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Nucleic Acids Research, 2003, Vol. 31, No. 1 345-347
© 2003 Oxford University Press

The Protein Information Resource

Cathy H. Wu*, Lai-Su L. Yeh1, Hongzhan Huang, Leslie Arminski1, Jorge Castro-Alvear1, Yongxing Chen1, Zhangzhi Hu1, Panagiotis Kourtesis1, Robert S. Ledley1, Baris E. Suzek1, C.R. Vinayaka1, Jian Zhang1 and Winona C. Barker1

Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057-1414, USA 1 National Biomedical Research Foundation, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057-1414, USA

*To whom correspondence should be addressed. Tel: +1 2026872121; Fax: +1 2026871662; Email: pirmail{at}georgetown.edu

ABSTRACT

The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering the entire taxonomic range. Family classification is used for sensitive identification, consistent annotation, and detection of annotation errors. The superfamily curation defines signature domain architecture and categorizes memberships to improve automated classification. To increase the amount of experimental annotation, the PIR has developed a bibliography system for literature searching, mapping, and user submission, and has conducted retrospective attribution of citations for experimental features. PIR also maintains NREF, a non-redundant reference database, and iProClass, an integrated database of protein family, function, and structure information. PIR-NREF provides a timely and comprehensive collection of protein sequences, currently consisting of more than 1 000 000 entries from PIR-PSD, SWISS-PROT, TrEMBL, RefSeq, GenPept, and PDB. The PIR web site (http://pir.georgetown.edu) connects data analysis tools to underlying databases for information retrieval and knowledge discovery, with functionalities for interactive queries, combinations of sequence and text searches, and sorting and visual exploration of search results. The FTP site provides free download for PSD and NREF biweekly releases and auxiliary databases and files.


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