What is beyond the scope of the GO project?

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Almost as important as understanding the scope of the GO project is understanding what the GO project is not. The most common misapprehensions are (1) that the GO is a system for naming genes and proteins and (2) that the GO attempts to describe all of biology. The GO neither names genes or gene products, nor does it attempt to provide structured vocabularies beyond its three domains: molecular function, biological process and cellular component. GO is not a nomenclature for genes or gene products. The vocabularies describe molecular phenomena (e.g. programmed cell death), not biological objects (e.g. proteins or genes). Sharing gene product names would entail tracking evolutionary histories and reflecting both orthologous and paralogous relationships between gene products. Different research communities have different naming conventions. Different organisms have different numbers of members in gene families. The GO project focuses on the development of vocabularies to describe attributes of biological objects, not on the naming of the objects themselves. This point is particularly important to understand because many genes and gene products are named for their function.