Nucleic Acids Research, Vol 27, Issue 1 69-73, Copyright © 1999 by Oxford University Press
PE Hodges, AH McKee, BP Davis, WE Payne and JI Garrels
The Yeast Proteome Database (YPD) is a model for the organization and
presentation of comprehensive protein information. Based on the detailed
curation of the scientific literature for the yeast Saccharomyces
cerevisiae, YPD contains more than 50 000 annotations lines derived from
the review of 8500 research publications. The information concerning each
of the approximately 6100 yeast proteins is structured around a convenient
one-page format, the Yeast Protein Report, with additional information
provided as pop-up windows. Protein classification schema have been revised
this year, defining each protein's cellular role, function and pathway, and
adding a Functional to the Yeast Protein Report. These changes provide the
user with a succinct summary of the protein's function and its place in the
biology of the cell, and they enhance the power of YPD Search functions.
Precalculated sequence alignments have been added, to provide a crossover
point for comparative genomics. The first transcript profiling data has
been integrated into the YPD Protein Reports, providing the framework for
the presentation of genome-wide functional data. The Yeast Proteome
Database can be accessed on the Web at http://www.proteome.com/YPDhome.html
ARTICLES
The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data
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 |
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