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Nucleic Acids Research, 2002, Vol. 30, No. 1 35-37
© 2002 Oxford University Press

The Protein Information Resource: an integrated public resource of functional annotation of proteins

Cathy H. Wu*, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhang-Zhi Hu, Robert S. Ledley, Kali C. Lewis, Hans-Werner Mewes1, Bruce C. Orcutt, Baris E. Suzek, Akira Tsugita2, C. R. Vinayaka, Lai-Su L. Yeh, Jian Zhang and Winona C. Barker

National Biomedical Research Foundation, Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20007, USA, 1GSF-Forschungszentrum f. Umwelt und Gesundheit, Munich Information Center for Protein Sequences am Max–Planck Instut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany and 2Japan International Protein Information Database, Science University of Tokyo, Noda, Japan

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases).

* To whom correspondence should be addressed. Tel: +1 202 687 2121; Fax: +1 202 687 1662; Email: pirmail{at}nbrf.georgetown.edu


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