A platform to standardize, store, and visualize proteomics experimental data.
With the development of functional genomics research, large-scale proteomics studies are now widespread, presenting significant challenges for data storage, exchange, and analysis. Here we present the Integrated Proteomics Exploring Database (IPED) as a platform for managing proteomics experimental data (both process and result data). IPED is based on the schema of the Proteome Experimental Data Repository (PEDRo), and complies with the General Proteomics Standard (GPS) drafted by the Proteomics Standards Committee of the Human Proteome Organization. In our work, we developed three components for the IPED platform: the IPED client editor, IPED server software, and IPED web interface. The client editor collects experimental data and generates an extensible markup language (XML) data file compliant with PEDRo and GPS; the server software parses the XML data file and loads information into a core database; and the web interface displays experimental results, to provide a convenient graphic representation of data. Given software convenience and data abundance, IPED is a powerful platform for data exchange and presents an important resource for the proteomics community. In its current release, IPED is available at http://www.biosino.org/iped2.
Zheng
Guangyong
G
Bioinformation Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Li
Hong
H
Wang
Chuan
C
Sheng
Quanhu
Q
Fan
Haiwei
H
Yang
Shaoyou
S
Liu
Boshu
B
Dai
Jianliang
J
Zeng
Rong
R
Xie
Lu
L
D000465:Algorithms; D002478:Cells, Cultured; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional; D042783:Endothelial Cells / Q000166:cytology / Q000187:drug effects / Q000378:metabolism; D006801:Humans; D019161:Hydroxymethylglutaryl-CoA Reductase Inhibitors / Q000494:pharmacology; D020407:Internet; D008148:Lovastatin / Q000494:pharmacology; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data*; D012984:Software; D014584:User-Computer Interface
D019161:Hydroxymethylglutaryl-CoA Reductase Inhibitors; D020543:Proteome; D008148:Lovastatin