The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI)

被引：46

作者：

Taylor, Chris F. ^{[1
]}

Hermjakob, Henning

Julian, Randall K., Jr.

Garavelli, John S.

Aebersold, Ruedi

Apweiler, Rolf

机构：

[1] EBI, EMBL, Cambridge CB10 1SD, England

[2] Indigo Biosyst, Indianapolis, IN USA

[3] Swiss Fed Inst Technol, Zurich, Switzerland

[4] Univ Zurich, Zurich, Switzerland

来源：

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY | 2006年 / 10卷 / 02期

关键词：

D O I：

10.1089/omi.2006.10.145

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

This article describes the origins, working practices and various development projects of the HUman Proteome Organisation's Proteomics Standards Initiative (HUPO PSI), specifically, our work on reporting requirements, data exchange formats and controlled vocabulary terms. We also offer our view of the two functional genomics projects in which the PSI plays a role (FuGE and FuGO), discussing their impact on our process and laying out the benefits we see as accruing, both to the PSI and to biomedical science as a whole as a result of their widespread acceptance. This paper is part of the special issue of OMICS on data standards.

引用

页码：145 / 151

页数：7

共 7 条

[1] Minimum information about a microarray experiment (MIAME) - toward standards for microarray data [J].

Brazma, A ;

Hingamp, P ;

Quackenbush, J ;

Sherlock, G ;

Spellman, P ;

Stoeckert, C ;

Aach, J ;

Ansorge, W ;

Ball, CA ;

Causton, HC ;

Gaasterland, T ;

Glenisson, P ;

Holstege, FCP ;

Kim, IF ;

Markowitz, V ;

Matese, JC ;

Parkinson, H ;

Robinson, A ;

Sarkans, U ;

Schulze-Kremer, S ;

Stewart, J ;

Taylor, R ;

Vilo, J ;

Vingron, M .

NATURE GENETICS, 2001, 29 (04) :365-371

[2] HUPO brain proteome project: aims and needs in proteomics [J].

Hamacher, M ;

Meyer, HE .

EXPERT REVIEW OF PROTEOMICS, 2005, 2 (01) :1-3

[3] The human Proteome organization a - Mission to advance proteome knowledge [J].

Hanash, S ;

Celis, JE .

MOLECULAR & CELLULAR PROTEOMICS, 2002, 1 (06) :413-414

[4] The HUPOPSI's Molecular Interaction format - a community standard for the representation of protein interaction data [J].

Hermjakob, H ;

Montecchi-Palazzi, L ;

Bader, G ;

Wojcik, R ;

Salwinski, L ;

Ceol, A ;

Moore, S ;

Orchard, S ;

Sarkans, U ;

von Mering, C ;

Roechert, B ;

Poux, S ;

Jung, E ;

Mersch, H ;

Kersey, P ;

Lappe, M ;

Li, YX ;

Zeng, R ;

Rana, D ;

Nikolski, M ;

Husi, H ;

Brun, C ;

Shanker, K ;

Grant, SGN ;

Sander, C ;

Bork, P ;

Zhu, WM ;

Pandey, A ;

Brazma, A ;

Jacq, B ;

Vidal, M ;

Sherman, D ;

Legrain, P ;

Cesareni, G ;

Xenarios, L ;

Eisenberg, D ;

Steipe, B ;

Hogue, C ;

Apweiler, R .

NATURE BIOTECHNOLOGY, 2004, 22 (02) :177-183

[5] Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database [J].

Omenn, GS ;

States, DJ ;

Adamski, M ;

Blackwell, TW ;

Menon, R ;

Hermjakob, H ;

Apweiler, R ;

Haab, BB ;

Simpson, RJ ;

Eddes, JS ;

Kapp, EA ;

Moritz, RL ;

Chan, DW ;

Rai, AJ ;

Admon, A ;

Aebersold, R ;

Eng, J ;

Hancock, WS ;

Hefta, SA ;

Meyer, H ;

Paik, YK ;

Yoo, JS ;

Ping, PP ;

Pounds, J ;

Adkins, J ;

Qian, XH ;

Wang, R ;

Wasinger, V ;

Wu, CY ;

Zhao, XH ;

Zeng, R ;

Archakov, A ;

Tsugita, A ;

Beer, I ;

Pandey, A ;

Pisano, M ;

Andrews, P ;

Tammen, H ;

Speicher, DW ;

Hanash, SM .

PROTEOMICS, 2005, 5 (13) :3226-3245

[6] The proteomics standards initiative [J].

Orchard, S ;

Hermjakob, H ;

Apweiler, R .

PROTEOMICS, 2003, 3 (07) :1374-1376

[7] A common open representation of mass spectrometry data and its application to proteomics research [J].

Pedrioli, PGA ;

Eng, JK ;

Hubley, R ;

Vogelzang, M ;

Deutsch, EW ;

Raught, B ;

Pratt, B ;

Nilsson, E ;

Angeletti, RH ;

Apweiler, R ;

Cheung, K ;

Costello, CE ;

Hermjakob, H ;

Huang, S ;

Julian, RK ;

Kapp, E ;

McComb, ME ;

Oliver, SG ;

Omenn, G ;

Paton, NW ;

Simpson, R ;

Smith, R ;

Taylor, CF ;

Zhu, WM ;

Aebersold, R .

NATURE BIOTECHNOLOGY, 2004, 22 (11) :1459-1466

← 1 →