The%20Gene%20Ontology%20Consortium

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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.geneontology.org/GO.tools.shtml
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http//www.geneontology.org/GO.tools.shtml
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http//www.godatabase.org/
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http//www.godatabase.org/
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Ontology Content
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Terms molecular_function 7913 biological_proces
s 10677 cellular_component 1805 defined 95
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Immunology improvements
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http//www.godatabase.org/
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Process ontology
Cell Ontology

• cone cell fate commitment

• retinal_cone_cell

• keratinocyte

• keratinocyte differentiation

• fat_cell

• adipocyte differentiation

• dendritic_cell

• dendritic cell activation

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Term id GO0030182 name neuron
differentiation namespace biological_process def
"The process whereby a relatively unspecialized
cell acquires specialized features of a neuron."
GOmah is_a GO0030154 ! cell
differentiation relationship part_of GO0048699
! neurogenesis
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Term id CL0000540 name neuron def "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." MESHA.08.663 xref_analog
FBbt00005106 xref_analog FBbt00005146 is_a
CL0000393 ! electrically responsive cell is_a
CL0000404 ! electrically signaling
cell relationship develops_from CL0000031 !
neuroblast
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Term id GO0030182 name neuron
differentiation namespace 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." MESHA.08.663, GOmah is_a
GO0030154 ! cell differentiation intersection
_of is_a GO0030154 ! cell
differentiation intersection_of has_participant
CL0000540 ! 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.shtmlsc
ript
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Mapping Files - Uniprot keywords and
Interpro2GO updated
http//www.geneontology.org/GO.indices.shtml
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Publications
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.
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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, 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.
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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 Gramene The Arabidopsis
Information Resource The Zebrafish Information
Network Berkeley Drosophila Genome
Project Saccharomyces Genome Database The
Institute for Genomic Research The GO Editorial
Office