Scripps VIVO scripps research logo

  • Index
  • Log in
  • Home
  • People
  • Organizations
  • Research
  • Events
Search form

A systematic approach to modeling, capturing, and disseminating proteomics experimental data

Academic Article
uri icon
  • Overview
  • Identity
  • Additional Document Info
  • View All
scroll to property group menus

Overview

authors

  • Taylor, C. F.
  • Paton, N. W.
  • Garwood, K. L.
  • Kirby, P. D.
  • Stead, D. A.
  • Yin, Z. K.
  • Deutsch, E. W.
  • Selway, L.
  • Walker, J.
  • Riba-Garcia, I.
  • Mohammed, S.
  • Deery, M. J.
  • Howard, J. A.
  • Dunkley, T.
  • Aebersold, R.
  • Kell, D. B.
  • Lilley, K. S.
  • Roepstorff, P.
  • Yates III, John
  • Brass, A.
  • Brown, A. J. P.
  • Cash, P.
  • Gaskell, S. J.
  • Hubbard, S. J.
  • Oliver, S. G.

publication date

  • 2003

journal

  • Nature Biotechnology  Journal

abstract

  • Both the generation and the analysis of proteome data are becoming increasingly widespread, and the field of proteomics is moving incrementally toward high-throughput approaches. Techniques are also increasing in complexity as the relevant technologies evolve. A standard representation of both the methods used and the data generated in proteomics experiments, analogous to that of the MIAME (minimum information about a microarray experiment) guidelines for transcriptomics, and the associated MAGE (microarray gene expression) object model and XML (extensible markup language) implementation, has yet to emerge. This hinders the handling, exchange, and dissemination of proteomics data. Here, we present a UML (unified modeling language) approach to proteomics experimental data, describe XML and SQL (structured query language) implementations of that model, and discuss capture, storage, and dissemination strategies. These make explicit what data might be most usefully captured about proteomics experiments and provide complementary routes toward the implementation of a proteome repository.

subject areas

  • Database Management Systems
  • Databases, Protein
  • Documentation
  • Hypermedia
  • Information Dissemination
  • Information Storage and Retrieval
  • Models, Molecular
  • Protein Conformation
  • Proteins
  • Proteomics
  • Sequence Analysis, Protein
  • Software
  • Software Design
  • User-Computer Interface
scroll to property group menus

Identity

International Standard Serial Number (ISSN)

  • 1087-0156

Digital Object Identifier (DOI)

  • 10.1038/nbt0303-247

PubMed ID

  • 12610571
scroll to property group menus

Additional Document Info

start page

  • 247

end page

  • 254

volume

  • 21

issue

  • 3

©2019 The Scripps Research Institute | Terms of Use | Powered by VIVO

  • About
  • Contact Us
  • Support