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Gene Ontology TM(GO) Consortium

http://www.geneontology.org/

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The problem:

Vast amounts of biological data held ingenome and protein databases.

Different names for the same concepts indifferent species.

Makes cross-species comparison difficult.

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Ontology (for our purposes)

an explicit specification of some topic Stanford Knowledge Systems Lab

Includes: a vocabulary of terms (names)

defined logical relationships to each

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W hat GO is not:

Not a way of unifying databases!

Not a dictated standardAdditional ontologies needed to model

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

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Molecular Function : elemental activity or task

Biological Process : broad objective or goal

Cellular Component : location or complex

The Three Ontologies

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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

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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

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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

nucleus, ribosome

The Three Ontologies

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Go network diagram

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GO:0009838 ; abscissionGO:0007568 ; agingGO:0030154 ; cell differentiationGO:0007349 ; cellularizationGO:0009790 ; embryonic developmentGO:0009292 ; genetic transfer GO:0040007 ; growthGO:0007320 ; inseminationGO:0002164 ; larval developmentGO:0010073 ; meristem maintenanceGO:0009933 ; meristem organization

M ore examples:

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GO annotation diagram

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Mitochondrial P450(CC24 PR01238; MITP450CC24)

Annotation

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

W here is it?

M itochondrialp450

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GO molecular function term:monooxygenase activity ; GO:0004497

W hat does it do?

substrate + O 2 = CO 2 +H 20 product

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

GO biological process term:electron transport ; GO:0006118

W hich process is this?

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monooxygenase activity ; GO:0004497

Other gene products:

MGI monooxygenase, DBH-like 1MGI prostaglandin I2 (prostacyclin) synthaseMGI splicing factor 3b, subunit 2SGD flavin-containing monooxygenaseTAIR FERULATE-5-HYDROXYLASE 1

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http://godatabase.org/cgi-bin/go.cgi

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mappings

EC:1.1.1.1 > GO:alcohol dehydrogenase activity ; GO:0004022EC:1.1.1.10 > GO:L-xylulose reductase activity ; GO:0050038EC:1.1.1.104 > GO:4-oxoproline reductase activity ; GO:0016617EC:1.1.1.105 > GO:retinol dehydrogenase activity ; GO:0004745

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Contributors

F lyBase Rat Genome DatabaseDictyBase W ormBaseGeneDB S. pombe CompugenMouse Genome Database GeneDB for protozoaGenome Knowledge Base EBI GOA project

TIGR GrameneThe Arabidopsis Information ResourceThe Zebrafish Information NetworkBerkeley Drosophila Genome ProjectSaccharomyces Genome DatabaseThe Institute for Genomic Research