gene ont

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The Gene Ontology Consortium

www.geneontology.org

Jennifer Clark, GO Editorial Office

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http://www.geneontology.org/

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Consortium Tools

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http://www.geneontology.org/GO.tools.shtml

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http://www.godatabase.org/

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Ontology Content

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Terms:

molecular_function: 7913

biological_process: 10677

cellular_component: 1805

defined: %95

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Immunology improvements

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cone cell fate commitment retinal_cone_cell

keratinocyte differentiation keratinocyte

adipocyte differentiation fat_cell

dendritic cell activation dendritic_cell

Process ontology Cell Ontology

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[Term]

id: GO:0030182

name: neuron differentiation

namespace: biological_process

def: "The process whereby a relatively unspecialized cell

acquires specialized features of a neuron." [GO:mah]

is_a: GO:0030154 ! cell differentiationrelationship: part_of GO:0048699 ! neurogenesis

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[Term]id: CL:0000540

name: neuron

def: "The basic cellular unit of nervous tissue. Each neuron

consists of a body\, an axon\, and dendrites. Their purposeis to receive\, conduct\, and transmit impulses in the

nervous system." [MESH:A.08.663]

xref_analog: FBbt:00005106

xref_analog: FBbt:00005146

is_a: CL:0000393 ! electrically responsive cell

is_a: CL:0000404 ! electrically signaling cell

relationship: develops_from CL:0000031 ! neuroblast

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[Term]

id: GO:0030182

name: neuron differentiation

namespace: biological_process

def: "The process whereby a relatively unspecialized cellacquires specialized features of a neuron. The basic cellular

unit of nervous tissue. Each neuron consists of a body\, an

axon\, and dendrites. Their purpose is to receive\, conduct\,

and transmit impulses in the nervous system."

[MESH:A.08.663, GO:mah]

is_a: GO:0030154 ! cell differentiation

intersection_of: is_a GO:0030154 ! cell differentiation

intersection_of: has_participant CL:0000540 ! neuron

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Other Ontologies that can be

aligned with GO

Chemical ontologies

3,4-dihydroxy-2-butanone-4-phosphate synthase activity

Anatomy ontologies metanephros development

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Annotation

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Gene Association file QC - Redundancy

http://www.geneontology.org/GO.annotation.shtml#script

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http://www.geneontology.org/GO.indices.shtml

Mapping Files -

Uniprot keywords and Interpro2GO updated

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Lomax J, The Gene Ontology Consortium

Get ready to GO! A biologist's guide to the Gene Ontology.Brief Bioinform. 2005 ; 6: 298-304.

Clark JI, Brooksbank C, Lomax J

It's all GO for plant scientists.

Plant Physiol. 2005 ; 138: 1268-1279.

Harris MA, Lomax J, Ireland A, Clark JI

The Gene Ontology project.

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Part 4,

Bioinformatics [Subramaniam S (ed.), Wiley and Sons, Inc., New York.].

2005

Arnaud MB, Costanzo MC, Skrzypek MS, Binkley G, Lane C, Miyasato SR,

Sherlock G

The Candida Genome Database (CGD), a community resource for Candida

albicans gene and protein information.

Nucleic Acids Res. 2005 ; 33: D358-D363.

Drabkin HJ, Hollenbeck C, Hill DP, Blake JA

Ontological visualization of protein-protein interactions.

BMC Bioinformatics. 2005 ; 6: 29.

de la Cruz N et al.

The Rat Genome Database (RGD): developments towards a phenome database.


Publications

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Lewis SE

Gene Ontology: looking backwards and forwards.

Genome Biology. 2005 ; 6: 103.

Haas BJ et al.

Complete reannotation of the Arabidopsis genome: methods, tools, protocols

and the final release.

BMC Biol. 2005 ; 3: 7.

Zhang P, Foerster H, Tissier CP, MuellerL, Paley S, Karp PD, Rhee SY

MetaCyc and AraCyc. Metabolic pathway databases for plant research.

Plant Physiol. 2005 ; 138: 27-37.

The Gene Ontology Consortium

The Gene Ontology (GO) project in 2006.


Stover NA, Krieger CJ, Binkley G, Dong Q, Fisk DG, Nash R, Sethuraman A,

Weng S, Cherry JM

Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena

thermophila research.

Nucleic Acids Res. 2006 ; 34: D500-503.

Hirschman JE et al.

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD)

presenting an overview of the Saccharomyces cerevisiae genome.

Nucleic Acids Res. 2006 ; 34: D442-445.

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Outreach to new annotation groups

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http://www.geneontology.org/

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Contributors

FlyBase Rat Genome Database

DictyBase WormBase

GeneDB S. pombe Compugen

Mouse Genome Database GeneDB for protozoa

Genome Knowledge Base EBI GOA project

TIGR GrameneThe Arabidopsis Information Resource

The Zebrafish Information Network

Berkeley Drosophila Genome Project

Saccharomyces Genome Database

The Institute for Genomic ResearchThe GO Editorial Office

gene ont

Documents