The Gene Ontology (GO) project provides a controlled vocabulary to facilitate high-quality functional gene annotation for all species. Genes in biological databases are linked to GO terms, allowing biologists to ask questions about gene function in a manner independent of species. This tutorial provides an introduction for biologists to the GO resources and covers three of the most common methods of querying GO: by individual gene, by gene function and by using a list of genes. [For the sake of brevity, the term gene is used throughout this paper to refer to genes and their products (proteins and RNAs). GO annotations are always based on the characteristics of gene products, even though it may be the gene that is cited in the annotation.].