Gene Ontology

Consortiumhttp://

www.geneontology.org/

Clark et al, (2005) Plant PhysSubmitted.

Ontology (for our purposes)

• “an explicit specification of some topic” – Stanford Knowledge Systems Lab

• Includes:– a vocabulary of terms (names for concepts)– defined logical relationships to each– definitions

TactitionTactile sense

Taction

?

Tactition Tactile senseTaction

perception of touch ; GO:0050975

Bud initiation?

= bud initiation

sensu Metazoa

= bud initiation

sensu Saccharomyces

= bud initiation

sensu Viridiplantae

Microarray analysis

Whole genome analysis(J. D. Munkvold et al., 2004)

What GO is not:

• Not a way of unifying databases!

• Not a dictated standard

• Additional ontologies needed to model

biology and experimentation. http://obo.sourceforge.net/

•Molecular Function: elemental activity or task

•Biological Process: broad objective or goal

•Cellular Component: location or complex

The Three Ontologies

•Molecular Function: elemental activity or taskDNA binding, catalysis of a reaction

•Biological Process: broad objective or goal

•Cellular Component: location or complex

The Three Ontologies

•Molecular Function: elemental activity or taskDNA binding, catalysis of a reaction

•Biological Process: broad objective or goalmitosis, signal transduction, metabolism

•Cellular Component: location or complex

The Three Ontologies

•Molecular Function: elemental activity or taskDNA binding, catalysis of a reaction

•Biological Process: broad objective or goalmitosis, signal transduction, metabolism

•Cellular Component: location or complexnucleus, ribosome

The Three Ontologies

•Molecular Function: elemental activity or taskDNA binding, catalysis of a reaction

•Biological Process: broad objective or goalmitosis, signal transduction, metabolism

•Cellular Component: location or complexnucleus, ribosome

The Three Ontologies

6 January 2005: Total terms = 1824493% have definitions

What’s in a GO term?

term: transcription initiation

id: GO:0006352

definition: Processes involved in starting transcription, where transcription is the synthesis of RNA by RNA polymerases using a DNA template.

Annotation

GO cellular component term:mitochondrial inner membrane ; GO:0005743

Where is it?

cytochrome c oxidase

GO molecular function term:cytochrome-c oxidase activity; GO:0004497

What does it do?

4 ferrocytochrome c + O2

=

4 ferricytochrome c + 2 H2O

http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html

GO biological process term:electron transport ; GO:0006118

Which process is this?

Request new terms

go@geneontology.orghttp://sourceforge.net/projects/geneontology

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Clark et al, (2005) Plant PhysSubmitted

GO Slim

http://www.geneontology.org/

Contributors

FlyBase Rat Genome Database DictyBase  WormBase GeneDB S. pombe CompugenMouse Genome Database GeneDB for protozoa Genome Knowledge Base EBI GOA project TIGR Gramene The Arabidopsis Information ResourceThe Zebrafish Information Network Berkeley Drosophila Genome ProjectSaccharomyces Genome DatabaseThe Institute for Genomic ResearchThe GO Editorial Office