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

Abstract

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).

Transcriptional Profiling of Sorghum Induced by Methyl Jasmonate, Salicylic Acid, and Aminocyclopropane Carboxylic Acid Reveals Cooperative Regulation and Novel Gene Responses

“…In Supplemental Table IV are annotation data for the full 17,733 element positions on the microarray, including the following information for both 3# and (when available) 5# sequences: clone name, PIRnref ID, GenBank ID, BLASTX identifications, expect values, and BLASTX scores. Provisional electronic annotation of ESTs was obtained by BLASTX (Altschul et al, 1990(Altschul et al, , 1997) against full-codinglength entries from the PIR-NREF database (Wu et al, 2002). Blast scores and e-values of genes given functional consideration in this paper are shown in the figures and tables.…”

MetaCyc: a multiorganism database of metabolic pathways and enzymes

“…MetaCyc is linked to the protein sequence databases, Swiss-Prot (6) and Protein Information Resource (PIR) (7), to the protein structural database, Protein Data Bank (PDB) (8) and to TAIR (9). We will also establish links from S.cerevisiae pathways in MetaCyc to SGD (10).…”

Gnare: Automated System For High-Throughput Genome Analysis With Grid Computational Backend

“…The Analysis Server automatically creates workflows in the abstract Virtual Data Language, based on predefined templates (Section 3.5), which it then executes on distributed Grid resources such as Grid2003 and TeraGrid. The Update Server updates the Integrated Database with recently changed data from a set of monitored public databases (currently including NCBI RefSeq [22], PIR [23], InterPro [6], and KEGG [24]). In the following sections, we describe the implementation details of each of the components of GNARE.…”