mentha

mentha aggregates curated protein–protein interaction (PPI) evidence from IMEx-compliant databases to generate harmonized organism-specific and cross-species interactomes.

Key Features:

• Integration of IMEx-compliant data: Aggregates curated interaction records from IMEx-compliant databases to increase coverage of literature-curated PPIs.
• Federation and standardization: Federates and standardizes interaction records from diverse literature-curated PPI sources to produce consistent interaction representations.
• Weekly interactome reconstruction: Continuously reconstructs interaction graphs on a weekly basis to update harmonized networks.
• Reliability scoring: Assigns a reliability score to each interaction derived from the volume and quality of supporting experimental evidence.
• Organism-specific interactomes: Provides organism-specific interactomes for eight model species.
• Cross-organism network: Produces a unified cross-organism interactome enabling multi-species network integration.
• Evidence provenance and neighborhood analysis: Retains supporting evidence sources and enables analysis of interaction neighborhoods and confidence scores within the network context.

Scientific Applications:

• Systems-level protein function analysis: Facilitates network-based investigation of protein function using harmonized PPI data.
• Signaling pathway and topology studies: Enables analysis of signaling pathways and interactome topology using curated interactions and confidence scores.
• Comparative interactomics: Supports cross-species comparisons via the unified cross-organism network and organism-specific interactomes.
• Interaction prioritization: Allows ranking and prioritization of PPIs for downstream experiments based on reliability scores and evidence volume.
• Neighborhood and evidence exploration: Enables examination of interaction neighborhoods and their supporting experimental evidence for hypothesis generation.

Methodology:

Aggregates and harmonizes interaction records from IMEx-compliant databases, standardizes federated literature-curated PPI entries, reconstructs interaction graphs weekly, and computes per-interaction reliability scores from the volume and quality of supporting experimental evidence.