OmniPath

OmniPath integrates literature-curated signaling pathway and interaction datasets into a high-coverage, directionally annotated knowledge base for human signaling.

Key Features:

• Integration of interaction types: Integrates causal (activity flow and enzyme–substrate), undirected, and process-description–derived interaction types across 27 curated sources.
• Directionality and sign harmonization: Resolves inconsistencies in directionality, effect sign, and mechanistic detail across heterogeneous resources.
• Annotation-rich interactions: Provides a uniform representation that incorporates references, localization, compound effects, and additional biochemical metadata for each interaction.
• Coverage: Encompasses tens of thousands of interactions and nearly 40% of human protein-coding genes, enriched in disease-associated, druggable, and cancer-related proteins.
• Evidence provenance: Supports all interactions with bibliographic evidence aggregated from thousands of publications to enable provenance tracking and reliability assessment.
• pypath integration: pypath, a Python library, enables dynamic retrieval, filtering, integration, custom network assembly, automated updates from underlying resources, and incorporation of functional, structural, and disease-linked metadata.

Scientific Applications:

• Pathway analysis: Performing high-confidence pathway analyses across biological and translational contexts.
• Signaling study design: Designing signaling studies and selecting appropriate interaction sources.
• Disease and drug target research: Investigating disease-associated, druggable, and cancer-related proteins.

Methodology:

Systematic evaluation and harmonization of publicly available human signaling resources; integration of causal, undirected, and process-description–derived interaction types across 27 curated sources; resolution of inconsistencies in directionality, effect sign, and mechanistic detail; aggregation of bibliographic evidence from thousands of publications; construction of a uniform representation with references, localization, compound effects, and biochemical metadata for each interaction; use of pypath for dynamic retrieval, filtering, integration, custom network assembly, and automated updates.