Proteins API

Proteins API provides programmatic access to curated UniProtKB sequence annotations, variation and proteomics datasets from large-scale studies (1000 Genomes, ExAC, COSMIC, PeptideAtlas, MaxQB, EPD, and the Human Protein Atlas) and genomic sequence coordinates to support integrative proteomics and genomics analyses.

Key Features:

• UniProtKB sequence positional annotations: Access to curated protein sequence positional annotations derived from UniProtKB.
• Variation and proteomics data mapping: Integration of variation and proteomics data mapped from large-scale studies including 1000 Genomes, ExAC, COSMIC, PeptideAtlas, MaxQB, EPD, and the Human Protein Atlas (HPA).
• Genomic coordinates service: Programmatic retrieval of genomic sequence coordinates for proteins cataloged in UniProtKB via a coordinates service.
• Flexible output formats: Search results and data exports available in JSON, XML, or GFF formats.
• RESTful API: Data access exposed through RESTful web services for programmatic query and retrieval.

Scientific Applications:

• Integrated proteomics–genomics analyses: Enable combined analyses of protein annotations, proteomics evidence, and genomic coordinates for multi-omic studies.
• Variant interpretation and disease mechanism studies: Map variants and proteomics signals to UniProtKB annotations and genomic coordinates to support investigations of disease mechanisms and targets for drug discovery.
• Proteomics evidence mapping: Link peptide and proteomics data from PeptideAtlas, MaxQB, EPD, and HPA to protein sequences and genomic loci for validation and annotation.

Methodology:

Implements RESTful web services that integrate UniProtKB and large-scale study datasets (1000 Genomes, ExAC, COSMIC, PeptideAtlas, MaxQB, EPD, HPA), provides a coordinates service to map proteins to genomic sequence coordinates, and returns results in JSON, XML, or GFF.