rWikiPathways

rWikiPathways provides programmatic access to WikiPathways pathway content via the WikiPathways API, enabling retrieval of curated, machine‑readable pathway data for integration with omics analyses.

Key Features:

• Curated Pathway Data: Contains curated biological pathways covering genes, proteins, and metabolites, including enhanced metabolite annotations and doubling of annotated metabolite nodes by associating unmapped metabolites with database identifiers.
• FAIR Interoperability: Applies FAIR principles to support integration with experimental omics data and linking of pathway components to external databases.
• Search and Integration: Provides search functionalities and increased links to metabolite databases to support pathway discovery and data integration.
• Community Curation: Supports community-driven curation and open-science contributions to pathway content and annotations.
• Database Restructuring and Automation: Incorporates database restructuring and automation to improve curation scalability and data stability.

Scientific Applications:

• Omics Data Analysis: Enables integration of pathway annotations with gene expression, protein interactions, and metabolic process data to interpret experimental results.
• Pathway Visualization: Supplies machine‑readable pathway data suitable for visualizing complex biological interactions and pathways.
• Metabolic Pathway Research: Facilitates exploration of metabolic networks through improved metabolite annotations and identifier mappings.

Methodology:

Access via the WikiPathways API to obtain machine‑readable pathway data, mapping of unmapped metabolites to database identifiers, and database restructuring combined with automation to support curation.