Transcript Slide 1
The Gene Ontology Project DNA gene gene gene gene mRNA protein gene http://cms.frontiersin.org/content/10.3389/neuro.02/007.2008/ html/fnmol-01-007/images/article/image_n/fnmol-01-007-g001.gif substrate + O2 = CO2 +H20 product http://ntri.tamuk.edu/cell/ mitochondrion/krebpic.html Gene product: • What does it do? • Where does it do it? • What is the bigger picture? Clark et al., 2005 is_a part_of Clark et al., 2005 is_a part_of Whole genome analysis (J. D. Munkvold et al., 2004) 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 attacked control Selected Gene Tree: pearson Coloredby by:: ne Tree: pear s on lw n3d ...lw n3d ...Colored Branch color classification: Set_LW_n3d_5p_... Gene List: r c lass ific ation: Set_LW_n3d_5p_... Gene Lis t: Copy of Copy (Def a... Copy of ofCC5_RMA opy of C5_RMA ( Def a... allall genes (14010)( 14010) genes Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI. 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. Future plans • Cross products • Function-process links Cross products: Identify ontologies within ontologies – make computable 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 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. Link out to other ontologies: • Open Biomedical Ontologies – 54 compatible ontologies – 26 other nearly compatible ontologies http://www.obofoundry.org/ Function-process links http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html biosynthetic UDP-glucose metabolic process process galactose carbohydrate metabolic catabolic response process to desiccation process glucose metabolic process Process hp hp hp hp hp hp UTP:glucose-1-phosphate uridylyltransferase activity α-D-glucose 1-phosphate + UTP -> UDP-D-glucose + diphosphate Function hp = has_part colanic acid biosynthetic process hp Lysine biosynthesis pathways Process lysine biosynthesis is_a is_a is_a is_a is_a is_a lysine biosynthesis 7? is_a lysine biosynthesis 1 Function lysine lysine biosynthesis biosynthesis 3 5 lysine lysine lysine biosynthesis biosynthesis biosynthesis 4 2 6 Process Lysine Biosynthesis Process B Process C = has_part Function Shared function? Non-shared function new GO term existing GO term Process Lysine Biosynthesis Process B Function Relationship explosion (or Editorial office explosion) Process C Tools OBO-Edit: Ontology Editor Tool Reasoner finds missing and redundant relationships. 2006 Consortium Meeting, St. Croix, U.S. Virgin Islands, March 30 - April 3, 2006 E. Coli hub http://www.geneontology.org Reactome 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: