Transcript grant-SOPs_slewis - Gene Ontology Consortium

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
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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
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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)
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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?