Introduction to the gene ontology
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Introduction to the Gene Ontology. GO Workshop 3-6 August 2010. 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. The GO Consortium.

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Introduction to the Gene Ontology

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Introduction to the Gene Ontology

GO Workshop

3-6 August 2010

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

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

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

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

GO Working Groups:

Information about:

  • Development projects

  • Meetings

  • Annotation projects

  • Changes to the GO

The Annotation Dilemma

  • Exponential increase in biological data

  • More important than ever to provide annotation for this data

  • How to keep up?

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

GO & PO: literature annotation for rice, computational annotation for rice, maize, sorghum, Brachypodia

  • Literature annotation for Agrobacterium tumefaciens, Dickeya dadantii, Magnaporthe grisea, Oomycetes

  • 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).

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!

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

‘sanity’ check


AgBase Quality Checks & Releases

AgBase Biocurators

‘sanity’ check




AgBase database

GO analysis tools

Microarray developers

‘sanity’ check

UniProt db

QuickGO browser

GO analysis tools

Microarray developers

EBI GOA Project

‘sanity’ check: checks to ensure all appropriate information is captured, no obsolete GO:IDs are used, etc.

‘sanity’ check


Public databases

AmiGO browser

GO analysis tools

Microarray developers

GO Consortium


Sources of GO

  • Primary sources of GO: from the GO Consortium (GOC) & GOC members

    • most up to date

    • most comprehensive

  • 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 annotation

  • 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.

Secondary Sources of GO annotation


    • public databases (eg. NCBI, UniProtKB)

    • genome browsers (eg. Ensembl)

    • array vendors (eg. Affymetrix)


    • What is the original source?

    • When was it last updated?

    • Are evidence codes displayed?

Differences in displaying GO annotations: secondary/tertiary sources.

Learning more about the GO

At the GO Consortium website:

  • FAQs

  • Mailing groups

  • Tools that use GO

  • News about changes and updates

  • publications

  • Login