Gene Ontology

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Gene Ontology Project http//www.geneontolog
y.org/
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Clark et al., 2005
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Clark et al., 2005
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Who uses GO?
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NIH funded experimental research that uses the GO

• 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)

Sample of 77 research papers, both intra-mural
extra-mural research.
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Publications

• Published articles
• mentioning GO 1063, in 284 journals
• Google Scholar
• gene ontology, tool for unification of biology
  1291 citations

25th September 2006
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Who is citing GO?
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1063 publications over 284 Journals
http//www.geneontology.org/cgi-bin/biblio.cgi
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Companies

• NLP Ontology Products BioWisdom, IBM
• Array Products and data analysis Affymetrix,
  Spotfire
• Products that use GO Clontech, Inpharmatica
• Reagents services Sigma, Abnova
• Big Pharmas AstraZeneca

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Whole genome analysis (J. D. Munkvold et al.,
2004)
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analysis of high-throughput data according to GO
MicroArray data analysis
Bregje Wertheim at the Centre for Evolutionary
Genomics, Department of Biology, UCL and Eugene
Schuster Group, EBI.
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How do GO annotations work?
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Clark et al., 2005
is_a
part_of
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Clark et al., 2005
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GO0047519
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Clark et al., 2005
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AmiGO The GO Browser
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How to use GO The GO website
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Clark et al., 2005
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is_a
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Whole genome analysis (J. D. Munkvold et al.,
2004)
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analysis of high-throughput data according to GO
MicroArray data analysis
Bregje Wertheim at the Centre for Evolutionary
Genomics, Department of Biology, UCL and Eugene
Schuster Group, EBI.
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Gene products for which nothing is known
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Molecular function ontology
Annotations
molecular function molecular function
unknown
is_a
10-4
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Molecular function ontology
Annotations
molecular function molecular function
unknown
10-4
is_a
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Molecular function ontology
Annotations
molecular function molecular function
unknown
10-4
is_a
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Adding terms to the GO
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2006 Consortium Meeting, St. Croix, U.S.
Virgin Islands, March 30 - April 3, 2006
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Contributors dictyBase FlyBase GeneDB
Gramene Reactome WormBase The GO Editorial
Office Berkeley Bioinformatics and Ontology
Project (BBOP) Gene Ontology Annotation _at_ EBI
(GOA) Mouse Genome Database (MGD) and Gene
Expression Database (GXD) Rat Genome Database
(RGD) Saccharomyces Genome Database (SGD) The
Arabidopsis Information Resource (TAIR) The
Institute for Genomic Research (TIGR) Zebrafish
Information Network (ZFIN)
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gohelp_at_geneontology.org
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Spare slides
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http//david.abcc.ncifcrf.gov/
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http//discover.nci.nih.gov/
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overview proteome with GO Slim
http//www.ebi.ac.uk/integr8
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http//www.ebi.uniprot.org/
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http//www.ncbi.nlm.nih.gov/
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