BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs

Jackson Callaghan; Colleen H. Xu; Jiwen Xin; Marco Alvarado Cano; Anders Riutta; Eric Zhou; Rohan Juneja; Yao Yao; Madhumita Narayan; Kristina Hanspers; Ayushi Agrawal; Alexander R. Pico; Chunlei Wu; Andrew I. Su

arXiv · 2304.09344

BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs

Jackson Callaghan·Colleen H. Xu·Jiwen Xin·Marco Alvarado Cano·Anders Riutta·Eric Zhou·Rohan Juneja·Yao Yao·Madhumita Narayan·Kristina Hanspers·Ayushi Agrawal·Alexander R. Pico·Chunlei Wu·Andrew I. Su

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Abstract

Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge graphs can easily represent heterogeneous types of information, and many algorithms and tools exist for querying and analyzing graphs. Biomedical knowledge graphs have been used in a variety of applications, including drug repurposing, identification of drug targets, prediction of drug side effects, and clinical decision support. Typically, knowledge graphs are constructed by centralization and integration of data from multiple disparate sources. Here, we describe BioThings Explorer, an application that can query a virtual, federated knowledge graph derived from the aggregated information in a network of biomedical web services. BioThings Explorer leverages semantically precise annotations of the inputs and outputs for each resource, and automates the chaining of web service calls to execute multi-step graph queries. Because there is no large, centralized knowledge graph to maintain, BioThing Explorer is distributed as a lightweight application that dynamically retrieves information at query time. More information can be found at https://explorer.biothings.io, and code is available at https://github.com/biothings/biothings_explorer.

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Jackson Callaghan, Colleen H. Xu, Jiwen Xin, Marco Alvarado Cano, Anders Riutta, Eric Zhou, Rohan Juneja, Yao Yao, Madhumita Narayan, Kristina Hanspers, Ayushi Agrawal, Alexander R. Pico, Chunlei Wu, Andrew I. Su. 2023-04-18. BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs. https://arxiv.org/abs/2304.09344

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