monarchr: an R package for querying biomedical knowledge graphs

O’Neil, Shawn T, Schilder, Brian M, Schaper, Kevin, Cox, Corey, Korn, Daniel, Gehrke, Sarah, Mungall, Christopher J, Haendel, Melissa A (October 2025) monarchr: an R package for querying biomedical knowledge graphs. Bioinformatics, 41 (10). ISSN 1367-4803

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Abstract

Biomedical knowledge graphs (KGs) aggregate and provide a wealth of information, linking genes and their variants, diseases, phenotypes, and much more. While these data are available in raw and API-hosted form, to date, functionality for working with KGs in the R programming language has been limited. We introduce monarchr, a package for querying and manipulating KG data. Support for the expansive Monarch Initiative KG is built in, and monarchr can accommodate any KG in the Knowledge Graph eXchange (KGX) format. This tidy-inspired interface offers researchers an intuitive, iterative approach to querying and visualizing KG data.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > computational biology
CSHL Authors:	Schilder, Brian
Communities:	CSHL labs > Koo Lab CSHL Post Doctoral Fellows
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	2 October 2025
Date Deposited:	27 Oct 2025 13:01
Last Modified:	27 Oct 2025 13:01
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41990

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