gene ontology consortium
TRANSCRIPT
Gene Ontology
Consortiumhttp://
www.geneontology.org/
Clark et al, (2005) Plant PhysSubmitted.
Ontology (for our purposes)
• “an explicit specification of some topic” – Stanford Knowledge Systems Lab
• Includes:– a vocabulary of terms (names for concepts)– defined logical relationships to each– definitions
TactitionTactile sense
Taction
?
Tactition Tactile senseTaction
perception of touch ; GO:0050975
Bud initiation?
= bud initiation
sensu Metazoa
= bud initiation
sensu Saccharomyces
= bud initiation
sensu Viridiplantae
Microarray analysis
Whole genome analysis(J. D. Munkvold et al., 2004)
What GO is not:
• Not a way of unifying databases!
• Not a dictated standard
• Additional ontologies needed to model
biology and experimentation. http://obo.sourceforge.net/
•Molecular Function: elemental activity or task
•Biological Process: broad objective or goal
•Cellular Component: location or complex
The Three Ontologies
•Molecular Function: elemental activity or taskDNA binding, catalysis of a reaction
•Biological Process: broad objective or goal
•Cellular Component: location or complex
The Three Ontologies
•Molecular Function: elemental activity or taskDNA binding, catalysis of a reaction
•Biological Process: broad objective or goalmitosis, signal transduction, metabolism
•Cellular Component: location or complex
The Three Ontologies
•Molecular Function: elemental activity or taskDNA binding, catalysis of a reaction
•Biological Process: broad objective or goalmitosis, signal transduction, metabolism
•Cellular Component: location or complexnucleus, ribosome
The Three Ontologies
•Molecular Function: elemental activity or taskDNA binding, catalysis of a reaction
•Biological Process: broad objective or goalmitosis, signal transduction, metabolism
•Cellular Component: location or complexnucleus, ribosome
The Three Ontologies
6 January 2005: Total terms = 1824493% have definitions
What’s in a GO term?
term: transcription initiation
id: GO:0006352
definition: Processes involved in starting transcription, where transcription is the synthesis of RNA by RNA polymerases using a DNA template.
Annotation
GO cellular component term:mitochondrial inner membrane ; GO:0005743
Where is it?
cytochrome c oxidase
GO molecular function term:cytochrome-c oxidase activity; GO:0004497
What does it do?
4 ferrocytochrome c + O2
=
4 ferricytochrome c + 2 H2O
http://ntri.tamuk.edu/cell/mitochondrion/krebpic.html
GO biological process term:electron transport ; GO:0006118
Which process is this?
Request new terms
[email protected]://sourceforge.net/projects/geneontology
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Number of terms
definedundefinedobsolete
Clark et al, (2005) Plant PhysSubmitted
GO Slim
http://www.geneontology.org/
Contributors
FlyBase Rat Genome Database DictyBase WormBase GeneDB S. pombe CompugenMouse Genome Database GeneDB for protozoa Genome Knowledge Base EBI GOA project TIGR Gramene The Arabidopsis Information ResourceThe Zebrafish Information Network Berkeley Drosophila Genome ProjectSaccharomyces Genome DatabaseThe Institute for Genomic ResearchThe GO Editorial Office