Open AccessSequence Ontology annotation guide
Author(s) -
Eilbeck Karen,
Lewis Suzanna E.
Publication year - 2004
Publication title -
comparative and functional genomics
Language(s) - English
Resource type - Journals
eISSN - 1532-6268
pISSN - 1531-6912
DOI - 10.1002/cfg.446
Subject(s) - annotation , computer science , information retrieval , sequence (biology) , ontology , software , construct (python library) , gene annotation , gene ontology , vocabulary , controlled vocabulary , visualization , natural language processing , data mining , artificial intelligence , programming language , genome , gene , biology , genetics , philosophy , gene expression , linguistics , epistemology
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. Copyright © 2005 John Wiley & Sons, Ltd.