The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information
The work
| Authors | John H Morris; Karthik Soman; Rabia E Akbas; Xiaoyuan Zhou; Brett Smith; Elaine C Meng; Conrad C Huang; Gabriel Cerono; Gundolf Schenk; Angela Rizk-Jackson; Adil Harroud; Lauren Sanders; Sylvain V Costes; Krish Bharat; Arjun Chakraborty; Alexander R Pico; Taline Mardirossian; Michael Keiser; Alice Tang; Josef Hardi; Yongmei Shi; Mark Musen; Sharat Israni; Sui Huang; Peter W Rose; Charlotte A Nelson; Sergio E Baranzini |
|---|---|
| Editors | Zhiyong Lu |
| Type | article |
| Year | 2023 |
| Citekey | morris2023scalable |
Where it appeared
| Published in | Bioinformatics |
|---|---|
| Publisher | Oxford University Press (OUP) |
| Volume | 39 |
| Issue | 2 |
| Article number | btad080 |
Identifiers
| DOI | 10.1093/bioinformatics/btad080 |
|---|---|
| ISSN | 1367-4811 |
Access
| Landing page | https://doi.org/10.1093/bioinformatics/btad080 |
|---|
From crossref.
Abstract
Abstract Motivation Knowledge graphs (KGs) are being adopted in industry, commerce and academia. Biomedical KG presents a challenge due to the complexity, size and heterogeneity of the underlying information. Results In this work, we present the Scalable Precision Medicine Open Knowledge Engine (SPOKE), a biomedical KG connecting millions of concepts via semantically meaningful relationships. SPOKE contains 27 million nodes of 21 different types and 53 million edges of 55 types downloaded from 41 databases. The graph is built on the framework of 11 ontologies that maintain its structure, enable mappings and facilitate navigation. SPOKE is built weekly by python scripts which download each resource, check for integrity and completeness, and then create a ‘parent table’ of nodes and edges. Graph queries are translated by a REST API and users can submit searches directly via an API or a graphical user interface. Conclusions/Significance: SPOKE enables the integration of seemingly disparate information to support precision medicine efforts. Availability and implementation The SPOKE neighborhood explorer is available at https://spoke.rbvi.ucsf.edu. Supplementary information Supplementary data are available at Bioinformatics online.
How it got here
| How it got here | agent via crossref |
|---|---|
| Added | 2026-10-23 13:47 UTC |
| Not denied by | a person 2026-10-29 17:12 UTC |
Cite it as
@article{morris2023scalable,
title = {The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information},
author = {John H Morris and Karthik Soman and Rabia E Akbas and Xiaoyuan Zhou and Brett Smith and Elaine C Meng and Conrad C Huang and Gabriel Cerono and Gundolf Schenk and Angela Rizk-Jackson and Adil Harroud and Lauren Sanders and Sylvain V Costes and Krish Bharat and Arjun Chakraborty and Alexander R Pico and Taline Mardirossian and Michael Keiser and Alice Tang and Josef Hardi and Yongmei Shi and Mark Musen and Sharat Israni and Sui Huang and Peter W Rose and Charlotte A Nelson and Sergio E Baranzini},
editor = {Zhiyong Lu},
year = {2023},
journal = {Bioinformatics},
publisher = {Oxford University Press (OUP)},
volume = {39},
number = {2},
issn = {1367-4811},
articleno = {btad080},
doi = {10.1093/bioinformatics/btad080},
}
This record lives at https://refs.drheap.org/morris2023scalable/ and will keep doing so.