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The Gene Ontology Consortium geneontology 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.

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The Gene Ontology Consortium geneontology Jennifer Clark, GO Editorial Office

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  1. The Gene Ontology Consortium www.geneontology.org Jennifer Clark, GO Editorial Office

  2. http://www.geneontology.org/

  3. Consortium Tools

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

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

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

  7. http://www.godatabase.org/

  8. http://www.godatabase.org/

  9. Ontology Content

  10. Terms: molecular_function: 7913 biological_process: 10677 cellular_component: 1805 defined: %95

  11. Immunology improvements

  12. http://www.godatabase.org/

  13. cone cell fate commitment retinal_cone_cell Process ontology Cell Ontology • keratinocyte • keratinocyte differentiation • fat_cell • adipocyte differentiation • dendritic_cell • dendritic cell activation

  14. [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

  15. [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

  16. [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

  17. Other Ontologies that can be aligned with GO • Chemical ontologies • 3,4-dihydroxy-2-butanone-4-phosphate synthase activity • Anatomy ontologies • metanephros development

  18. Annotation

  19. Gene Association file QC - Redundancy http://www.geneontology.org/GO.annotation.shtml#script

  20. Mapping Files - Uniprot keywords and Interpro2GO updated http://www.geneontology.org/GO.indices.shtml

  21. 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.

  22. 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.

  23. Outreach to new annotation groups

  24. http://www.geneontology.org/

  25. 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

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