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Molecular Biology Ontologies for Research Advancement

Providing structured vocabularies and ontologies for molecular biology, supporting gene product annotation, extending GO Consortium, and building informatics resources. Visit GODatabase.org for resources and tools.

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Molecular Biology Ontologies for Research Advancement

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  1. Mouse; NOTC1; Q01705 Function: protein binding Process: Notch signaling pathway Process: positive regulation of transcription from RNA polymerase II promoter Process: cell fate specification Process: compartment specification Process: determination of left/right symmetry Process: positive regulation of apoptosis Process: somatic stem cell division Process: epithelial to mesenchymal transition Process: epidermis development Process: hair follicle development Process: heart development Rat; NOTC1; Q07008 Function: Process: embryonic development Genetic assay Mutant phenotype Direct assay Curator review Protein interaction Sequence similarity

  2. Specific Aims circa 2003 • Provide structured vocabularies and ontologies for molecular biology • Support and promote the use of the ontologies to annotate gene products. • Extend the GO Consortium to include new model organism databases. • Build and disseminate informatics resources and tools to support community use of the GO vocabularies.

  3. GODatabase.org • Hits = 77,012 • Visits = 14,063 • Sites = 6,638 • Averages per week

  4. Number of links to a site: as reported by Google www.geneontology.org 7,240 www.godatabase.org 33 obo.sourceforge.net 10 song.sourceforge.net 6 genome.ucsc.edu 3,670 www.ncbi.nih.gov 12,000 www.ebi.ac.uk 14,900 sciencemag.org 14,900 www.ncbi.nlm.nih.gov 34,500

  5. 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. National Eye Institute (NEI) 14. National Institute of General Medical Sciences (NIGMS) 15. National Institute of Child Health and Human Development (NICHD) 16. National Human Genome Research Institute (NHGRI) 17. National Heart, Lung and Blood Institute (NHLBI) 18. National Library of Medicine (NLM) 19. National Center on Minority Health and Health Disparities (NCMHD) 20. National Institute of Mental Health (NIMH) 21. National Institute of Nursing Research (NINR) 22. National Institute of Neurological Disorders and Stroke (NINDS) 23. National Center for Research Resources (NCRR) 24. Fogarty International Center (FIC) NIH funded experimental research that uses the GO Sample of 77 research papers, both intra-mural & extra-mural research.

  6. Publications • PubMed – GO in abstract ( 459) includes papers in 162 journals • Endocrinology, J. Neurosci Res., J. Dent Res, etc. • Google Scholar • ‘gene ontology, tool for unification of biology’ 1348 citations as of April 1, 2006

  7. Survey: close to 1500 replies in 3 weeks, almost all positive www.advancedsurvey.com/survey/header.asp

  8. Congratulations! We are successful

  9. Specific Aims circa 2003 • Provide structured vocabularies and ontologies for molecular biology • Support and promote the use of the ontologies to annotate gene products. • Extend the GO Consortium to include new model organism databases. • Build and disseminate informatics resources and tools to support community use of the GO vocabularies.

  10. Specific Aims • 2006: We will maintain comprehensive, logically rigorous and biologically accurate ontologies. • 2003: Support and promote the use of the ontologies to annotate gene products. • 2003: Extend the GO Consortium to include new model organism databases. • 2003: Build and disseminate informatics resources and tools to support community use of the GO vocabularies.

  11. Specific Aims • 2006: We will maintain comprehensive, logically rigorous and biologically accurate ontologies. • 2006: We will comprehensively annotate 9 reference genomes in as complete detail as possible. • 2003: Extend the GO Consortium to include new model organism databases. • 2003: Build and disseminate informatics resources and tools to support community use of the GO vocabularies.

  12. Specific Aims • 2006: We will maintain comprehensive, logically rigorous and biologically accurate ontologies. • 2006: We will comprehensively annotate 9 reference genomes in as complete detail as possible. • 2006: We will support annotation across all organisms. • 2003: Build and disseminate informatics resources and tools to support community use of the GO vocabularies.

  13. Specific Aims • 2006: We will maintain comprehensive, logically rigorous and biologically accurate ontologies. • 2006: We will comprehensively annotate 9 reference genomes in as complete detail as possible. • 2006: We will support annotation across all organisms. • 2006: We will provide our annotations and tools to the research community.

  14. Defining the roles of a group

  15. Reference genomes group

  16. Scientific Advisory Board Sets objectives & priorities Ashburner, Blake, Cherry, Lewis Harris Ontology Content Hill Annotator-Ontology liaison Clark Annotation outreach Chisholm Reference Annotation Hong Community Advocacy Mungall Computational architecture Manages projects & deliverables Human* Mouse* Zebrafish Fly Weed* Worm* Slime mold* Budding Yeast* Microbes *one of the GO supported annotators works on this project …and we all carry out the work, just as we do now.

  17. Specific Aims 2006 • We will maintain comprehensive, logically rigorous and biologically accurate ontologies. • We will comprehensively annotate 9 reference genomes in as complete detail as possible. • We will support annotation across all organisms. • We will provide our annotations and tools to the research community.

  18. Defining the roles of a group

  19. Scientific Advisory Board Sets objectives & priorities Ashburner, Blake, Cherry, Lewis Harris Ontology Content Hill Annotator-Ontology liaison Clark Annotation outreach Chisholm Reference Annotation Hong Community Advocacy Mungall Computational architecture Manages projects & deliverables Human* Mouse* Zebrafish Fly Weed* Worm* Slime mold* Budding Yeast* Microbes *one of the GO supported annotators works on this project …and we all carry out the work, just as we do now.

  20. Send us please.. • Additional Notes to Kimberley • Any slides to Suzi

  21. Next meeting November (between Guy Fawkes and Thanksgiving) Hinxton? Marseille?

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