Mouse; NOTC1; Q01705Function: protein bindingProcess: Notch signaling pathwayProcess: positive regulation of transcription from RNA polymerase II promoterProcess: cell fate specificationProcess: compartment specificationProcess: determination of left/right symmetryProcess: positive regulation of apoptosisProcess: somatic stem cell divisionProcess: epithelial to mesenchymal transitionProcess: epidermis developmentProcess: hair follicle developmentProcess: heart development

Rat; NOTC1; Q07008Function: Process: embryonic development

Genetic assayMutant phenotypeDirect assayCurator reviewProtein interactionSequence 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

0 2 4

30

80

168

244

0

20

40

60

80

100

120

140

160

180

1999 2000 2001 2002 2003 2004 2005

www.geneontology.org 7,240www.godatabase.org 33obo.sourceforge.net 10song.sourceforge.net 6

genome.ucsc.edu 3,670www.ncbi.nih.gov 12,000www.ebi.ac.uk 14,900sciencemag.org 14,900

www.ncbi.nlm.nih.gov 34,500

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

www.advancedsurvey.com/survey/header.asp

Congratulations!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 groupPurpose 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 groupPurpose 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

MungallComputation

al architectur

e

ChisholmReferenc

e Annotati

on

HongCommunity Advocacy

Human*

HarrisOntolog

y Content

MicrobesWorm*Fly Weed*Mouse* Budding Yeast*Zebrafish

ClarkAnnotatio

n outreach

*one of the GO supported annotators works on this project

Slime mold*

HillAnnotator-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 groupPurpose 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

MungallComputation

al architectur

e

ChisholmReferenc

e Annotati

on

HongCommunity Advocacy

Human*

HarrisOntolog

y Content

MicrobesWorm*Fly Weed*Mouse* Budding Yeast*Zebrafish

ClarkAnnotatio

n outreach

*one of the GO supported annotators works on this project

Slime mold*

HillAnnotator-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?