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monarchr: an R package for querying biomedical knowledge graphs.

Shawn T O'Neil1, Brian M Schilder2, Kevin Schaper1

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Summary
This summary is machine-generated.

Researchers can now query and manipulate biomedical knowledge graphs (KGs) using the R programming language with the new monarchr package. This tool simplifies access to complex biological data, enhancing research capabilities.

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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.