RA-map

RA-map provides a curated, SBGN-formatted molecular map of signaling pathways implicated in rheumatoid arthritis for integrative analysis and omics data visualization.

Key Features:

• SBGN representation: Represents molecular and signaling processes using the Systems Biology Graphical Notation (SBGN) standard.
• Expert curation: Is fully annotated and expert-validated through manual curation focused on human-specific studies and small-scale experiments to minimize false positives.
• Source integration: Integrates evidence from 353 peer-reviewed publications covering 506 species, including 303 proteins, 61 complexes, 106 genes, 106 RNA entities, 2 ions, and 7 simple molecules.
• Reactions and phenotypes: Details 446 reactions and annotates 8 phenotypes associated with rheumatoid arthritis.
• Signal transduction mapping: Depicts signal transduction pathways from receptors to the nucleus.
• Disease Maps Project affiliation: Contributes a disease-specific molecular map within the framework of the Disease Maps Project.
• Omics visualization template: Serves as a template for overlaying and visualizing omics datasets on RA molecular pathways.

Scientific Applications:

• Disease knowledge organization: Formalizes and structures RA-specific molecular knowledge to support mechanistic interpretation of implicated factors.
• Omics data interpretation: Provides a scaffold for visualizing and contextualizing transcriptomics, proteomics, or other omics data within RA signaling networks.
• Pathway-level hypothesis generation: Supports generation and refinement of hypotheses about signaling mechanisms and phenotype associations in RA.

Methodology:

Construction uses the Systems Biology Graphical Notation (SBGN), manual expert curation focused on human-specific and small-scale studies, and integration of evidence from 353 peer-reviewed publications.