The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information.
Document Type
Article
Publication Date
2-3-2023
Publication Title
Bioinformatics (Oxford, England)
Keywords
washington; isb
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.
Department
Institute for Systems Biology
Recommended Citation
Morris, John H; Soman, Karthik; Akbas, Rabia E; Zhou, Xiaoyuan; Smith, Brett; Meng, Elaine C; Huang, Conrad C; Cerono, Gabriel; Schenk, Gundolf; Rizk-Jackson, Angela; Harroud, Adil; Sanders, Lauren; Costes, Sylvain V; Bharat, Krish; Chakraborty, Arjun; Pico, Alexander R; Mardirossian, Taline; Keiser, Michael; Tang, Alice; Hardi, Josef; Shi, Yongmei; Musen, Mark; Israni, Sharat; Huang, Sui; Rose, Peter W; Nelson, Charlotte A; and Baranzini, Sergio E, "The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information." (2023). Articles, Abstracts, and Reports. 7129.
https://digitalcommons.providence.org/publications/7129
