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The Gene Ontology (GO) is widely recognized as the premier tool for the organization and functional annotation of molecular aspects of cellular systems. However, for many immunologists the use of GO is a very foreign concept. Indeed, as a controlled vocabulary, GO can almost be considered a new language, and it can be difficult to appreciate the use and value of this approach for understanding the immune system. This review reflects on the application of GO to the field of immunology and explains the process of GO annotation. Finally, this review hopes to inspire immunologists to invest time and energy in improving both the content of the GO and the quality of GO annotations associated with genes of immunological interest.

Until recently, biologists have concentrated on studying specifi c pathways or individual molecules as an approach to unravelling the intricate details of cellular events. However recent advances in high-throughput proteomic methodologies have made it possible to profi le the global compositions of entire tissues, organelles or interactomes at specifi c time points or under particular developmental or disease states. While such methods provide researchers with a greater understanding of large-scale, complex biological changes, it has necessitated an increasing reliance on standardised annotation to link results to known biological activities. The Gene Ontology (GO) Consortium provides standardised functional annotations, which support high-throughput analyses and systems biology by enabling genes or proteins to be classifi ed and grouped according to their function, involvement in a particular process or subcellular location, providing researchers with an indication of underlying mechanisms behind a certain phenotype. In this article we provide an overview of the Gene Ontology, its uses and the software available for the analysis of proteomic data. Many of the examples presented in this paper relate to cardiovascular studies, the focus of a new GO annotation initiative. Abbreviations

SUMMARY A Vickers M85A flying-spot microdensitometer has been linked to a standard BBC model B microcomputer with a commercially available interface, and programs developed in which the computer controls step-wise scanning of the specimen. At each image point thirty-two absorbance readings are made and the average value is stored in the computer memory at 8-bit resolution; a complete 48x48 raster takes less than 5 s. An image of the specimen displayed on the monitor uses eight different pseudo-grey-level characters, and the manner in which the 256 possible absorbance values are represented on the screen can be altered by the user. A mask of arbitrary shape and size, drawn on the screen under key-board control, makes it possible to measure the integrated absorbance of even small, irregular and closely packed specimens such as individual bands in Drosophila polytene chromosomes. The coefficient of variation of repeated measurements of a Feulgen-stained frog nucleus is typically better than 1%. Displayed images can be printed on a dot-matrix printer, and data stored on disc for subsequent analysis. The techniques can readily be modified and adapted for other purposes, some of which are briefly discussed.