The Gene Ontology Project
description
Transcript of The Gene Ontology Project
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The Gene Ontology Project
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DNA
gene gene gene gene gene
mRNA
protein
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http://cms.frontiersin.org/content/10.3389/neuro.02/007.2008/html/fnmol-01-007/images/article/image_n/fnmol-01-007-g001.gif
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substrate + O2 = CO2 +H20 product
http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html
Gene product:• What does it do?• Where does it do it?• What is the bigger picture?
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Clark et al., 2005
part_of
is_a
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Clark et al., 2005
part_of
is_a
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Whole genome analysis(J. D. Munkvold et al., 2004)
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Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...
Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)
attacked
time
control
Puparial adhesionMolting cyclehemocyanin
Defense responseImmune responseResponse to stimulusToll regulated genesJAK-STAT regulated genes
Immune responseToll regulated genes
Amino acid catabolismLipid metobolism
Peptidase activityProtein catabolismImmune response
Selected Gene Tree: pearson lw n3d ...Branch color classification:Set_LW_n3d_5p_...
Colored by: Copy of Copy of C5_RMA (Defa...Gene List: all genes (14010)
See which processes are upregulated or downregulated.
Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.
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Current metrics
• 3 ontologies– Biological process– Molecular function– Cellular component
• 26,933 terms• 5 relationship types• 47,000+ relationships• 40,000,000+ annotations• 88,193 species.
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Future plans
• Cross products
• Function-process links
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Cross products: Identify ontologies within ontologies – make computable
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Intersection tags / cross products
[Term]
id: GO:0010064 ! embryonic shoot morphogenesis
intersection_of: GO:0010016 ! shoot morphogenesis
intersection_of: part_of GO:0009790 ! embryonic development
[Term]
id: GO:0010101 ! post-embryonic root morphogenesis
intersection_of: GO:0010015 ! root morphogenesis
intersection_of: part_of GO:0009791 ! post-embryonic development
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Cross products (xp) in progress
• XPs being set up amongst GO ontologies.
• Also with:
cell type ontology,
uberon (anatomy) ontology,
ChEBI (chemical) ontology.
• 170+ new relationship types planned.
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Link out to other ontologies:
• Open Biomedical Ontologies– 54 compatible ontologies– 26 other nearly compatible ontologies
http://www.obofoundry.org/
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Function-process links
http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html
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UTP:glucose-1-phosphate uridylyltransferase activity α-D-glucose 1-phosphate + UTP ->
UDP-D-glucose + diphosphate
glucose metabolic process
UDP-glucosemetabolicprocess galactose
metabolic process
biosyntheticprocess
colanic acidbiosyntheticprocess
responseto desiccation
carbohydrate catabolic process
Function
Processhp hp
hphp hp
hp hp
hp = has_part
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Lysine biosynthesis pathways
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lysinebiosynthesis
lysinebiosynthesis1
lysinebiosynthesis3
lysinebiosynthesis2
lysinebiosynthesis4
lysinebiosynthesis5
lysinebiosynthesis6
Function
Process
is_a
is_ais_a is_a is_a
is_a
lysinebiosynthesis 7?
is_a
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Process
Function
Lysine Biosynthesis
Process B Process C
Shared function?
= has_part
Non-shared function
new GO term
existing GO term
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Process
Function
Lysine Biosynthesis
Process B Process CRelationship explosion
(or Editorial office explosion)
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Tools
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OBO-Edit: Ontology Editor Tool
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Reasoner finds missing and redundant relationships.
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2006 Consortium Meeting,
St. Croix,
U.S. Virgin Islands, March 30 - April 3, 2006
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http://www.geneontology.org
Reactome
E. Coli hub
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Particular thanks to:
Chris Mungall - OBOL,
Rule Based Reasoner
Cross product system
Function process link plan – The electron transport working group
OBO-Edit:
John Day-Richter,
Nomi Harris,
Amina Abdulla: