Update on genome completion and annotations: Protein Information Resource

Abstract

The Protein Information Resource (PIR) recently joined the European Bioinformatics Institute (EBI) and Swiss Institute of Bioinformatics (SIB) to establish UniProt--the Universal Protein Resource--which now unifies the PIR, Swiss-Prot and TrEMBL databases. The PIRSF (SuperFamily) classification system is central to the PIR/UniProt functional annotation of proteins, providing classifications of whole proteins into a network structure to reflect their evolutionary relationships. Data integration and associative studies of protein family, function and structure are supported by the iProClass database, which offers value-added descriptions of all UniProt proteins with highly informative links to more than 50 other databases. The PIR system allows consistent, rich and accurate protein annotation for all investigators.

Figure 1

Diagram of the interrelated links of the iProClass database. Comprehensive protein and superfamily views exist in two types of summary reports. The protein sequence report covers information on family, structure, function, gene, genetics, disease, ontology, taxonomy and literature, with cross-references to relevant molecular databases and executive summary lines, as well as graphical display of domain and motif regions. The superfamily report provides PIR superfamily membership information with length, taxonomy and keyword statistics, complete member listing separated by major kingdoms, family relationships at the whole protein and domain and motif levels with direct mapping to other classifications, structure and function cross-references, and domain and motif graphical display.