monarchr: an R package for querying biomedical knowledge graphs

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Biomedical knowledge graphs (KGs) integrate vast amounts of biological data, including genes, variants, diseases, and phenotypes.
• Existing tools for accessing and manipulating KG data within the R programming language are limited.

Purpose of the Study:

• To introduce monarchr, an R package designed for querying and manipulating biomedical KG data.
• To provide R users with enhanced functionality for working with KGs, including the Monarch Initiative KG and any KG in the KGX format.

Main Methods:

• Development of the monarchr R package with a tidy-inspired interface.
• Implementation of support for the Monarch Initiative KG.
• Accommodation of any KG conforming to the Knowledge Graph eXchange (KGX) format.

Main Results:

• monarchr offers an intuitive and iterative approach to KG data analysis.
• The package enables seamless querying and visualization of complex biomedical data within the R environment.

Conclusions:

• monarchr addresses the limitations of working with KGs in R, providing a powerful new tool for researchers.
• The package facilitates easier access and manipulation of biomedical KG data, supporting a wide range of research applications.