<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>The central dogma of molecular biology has provided a meaningful principle
for data integration in the field of genomics. In this context, integration reflects
the known transitions from a chromosome to a protein sequence: transcription,
intron splicing, exon assembly and translation. There is no such clear principle for
integrating proteomics data, since the laws governing protein folding and interactivity
are not quite understood. In our effort to bring together independent pieces of
information relative to proteins in a biologically meaningful way, we assess the bias of
bioinformatics resources and consequent approximations in the framework of small-scale
studies. We analyse proteomics data while following both a data-driven (focus
on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial
proteomes) approach. These applications are potentially the source of specialized
complements to classical biological ontologies.</p>
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Comp Funct Genomics. 2004 Mar; 5(2):190-195