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Comp Funct Genomics. 2004 December; 5(8): 642–647. doi: 10.1002/cfg.446. | PMCID: PMC2447471 |
Copyright © 2004 Hindawi Publishing Corporation. Sequence Ontology Annotation Guide Karen Eilbeck  and Suzanna E. Lewis Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, California, 94729-3200, USA, Received November 17, 2004; Revised November 24, 2004; Accepted November 25, 2004. 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. 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. part_of, kind_of, annotations described with SO terms are also better substrates
for validation and visualization software. 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. The Full Text of this article is available as a PDF (223K). These references are in PubMed. This may not be the complete list of references from this article. - Benson Dennis A, Karsch-Mizrachi Ilene, Lipman David J, Ostell James, Wheeler David L. GenBank. Nucleic Acids Res. 2003 Jan 1;31(1):23–27. [PubMed]
- Lewis SE, Searle SMJ, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smithy CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME. Apollo: a sequence annotation editor. Genome Biol. 2002;3(12):RESEARCH0082. [PubMed]
- Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics. 2000 Oct;16(10):944–945. [PubMed]
- Stein Lincoln D, Mungall Christopher, Shu ShengQiang, Caudy Michael, Mangone Marco, Day Allen, Nickerson Elizabeth, Stajich Jason E, Harris Todd W, Arva Adrian, Lewis Suzanna. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 Oct;12(10):1599–1610. [PubMed]
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