International protein index (IPI)

International protein index (IPI) provides comprehensive, nonredundant reference proteome datasets for human, mouse, and rat by integrating protein sequences and cross-references from Swiss-Prot, TrEMBL, Ensembl, and RefSeq.

Key Features:

• Nonredundant reference proteomes: Provides comprehensive, minimally redundant protein sets representing the proteomes of human, mouse, and rat.
• Data integration: Constructs datasets by integrating protein sequences and annotations from Swiss-Prot, TrEMBL, Ensembl, and RefSeq.
• Cross-references: Maintains a database of cross-references among the integrated primary data sources.
• One sequence per transcript: Produces datasets that contain a single sequence for each transcript to minimize redundancy.
• Stable incremental versioned identifiers: Assigns stable identifiers that incorporate incremental versioning to track sequence changes over time.
• Coverage of known and predicted proteins: Consolidates information to provide full coverage of both known and predicted proteins across featured species.

Scientific Applications:

• Proteomic reference generation: Serves as a reference resource for proteomic experiments and protein identification.
• Longitudinal and comparative analyses: Enables tracking and comparison of protein sequences across dataset versions for longitudinal studies.
• Biological and disease research: Supports research into human health, disease mechanisms, and the fundamental biology of model organisms.

Methodology:

Integrates protein sequences and annotations from Swiss-Prot, TrEMBL, Ensembl, and RefSeq; constructs nonredundant datasets with one sequence per transcript; maintains cross-reference mappings among sources; and assigns stable identifiers with incremental versioning.