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1.  Gene Ontology: looking backwards and forwards 
Genome Biology  2004;6(1):103.
The Gene Ontology consortium began six years ago with a group of scientists who decided to connect our data by sharing the same language for describing it. Its most significant achievement lies in uniting many independent biological database efforts into a cooperative force.
The Gene Ontology consortium began six years ago with a group of scientists who decided to connect our data by sharing the same language for describing it. Its most significant achievement lies in uniting many independent biological database efforts into a cooperative force.
doi:10.1186/gb-2004-6-1-103
PMCID: PMC549054  PMID: 15642104
2.  Sequence Ontology Annotation Guide 
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.
doi:10.1002/cfg.446
PMCID: PMC2447471  PMID: 18629179

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