Transcript 2006-01_PAG_GO_update_jclark

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: 7913
biological_process: 10677
cellular_component: 1805
defined: %95
Immunology improvements
http://www.godatabase.org/
Process ontology
Cell Ontology
• cone cell fate commitment
• retinal_cone_cell
• keratinocyte differentiation
• keratinocyte
• adipocyte differentiation
• fat_cell
• dendritic cell activation
• dendritic_cell
[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 differentiation
relationship: part_of GO:0048699 ! neurogenesis
[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 purpose
is 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
[Term]
id: GO:0030182
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."
[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
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
Mapping Files Uniprot keywords and Interpro2GO updated
http://www.geneontology.org/GO.indices.shtml
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.
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
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