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

7, obo.sourceforge.netobo.sourceforge.net 10 song.sourceforge.netsong.sourceforge.net 6 genome.ucsc.edugenome.ucsc.edu 3, , ,900 sciencemag.orgsciencemag.org 14, ,500 Number of links to a site: as reported by Google

NIH funded experimental research that uses the GO 1.National Institute on Alcohol Abuse and Alcoholism (NIAAA) 2.National Institute on Aging (NIA) 3.National Institute of Allergy and Infectious Diseases (NIAID) 4.National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) 5.National Center for Complementary and Alternative Medicine (NCCAM) 6.National Cancer Institute (NCI) 7.National Institute on Drug Abuse (NIDA) 8.National Institute on Deafness and Other Communication Disorders (NIDCD) 9.National Institute of Dental & Craniofacial Research (NIDCR) 10.National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) 11.National Institute of Biomedical Imaging and Bioengineering (NIBIB) 12.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) 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

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 calendar How often do they meet? Through what communication channels? What are the milestones? Metrics of success What are the group’s objectives? How is the group 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 Ashburner, Blake, Cherry, Lewis Mungall Computational architecture Chisholm Reference Annotation Hong Community Advocacy Human* Harris Ontology Content MicrobesWorm*FlyWeed*Mouse*Budding Yeast*Zebrafish Clark Annotation outreach *one of the GO supported annotators works on this project Slime mold* Hill Annotator- Ontology liaison Sets objectives & priorities Manages projects & deliverables …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 calendar How often do they meet? Through what communication channels? What are the milestones? Metrics of success What are the group’s objectives? How is the group 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 Ashburner, Blake, Cherry, Lewis Mungall Computational architecture Chisholm Reference Annotation Hong Community Advocacy Human* Harris Ontology Content MicrobesWorm*FlyWeed*Mouse*Budding Yeast*Zebrafish Clark Annotation outreach *one of the GO supported annotators works on this project Slime mold* Hill Annotator- Ontology liaison Sets objectives & priorities Manages projects & deliverables …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?