rWikiPathways

rWikiPathways is a tool associated with WikiPathways, a collaborative platform capturing collective knowledge in biological pathways. With a curated and machine-readable database, WikiPathways facilitates omics data analysis and visualization, serving research groups across various fields. While the platform has been valuable for genes and proteins, recent curation efforts have significantly enhanced the annotation of metabolites and metabolic pathways, including associating unmapped metabolites with database identifiers and providing detailed interaction knowledge. Notable outcomes include a doubling of annotated metabolite nodes in WikiPathways. The tool introduces an OpenAPI documentation of web services and adheres to FAIR principles (Findable, Accessible, Interoperable, and Reusable), enhancing interoperability between pathway knowledge and experimental omics data. Additional features, such as new search options, monthly downloads, increased links to metabolite databases, and new portals, improve accessibility for individual researchers and research communities.