The Protein Information Resource: an integrated public resource of functional annotation of proteins.
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).
Wu
Cathy H
CH
National Biomedical Research Foundation, Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20007, USA. pirmail@nbrf.georgetown.edu
Huang
Hongzhan
H
Arminski
Leslie
L
Castro-Alvear
Jorge
J
Chen
Yongxing
Y
Hu
Zhang-Zhi
ZZ
Ledley
Robert S
RS
Lewis
Kali C
KC
Mewes
Hans-Werner
HW
Orcutt
Bruce C
BC
Suzek
Baris E
BE
Tsugita
Akira
A
Vinayaka
C R
CR
Yeh
Lai-Su L
LS
Zhang
Jian
J
Barker
Winona C
WC
D000595:Amino Acid Sequence; D000818:Animals; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval; D007390:International Agencies; D020407:Internet; D011506:Proteins / Q000145:classification / Q000235:genetics; D018511:Systems Integration
D011506:Proteins