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. 2025 Oct 2;41(10):btaf549.
doi: 10.1093/bioinformatics/btaf549.

monarchr: an R package for querying biomedical knowledge graphs

Shawn T O'Neil  1 , Brian M Schilder  2 , Kevin Schaper  1 , Corey Cox  1 , Daniel Korn  1 , Sarah Gehrke  1 , Christopher J Mungall  3 , Melissa A Haendel  1
Affiliations

monarchr: an R package for querying biomedical knowledge graphs

Shawn T O'Neil et al. Bioinformatics. .

Abstract

Summary: 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.

Availability and implementation: Source code, documentation, and installation instructions are available at https://github.com/monarch-initiative/monarchr.

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Figures

Figure 1.
Figure 1.
All genetic variants and genes associated with Noonan syndrome or its subtypes. Nodes are colored by pcategory and visualized with cytoscape() followed by adjustments in the Cytoscape GUI. Noonan syndrome and its subtypes are shown in the central ring, genes in middle, and genetic variants at the periphery.
See this image and copyright information in PMC

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