monarchr: an R package for querying biomedical knowledge graphs.
Where this comes from
- Record sourced from PubMed, PMID 41002262.
- Also identified by DOI 10.1093/bioinformatics/btaf549 and PMC identifier 12757009.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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. Source code, documentation, and installation instructions are available at https://github.com/monarch-initiative/monarchr.
Medical subject headings
- Software
- Computational Biology