Introduction to the Gene Ontology

GO Workshop3-6 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

http://www.geneontology.org/

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

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:

http://wiki.geneontology.org/index.php/Main_Page

http://wiki.geneontology.org/index.php/Main_Page

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

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).

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

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.

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

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

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

Differences in displaying GO annotations: secondary/tertiary sources.

At the GO Consortium website: FAQs Mailing groups Tools that use GO News about changes and updates publications

Learning more about the GO