OmniPath

OmniPath is a biomedical knowledgebase that consolidates literature-curated information on cell signaling into a single, searchable resource. It aims to provide a comprehensive view of signaling from extracellular cues to transcriptional responses, by assembling interactions, edges and regulators across multiple sources and species. The database focuses on high-quality, curated relationships rather than high-throughput associations alone.

Contents and scope: OmniPath gathers data on ligand–receptor interactions, protein–protein interactions, enzyme–substrate relationships, and transcription factor targets, as well as post-translational modification events that modulate signaling. Each relationship is supported by experimental evidence and linked to original publications. The resource uses standardized gene and protein identifiers to facilitate cross-platform integration.

Access and tools: OmniPath provides a web portal for browsing and downloading data, and offers programmatic access through software packages such as OmnipathR for R and OmnipathPy for Python, as well as a Cytoscape app for network visualization. Data can be downloaded in common network formats for use in modeling and analysis pipelines.

Applications and impact: Researchers use OmniPath to reconstruct signaling networks, interpret omics data, perform pathway enrichment and network propagation analyses, and build computational models of cellular signaling. The resource is regularly updated with new literature curation and is intended to complement pathway databases by emphasizing curated, evidence-backed interactions.

OmniPath is maintained by a collaboration of researchers and is freely available to the scientific community.