Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
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 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. GODatabase.org Hits = 77,012 Visits = 14,063 Sites = 6,638 Averages per week 244 180 168 160 140 120 100 80 80 60 40 30 20 0 0 1999 2 4 2000 2001 2002 2003 2004 2005 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 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. 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 Survey: close to 1500 replies in 3 weeks, almost all positive www.advancedsurvey.com/survey/header.asp Congratulatio ns! We are successful 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. 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. 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. 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. 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. Defining the roles of a group Purpose What is the group’s purpose? What makes this group necessary and unique? What is the lifespan? Group Leader Who tracks progress and makes sure that milestones are met? Activities What are the key deliverables of this group? What criteria are used to set priorities? Members What is the criteria for membership, and what role does each member play? Meeting How often do they meet? Through what communication calendar channels? What are the milestones? Metrics of What are the group’s objectives? How is the group success success evaluated? Linkages How does the group interact and share information with other key groups? Process What are the key decisions? How are decisions made? What is the flow of choices? What tools might be used to make this more efficient? Reference genomes group Purpose We will comprehensively annotate 9 reference genomes in as complete detail as possible. Group Leader Rex Activities Annotations and protein sets Members Representatives from each of the 9 genomes Meeting calendar How often do they meet? Through what communication channels? What are the milestones? Fortnightly phone calls. Metrics of success % of genome annotated, depth measurements Linkages Annotator driven ontology development, user community, computational group (NLP), and outreach group Process What are the key decisions? How are decisions made? What is the flow of choices? What tools might be used to make this more efficient Scientific Advisory Board Sets objectives & priorities Harris Ontology Content Hill AnnotatorOntology liaison Ashburner, Blake, Cherry, Lewis 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. 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. Defining the roles of a group Purpose What is the group’s purpose? What makes this group necessary and unique? What is the lifespan? Group Leader Who tracks progress and makes sure that milestones are met? Activities What are the key deliverables of this group? What criteria are used to set priorities? Members What is the criteria for membership, and what role does each member play? Meeting How often do they meet? Through what communication calendar channels? What are the milestones? Metrics of What are the group’s objectives? How is the group success success evaluated? Linkages How does the group interact and share information with other key groups? Process What are the key decisions? How are decisions made? What is the flow of choices? What tools might be used to make this more efficient? Scientific Advisory Board Sets objectives & priorities Harris Ontology Content Hill AnnotatorOntology liaison Ashburner, Blake, Cherry, Lewis 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. Send us please.. Additional Notes to Kimberley Any slides to Suzi Next meeting November (between Guy Fawkes and Thanksgiving) Hinxton? Marseille?