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 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 AgBase biocuration interface AgBase database ‘sanity’ check & GOC QC EBI GOA Project GO Consortium database ‘sanity’ check & GOC QC ‘sanity’ check GO analysis tools Microarray developers UniProt db QuickGO browser GO analysis tools Microarray developers Public databases AmiGO browser GO analysis tools Microarray 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