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The Gene Ontology Project

The Gene Ontology Project. DNA. gene gene gene gene gene. mRNA. protein. http://cms.frontiersin.org/content/10.3389/neuro.02/007.2008/ html/fnmol-01-007/images/article/image_n/fnmol-01-007-g001.gif.

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The Gene Ontology Project

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  1. The Gene Ontology Project

  2. DNA gene gene gene gene gene mRNA protein

  3. http://cms.frontiersin.org/content/10.3389/neuro.02/007.2008/http://cms.frontiersin.org/content/10.3389/neuro.02/007.2008/ html/fnmol-01-007/images/article/image_n/fnmol-01-007-g001.gif

  4. substrate + O2 = CO2 +H20 product • Gene product: • What does it do? • Where does it do it? • What is the bigger picture? http://ntri.tamuk.edu/cell/ mitochondrion/krebpic.html

  5. Clark et al., 2005 is_a part_of

  6. Clark et al., 2005 is_a part_of

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

  8. See which processes are upregulated or downregulated. time Defense response Immune response Response to stimulus Toll regulated genes JAK-STAT regulated genes Puparial adhesion Molting cycle hemocyanin Amino acid catabolism Lipid metobolism Peptidase activity Protein catabolism Immune response Immune response Toll regulated genes control attacked Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

  9. Current metrics • 3 ontologies • Biological process • Molecular function • Cellular component • 26,933 terms • 5 relationship types • 47,000+ relationships • 40,000,000+ annotations • 88,193 species.

  10. Future plans • Cross products • Function-process links

  11. Cross products: Identify ontologies within ontologies – make computable

  12. Intersection tags / cross products [Term] id: GO:0010064 ! embryonic shoot morphogenesis intersection_of: GO:0010016 ! shoot morphogenesis intersection_of: part_of GO:0009790 ! embryonic development [Term] id: GO:0010101 ! post-embryonic root morphogenesis intersection_of: GO:0010015 ! root morphogenesis intersection_of: part_of GO:0009791 ! post-embryonic development

  13. Cross products (xp) in progress • XPs being set up amongst GO ontologies. • Also with: cell type ontology, uberon (anatomy) ontology, ChEBI (chemical) ontology. • 170+ new relationship types planned.

  14. Link out to other ontologies: • Open Biomedical Ontologies • 54 compatible ontologies • 26 other nearly compatible ontologies http://www.obofoundry.org/

  15. Function-process links http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html

  16. biosynthetic process UDP-glucose metabolic process colanic acid biosynthetic process UTP:glucose-1-phosphate uridylyltransferase activity α-D-glucose 1-phosphate + UTP -> UDP-D-glucose + diphosphate galactose metabolic process carbohydrate catabolic process response to desiccation glucose metabolic process hp hp hp hp hp hp hp Process Function hp = has_part

  17. Lysine biosynthesis pathways

  18. Process lysine biosynthesis is_a lysine biosynthesis 7? is_a is_a is_a is_a is_a is_a lysine biosynthesis 1 lysine biosynthesis 3 lysine biosynthesis 5 lysine biosynthesis 4 lysine biosynthesis 2 lysine biosynthesis 6 Function

  19. Process Lysine Biosynthesis Process B Process C = has_part new GO term Shared function? Function existing GO term Non-shared function

  20. Process Lysine Biosynthesis Relationship explosion Process B Process C (or Editorial office explosion) Function

  21. Tools

  22. OBO-Edit: Ontology Editor Tool

  23. Reasoner finds missing and redundant relationships.

  24. 2006 Consortium Meeting, St. Croix, U.S. Virgin Islands, March 30 - April 3, 2006

  25. E. Coli hub http://www.geneontology.org Reactome

  26. Particular thanks to: Chris Mungall - OBOL, Rule Based Reasoner Cross product system Function process link plan – The electron transport working group OBO-Edit: John Day-Richter, Nomi Harris, Amina Abdulla:

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