Publication Type

Journal Article

Version

publishedVersion

Publication Date

3-2006

Abstract

In the field of proteomics, the increasing difficulty to unify the data format, due to the different platforms/instrumentation and laboratory documentation systems, greatly hinders experimental data verification, exchange, and comparison. Therefore, it is essential to establish standard formats for every necessary aspect of proteomics data. One of the recently published data models is the proteomics experiment data repository [Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D. et al., Nat. Biotechnol. 2003, 21, 247-254]. Compliant with this format, we developed the systematic proteomics laboratory analysis and storage hub (SPLASH) database system as an informatics infrastructure to support proteomics studies. It consists of three modules and provides proteomics researchers a common platform to store, manage, search, analyze, and exchange their data. (i) Data maintenance includes experimental data entry and update, uploading of experimental results in batch mode, and data exchange in the original PEDRo format. (ii) The data search module provides several means to search the database, to view either the protein information or the differential expression display by clicking on a gel image. (iii) The data mining module contains tools that perform biochemical pathway, statistics-associated gene ontology, and other comparative analyses for all the sample sets to interpret its biological meaning. These features make SPLASH a practical and powerful tool for the proteomics community.

Keywords

Database, PEDRo, Proteomics data exchange, Proteomics data mining, XML

Discipline

Computer Engineering | Data Storage Systems

Research Areas

Data Science and Engineering

Publication

Proteomics

Volume

6

Issue

6

First Page

1758

Last Page

1769

ISSN

1615-9853

Identifier

10.1002/pmic.200500378

Publisher

Wiley: 12 months

Additional URL

https://doi.org/10.1002/pmic.200500378

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