Introduction to the Gene Ontology
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Transcript of Introduction to the Gene Ontology
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Introduction to the Gene Ontology
GO Workshop3-6 August 2010
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Introduction to GO
GO and the GO Consortium (GOC) What the GOC does (and doesn’t do) GO Groups Working groups GO Wiki Dilemma: annotation strategies Sources for GO
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http://www.geneontology.org/
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The GO Consortium
began as a collaboration between FlyBase (Drosophila), the Saccharomyces Genome Database (SGD) and the Mouse Genome Database (MGD), in 1998
GO Consortium groups are actively involved in developing the GO, providing annotations and supporting use of the GO
http://www.geneontology.org/GO.consortiumlist.shtml
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The GO Consortium provides:
central repository for ontology updates and annotations
central mechanism for changing GO terms (adding, editing, deleting)
quality checking for annotations consistency checks for how annotations
are made by different groups central source of information for users co-ordination of annotation effort
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GO Consortium and GO Groups:
groups decide gene product set to annotate
biocurator training tool development mostly by groups
many non-consortium groups education and training by groups outreach to biocurators/databases by
GOC
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GO Working Groups:
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http://wiki.geneontology.org/index.php/Main_Page
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http://wiki.geneontology.org/index.php/Main_Page
Information about: Development projects Meetings Annotation projects Changes to the GO
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The Annotation Dilemma
Exponential increase in biological data More important than ever to provide
annotation for this data How to keep up?
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Annotation Strategy
Experimental data Many species have a body of published,
experimental data Detailed, species-specific annotation: ‘depth’ Requires manual annotation of literature slow
Computational analysis Can be automated faster Gives ‘breadth’ of coverage across the genome Annotations are general Relatively few annotation pipelines
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GO & PO: literature annotation for rice, computational annotation for rice, maize, sorghum, Brachypodia
1. Literature annotation for Agrobacterium tumefaciens, Dickeya dadantii, Magnaporthe grisea, Oomycetes
2. Computational annotation for Pseudomonas syringae pv tomato, Phytophthora spp and the nematode Meloidogyne hapla.
Literature annotation for chicken, cow, maize, cotton;
Computational annotation for agricultural species & pathogens.
literature annotation for human; computational annotation for UniProtKB entries (237,201 taxa).
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Community Annotation Researchers are the domain experts – but
relatively few contribute to annotation time 'reward' & 'employer/funding agency recognition' training – easy to use tools, clear instructions
Required submission Community annotation
Groups with special interest do focused annotation or ontology development
As part of a meeting/conference or distributed (eg. wikis)
Students!
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Releasing GO Annotations GO annotations are stored at individual
databases Sanity checks as data is entered – is all the
data required filled in? Databases do quality control (QC) checks
and submit to GO GO Consortium runs additional QC and
collates annotations Checked annotations are picked up by GO
users eg. public databases, genome browsers, array
vendors, GO expression analysis tools
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AgBase Biocurators
AgBasebiocuration
interface
AgBase database
‘sanity’ check
‘sanity’ check& GOC QC
EBI GOA Project
GO Consortiumdatabase
‘sanity’ check& GOC
QC ‘sanity’ check
GO analysis tools Microarray developers
UniProt dbQuickGO browserGO analysis toolsMicroarray developers
Public databases AmiGO browserGO analysis toolsMicroarray developers
AgBase Quality Checks & Releases
‘sanity’ check: checks to ensure all appropriate information is captured, no obsolete GO:IDs are used, etc.
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1. Primary sources of GO: from the GO Consortium (GOC) & GOC members
most up to date most comprehensive
2. Secondary sources: other resources that use GO provided by GOC members
public databases (eg. NCBI, UniProtKB) genome browsers (eg. Ensembl) array vendors (eg. Affymetrix) GO expression analysis tools
Sources of GO
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Different tools and databases display the GO annotations differently.
Since GO terms are continually changing and GO annotations are continually added, need to know when GO annotations were last updated.
Sources of GO annotation
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EXAMPLES: public databases (eg. NCBI, UniProtKB) genome browsers (eg. Ensembl) array vendors (eg. Affymetrix)
CONSIDERATIONS: What is the original source? When was it last updated? Are evidence codes displayed?
Secondary Sources of GO annotation
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Differences in displaying GO annotations: secondary/tertiary sources.
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At the GO Consortium website: FAQs Mailing groups Tools that use GO News about changes and updates publications
Learning more about the GO