Authors: Shawn O’Neil, Brian Schilder
README updated: Oct-01-2026
monarchr: Monarch Knowledge Graph Queries
monarchr provides a tidy interface for querying and analyzing biomedical knowledge graphs (KGs), including the Monarch Initiative KG, which integrates data on biological entities such as genes, disease, and phenotypes, and the relationships between them within and across species. The same set of functions queries the Monarch-hosted Neo4j database, other Neo4j databases, or local files in the KGX format (such as those available from KG-Hub), fetching nodes by identifier or property and expanding along edges by category and predicate. Results are tidygraph objects that can be manipulated with dplyr verbs and joined with other graphs. The package also provides transitive closure and reduction, aggregation over ontology hierarchies, and graph visualization.
- Website
- Get started
- Monarch Initiative
- KG-Hub (more knowledge graphs in KGX format)
Installation:
if(!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("monarch-initiative/monarchr", update=FALSE)
library(monarchr)