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Protein Information Resource

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The Protein Information Resource (PIR), located at Georgetown University Medical Center (GUMC), is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies.It contains protein sequences databases [1][2][3][4][5][6][7]

History

PIR was established in 1984 by the National Biomedical Research Foundation (NBRF) as a resource to assist researchers and customers in the identification and interpretation of protein sequence information. Prior to that, the NBRF compiled the first comprehensive collection of macromolecular sequences in the Atlas of Protein Sequence and Structure, published from 1964 to 1974 under the editorship of Margaret Dayhoff. Dayhoff and her research group pioneered in the development of computer methods for the comparison of protein sequences, for the detection of distantly related sequences and duplications within sequences, and for the inference of evolutionary histories from alignments of protein sequences.[8]

Winona Barker and Robert Ledley assumed leadership of the project after the death of Dayhoff in 1983. In 1999, Cathy H. Wu joined NBRF, and later on GUMC, to head the bioinformatics efforts of PIR, and has served first as Principal Investigator and, since 2001, as Director.[citation needed]

For four decades, PIR has provided many protein databases and analysis tools freely accessible to the scientific community, including the Protein Sequence Database (PSD), the first international database (see PIR-International), which grew out of Atlas of Protein Sequences and Structure.[citation needed]

In 2002, PIR – along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics) – were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. As of 2010, PIR offers a wide variety of resources mainly oriented to assist the propagation and standardization of protein annotation: PIRSF,[9] iProClass, and iProLINK.

The Protein Ontology (PRO) is another popular database released by the Protein Information Resource.[10][11]

References

  1. ^ http://pir.georgetown.edu/ Archived 2014-03-12 at the Wayback Machine Official website of PIR at Georgetown University.
  2. ^ Wu, Cathy; Nebert, Daniel W. (2004). "Update on genome completion and annotations: Protein Information Resource". Human Genomics. 1 (3): 229–33. doi:10.1186/1479-7364-1-3-229. PMC 3525084. PMID 15588483.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  3. ^ Wu, C. H. (2003). "The Protein Information Resource". Nucleic Acids Research. 31 (1): 345–347. doi:10.1093/nar/gkg040. PMC 165487. PMID 12520019.
  4. ^ Wu, CH; Huang, H; Arminski, L; Castro-Alvear, J; Chen, Y; Hu, ZZ; Ledley, RS; Lewis, KC; Mewes, HW; Orcutt, BC; Suzek, BE; Tsugita, A; Vinayaka, CR; Yeh, LS; Zhang, J; Barker, WC (2002-01-01). "The Protein Information Resource: an integrated public resource of functional annotation of proteins". Nucleic Acids Research. 30 (1): 35–37. doi:10.1093/nar/30.1.35. ISSN 1362-4962. PMC 99125. PMID 11752247.
  5. ^ Barker, W. C.; Garavelli, J. S.; Hou, Z.; Huang, H.; Ledley, R. S.; McGarvey, P. B.; Mewes, H. W.; Orcutt, B. C.; Pfeiffer, F.; Tsugita, A.; Vinayaka, C. R.; Xiao, C.; Yeh, L. S.; Wu, C. (2001). "Protein Information Resource: A community resource for expert annotation of protein data". Nucleic Acids Research. 29 (1): 29–32. doi:10.1093/nar/29.1.29. PMC 29802. PMID 11125041.
  6. ^ Barker, W. C. (2000). "The Protein Information Resource (PIR)". Nucleic Acids Research. 28 (1): 41–44. doi:10.1093/nar/28.1.41. PMC 102418. PMID 10592177.
  7. ^ George, D. G.; Dodson, R. J.; Garavelli, J. S.; Haft, D. H.; Hunt, L. T.; Marzec, C. R.; Orcutt, B. C.; Sidman, K. E.; Srinivasarao, G. Y.; Yeh, L.-S. L.; Arminski, L. M.; Ledley, R. S.; Tsugita, A.; Barker, W. C. (1997). "The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database". Nucleic Acids Research. 25 (1): 24–27. doi:10.1093/nar/25.1.24. PMC 146415. PMID 9016497.
  8. ^ Izet, M (2016). "The Most Influential Scientists in the Development of Medical informatics (13): Margaret Belle Dayhoff". Acta Inform Med. 24 (4).
  9. ^ Wu, C. H.; Nikolskaya, A.; Huang, H.; Yeh, L. S.; Natale, D. A.; Vinayaka, C. R.; Hu, Z. Z.; Mazumder, R.; Kumar, S.; Kourtesis, P.; Ledley, R. S.; Suzek, B. E.; Arminski, L.; Chen, Y.; Zhang, J.; Cardenas, J. L.; Chung, S.; Castro-Alvear, J.; Dinkov, G.; Barker, W. C. (2004). "PIRSF: Family classification system at the Protein Information Resource". Nucleic Acids Research. 32 (90001): 112D–114. doi:10.1093/nar/gkh097. PMC 308831. PMID 14681371.
  10. ^ "GeorgeTown.edu - Protein Ontology". Archived from the original on 2011-03-10. Retrieved 2017-12-04.
  11. ^ Chicco, Davide; Masseroli, Marco (2019). "Biological and Medical Ontologies: Protein Ontology (PRO)". Encyclopedia of Bioinformatics and Computational Biology. pp. 832–837. doi:10.1016/B978-0-12-809633-8.20396-8. ISBN 9780128114322.
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