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Gene Ontology Project http://www.geneontology.org/ Who is citing GO? 450 Gene Expression studies Clinical applications Other GO Tools Biological Databases GO Annotation Predictions Data and Text mining OBO Ontologies EST annotation Proteomics studies Protein Annotation GO Consortium Genome Annotation 1063 publications GO annotations Comparative genomics and evolutionary analysis over 284 Journals Supporting predictions Network modeling and analysis overviews of GO 0 50 100 150 200 250 300 350 400 450 http://www.geneontology.org/cgi-bin/biblio.cgi 500 Week ending 25th September 2006 NIH funded experimental research that uses the GO 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. National Institute on Alcohol Abuse and Alcoholism (NIAAA) National Institute on Aging (NIA) National Institute of Allergy and Infectious Diseases (NIAID) National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) National Center for Complementary and Alternative Medicine (NCCAM) National Cancer Institute (NCI) National Institute on Drug Abuse (NIDA) National Institute on Deafness and Other Communication Disorders (NIDCD) National Institute of Dental & Craniofacial Research (NIDCR) National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) National Institute of Biomedical Imaging and Bioengineering (NIBIB) National Institute of Environmental Health Sciences (NIEHS) 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. National Eye Institute (NEI) National Institute of General Medical Sciences (NIGMS) National Institute of Child Health and Human Development (NICHD) National Human Genome Research Institute (NHGRI) National Heart, Lung and Blood Institute (NHLBI) National Library of Medicine (NLM) National Center on Minority Health and Health Disparities (NCMHD) National Institute of Mental Health (NIMH) National Institute of Nursing Research (NINR) National Institute of Neurological Disorders and Stroke (NINDS) National Center for Research Resources (NCRR) Fogarty International Center (FIC) Sample of 77 research papers, both intra-mural & extra-mural research. Companies • NLP & Ontology Products BioWisdom, IBM • Array Products and data analysis Affymetrix, Spotfire • Products that use GO Clontech, Inpharmatica • Reagents & services Sigma, Abnova • Big Pharmas AstraZeneca Clark et al., 2005 is_a part_of Clark et al., 2005 Whole genome analysis (J. D. Munkvold et al., 2004) …analysis of high-throughput data according to GO MicroArray data analysis 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 catabloism Immune response Immune response Toll regulated genes attacked control Selected Gene Tree: pearson Coloredby by:: ene Tree: pear s on lw n3d ...lw n3d ...Colored Branch color classification: Set_LW_n3d_5p_... Gene List: or c lass ific ation: Set_LW_n3d_5p_... Gene Lis t: Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI. Copy of Copy (Def a... Copy of ofCC5_RMA opy of C5_RMA ( Def a... allall genes (14010)( 14010) genes P05147 P05147 PMID: 2976880 P05147 PMID: 2976880 GO:0047519 P05147 PMID: 2976880 IDA GO:0047519 P05147 PMID: 2976880 IDA GO:0047519 P05147 PMID: 2976880 IDA GO:0047519 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) …analysis of high-throughput data according to GO MicroArray data analysis 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 catabloism Immune response Immune response Toll regulated genes attacked control Selected Gene Tree: pearson Coloredby by:: ene Tree: pear s on lw n3d ...lw n3d ...Colored Branch color classification: Set_LW_n3d_5p_... Gene List: or c lass ific ation: Set_LW_n3d_5p_... Gene Lis t: Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI. Copy of Copy (Def a... Copy of ofCC5_RMA opy of C5_RMA ( Def a... allall genes (14010)( 14010) genes http://www.psb.ugent.be/ 2006 Consortium Meeting, St. Croix, U.S. Virgin Islands, March 30 - April 3, 2006 Contributors dictyBase FlyBase GeneDB Gramene Reactome WormBase The GO Editorial Office Berkeley Bioinformatics and Ontology Project (BBOP) Gene Ontology Annotation @ EBI (GOA) Mouse Genome Database (MGD) and Gene Expression Database (GXD) Rat Genome Database (RGD) Saccharomyces Genome Database (SGD) The Arabidopsis Information Resource (TAIR) The Institute for Genomic Research (TIGR) Zebrafish Information Network (ZFIN)