The Gene Ontology Consortium Jennifer Clark, GO Editorial Office.

The Gene Ontology Consortium

www.geneontology.org

Jennifer Clark, GO Editorial Office

http://www.geneontology.org/

Consortium Tools

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

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

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

http://www.godatabase.org/

http://www.godatabase.org/

Ontology Content

Terms:

molecular_function: 7913biological_process: 10677cellular_component: 1805

defined: %95

Immunology improvements

http://www.godatabase.org/

• cone cell fate commitment • retinal_cone_cell

• keratinocyte differentiation • keratinocyte

• adipocyte differentiation • fat_cell

• dendritic cell activation • dendritic_cell

Process ontology Cell Ontology

[Term]id: GO:0030182name: neuron differentiationnamespace: 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

[Term]id: CL:0000540name: neuron

def: "The basic cellular unit of nervous tissue. Each neuronconsists 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:00005106xref_analog: FBbt:00005146is_a: CL:0000393 ! electrically responsive cellis_a: CL:0000404 ! electrically signaling cellrelationship: develops_from CL:0000031 ! neuroblast

[Term]id: GO:0030182name: neuron differentiationnamespace: biological_process

def: "The process whereby a relatively unspecialized cell acquires 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 differentiationintersection_of: is_a GO:0030154 ! cell differentiationintersection_of: has_participant CL:0000540 ! neuron

Other Ontologies that can be aligned with GO

• Chemical ontologies– 3,4-dihydroxy-2-butanone-4-phosphate synthase activity

• Anatomy ontologies– metanephros development

Annotation

Gene Association file QC - Redundancy

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

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

Mapping Files -

Uniprot keywords and Interpro2GO updated

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. Nucleic Acids Res. 2005 ; 33: D485-D491.

Publications

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, Mueller L, 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. Nucleic Acids Res. 2006 ; 34: D322-D326.

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.

Outreach to new annotation groups

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