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Gene Ontology Consortium geneontology/

Gene Ontology Consortium http://www.geneontology.org/. Clark et al, (2005) Plant Phys Submitted. Ontology (for our purposes). “an explicit specification of some topic” – Stanford Knowledge Systems Lab Includes: a vocabulary of terms (names for concepts)

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Gene Ontology Consortium geneontology/

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  1. Gene Ontology Consortium http://www.geneontology.org/

  2. Clark et al, (2005) Plant Phys Submitted.

  3. Ontology (for our purposes) • “an explicit specification of some topic”– Stanford Knowledge Systems Lab • Includes: • a vocabulary of terms (names for concepts) • defined logical relationships to each • definitions

  4. Taction Tactition Tactile sense ?

  5. Taction Tactition Tactile sense perception of touch ; GO:0050975

  6. Bud initiation?

  7. = bud initiation sensu Metazoa = bud initiation sensu Saccharomyces = bud initiation sensu Viridiplantae

  8. Microarray analysis Whole genome analysis (J. D. Munkvold et al., 2004)

  9. What GO is not: • Not a way of unifying databases! • Not a dictated standard • Additional ontologies needed to model • biology and experimentation. • http://obo.sourceforge.net/

  10. The Three Ontologies • Molecular Function: elemental activity or task • Biological Process: broad objective or goal • Cellular Component: location or complex

  11. The Three Ontologies • Molecular Function: elemental activity or task • DNA binding, catalysis of a reaction • Biological Process: broad objective or goal • Cellular Component: location or complex

  12. The Three Ontologies • Molecular Function: elemental activity or task • DNA binding, catalysis of a reaction • Biological Process: broad objective or goal • mitosis, signal transduction, metabolism • Cellular Component: location or complex

  13. The Three Ontologies • Molecular Function: elemental activity or task • DNA binding, catalysis of a reaction • Biological Process: broad objective or goal • mitosis, signal transduction, metabolism • Cellular Component: location or complex • nucleus, ribosome

  14. The Three Ontologies • Molecular Function: elemental activity or task • DNA binding, catalysis of a reaction • Biological Process: broad objective or goal • mitosis, signal transduction, metabolism • Cellular Component: location or complex • nucleus, ribosome 6 January 2005: Total terms = 18244 93% have definitions

  15. What’s in a GO term? term: transcription initiation id: GO:0006352 definition: Processes involved in starting transcription, where transcription is the synthesis of RNA by RNA polymerases using a DNA template.

  16. Annotation

  17. Where is it? cytochrome c oxidase GO cellular component term: mitochondrial inner membrane ; GO:0005743

  18. What does it do? 4 ferrocytochrome c + O2 = 4 ferricytochrome c + 2 H2O GO molecular function term: cytochrome-c oxidase activity; GO:0004497

  19. Which process is this? GO biological process term: electron transport ; GO:0006118 http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html

  20. Request new terms go@geneontology.org http://sourceforge.net/projects/geneontology Clark et al, (2005) Plant Phys Submitted

  21. GO Slim

  22. http://www.geneontology.org/

  23. 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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