<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>This Sequence Ontology (SO) [13] aims to unify the way in which we describe
sequence annotations, by providing a controlled vocabulary of terms and the
relationships between them. Using SO terms to label the parts of sequence annotations
greatly facilitates downstream analyses of their contents, as it ensures that annotations
produced by different groups conform to a single standard. This greatly facilitates
analyses of annotation contents and characteristics, e.g. comparisons of UTRs,
alternative splicing, etc. Because SO also specifies the relationships between features,
e.g. <italic>part_of, kind_of</italic>, annotations described with SO terms are also better substrates
for validation and visualization software.</p> <p>This document provides a step-by-step guide to producing a SO compliant file
describing a sequence annotation. We illustrate this by using an annotated gene as an
example. First we show where the terms needed to describe the gene's features are
located in SO and their relationships to one another. We then show line by line how
to format the file to construct a SO compliant annotation of this gene.</p>
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Comp Funct Genomics. 2004 Dec; 5(8):642-647