A, Khankhanian P, Baranzini SE. eLife. 2017 Sep 22;6. pii: e26726.
Multi-omics resolves a sharp disease-state shift between mild and moderate COVID-19. Su Y, Chen D, [...] Goldman JD, Heath JR. Cell. 2020 Dec 10;183(6):1479-1495.e20.
ProtCID: a data resource for structural information on protein interactions. Xu Q, Dunbrack RL Jr. Nat Commun. 2020 Feb 5;11(1):711.