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Annotation and Assigning a Gene Function

Human curators and automated programs such as RAST assign functional roles to genes, and the process is called annotation. In most contexts, people use the term annotation to refer to assignments of function to the genes within a single organism. We certainly use the term in this sense, but we also use it to describe the process of assigning functions to corresponding genes from numerous genomes. Our basic approach to annotation is to ask our curators to annotate the genes included in a subsystem (e.g., glycolysis) across all genomes. This process of annotation of the genes within a subsystem across a set of genomes, rather than annotation of genes within a single genome, allows our curators to focus on a constrained set of functional roles and attempt to accurately identify exactly what variant, if any, of a subsystem exists in each of the genomes.

We use the term annotation to refer to assigning functions or commentary notes to genes (either within a single organism or to a constrained set of gene/protein families across a set of organisms). This activity is closely related to the construction of subsystems and protein families (which we call FIGfams).

Further reading:

• Assertions
• Annotation Clearinghouse
• Functional Roles
• How to Annotate a Genome