The Gene Ontology Project:
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Transcript of The Gene Ontology Project:
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The Gene Ontology
Project:Content for the Semantic Web
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• Compile structured vocabularies describing aspects of molecular biology
• Describe gene products using vocabulary terms (annotation)
• Develop tools:• to query and modify the vocabularies and annotations• annotation tools for curators
GO Project Goals
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GO provides two bodies of data:
• Terms with definitions and cross- references
• Gene product annotations with supporting data
GO Data
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•Molecular Function — elemental activity or task
nuclease, DNA binding, transcription factor
•Biological Process — broad objective or
goalmitosis, signal transduction, metabolism
•Cellular Component — location or complexnucleus, ribosome, origin recognition complex
The Three Ontologies
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DAG Structure
Directed acyclic graph: each child may have one or more
parents
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• is-asubclass; a is a type of b
• part-ofphysical part of (component)subprocess of (process)
Relationship Types
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Every path from a node back to the root must be biologically accurate
The True Path Rule
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• ID
• Text string
• Definition with source
• Synonyms (optional)
• Cross-references (optional)
GO Terms: Associated Data
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• Enzyme Commission (EC)
• Transport Commission (TC)
• University of Minnesota Biocatalysis/ Biodegradation Database (UM-BBD)
• MetaCyc
GO Terms: Cross-References
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• Association between gene product and applicable GO terms
• Provided by member databases
• Made by manual or automated methods
GO Annotation
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• Database object: gene or gene product
• GO term ID
• Reference
•publication or computational method
• Evidence supporting annotation
GO Annotation: Data
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DAG Structure
Annotate to any level within DAG
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• Improve coverage:• Developmental processes• Physiological processes
• Relational database
• Support ontology development for additional domains of biology
The Future of GO:
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• Names of gene products
• Protein domains
• Protein sequence features
• Phenotypes; diseases
• Anatomical terms (except as part of terms generated by cross-products)
Terms outside the Scope of GO
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• Global Open Biology Ontologies
• Umbrella site for shared genomics and proteomics vocabularies
• Present incarnation: subdirectory within GO repository:
ftp://ftp.geneontology.org/pub/go/gobo/README
The GOBO Proposal
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• FlyBase & Berkeley Drosophila Genome Project • WormBase• Saccharomyces Genome Database • DictyBase• Mouse Genome Informatics • Compugen, Inc• The Arabidopsis Information Resource• Swiss-Prot/TrEMBL/InterPro
• Pathogen Sequencing Unit (Sanger Institute)
• PomBase (Sanger Institute)
• Rat Genome Database
• Genome Knowledge Base (CSHL)
• The Institute for Genomic Research
www.geneontology.org
The Gene Ontology Consortium is supported by NHGRI grant HG02273 (R01). The Gene Ontology project thanks AstraZeneca for financial support. The Stanford group acknowledges a gift from Incyte Genomics.
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Conference:
Standards and Ontologies for Functional Genomics (SOFG)
Towards unified ontologies for describing biology and biomedicine
17 – 20 November 2002
Hinxton Hall Conference CentreHinxton, Cambridge, UK
www.ebi.ac.uk/SOFG/
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First Standards and Ontologies for Functional Genomics
(SOFG)
Keynote SpeakersKen Buetow, NCI, USA
Win Hide, SANBI, South Africa Peter Karp, SRI International, USA
17-20 November 2002,
Hinxton, UK
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Aims and Objectives
• Bring together scientists developing standards and ontologies, both biologists, bioinformaticians and computer scientists
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Topics
• Introduction to Ontologies• Tools for building ontologies• Go and related ontologies• Species specific ontologies• Implementation• Inter-ontology mapping• Ontologies for pathology, toxicology• Chemical ontologies
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Structure
• 3 keynote speakers
• ~20 invited talks
• 10 short talks selected from poster abstracts
• Panel discussion
• Parallel working groups/tutorials
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Programme CommitteeMichael Ashburner, University of Cambridge, UK (Chair)
Cathy Ball, Stanford University, USA Mike Bittner, NHGRI, USA
Alvis Brazma, EMBL-EBI, UK Catherine Brooksbank, EMBL-EBI, UK
Duncan Davidson, MRC HGU, Edinburgh, UK Liz Ford, EMBL-EBI, UK
Midori Harris, EMBL-EBI, UKVictor Markowitz, Gene Logic, USA
Helen Parkinson, EMBL-EBI, UKJohn Quackenbush, TIGR, USA
Martin Ringwald, The Jackson Laboratories, USASteffen Schulze-Kremer, RZPD, Germany
Paul Spellman, U.C. Berkeley, USA Robert Stevens, University of Manchester, UK
Chris Stoeckert, University of Pennsylvania, USA
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URL
http://www.ebi.ac.uk/microarray/General/Events/SOFG/SOFG.html
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chitin metabolism: before revision
The True Path Rule
chitin biosynthesis
cuticle synthesis
chitin catabolism
cell wall biosynthesis
chitin metabolism
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chitin metabolism: after revision
The True Path Rule
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chitin metabolism: after revision
The True Path Rule
cuticle synthesischitin metabolism
cuticle chitin biosynthesis
chitin biosynthesis cuticle chitin metabolism
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• Open source
• Can be instantiated in DAML+OIL or GO syntax
• Orthogonal
• Shared ID space
• Defined terms
GOBO Criteria
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hexose glucose fructose
DAG Cross-Products
metabolism biosynthesis catabolism
hexose metabolism hexose biosynthesis glucose biosynthesis fructose biosynthesis hexose catabolism glucose catabolism fructose catabolism glucose metabolism
... etc.
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gene gene_attribute gene_structure SO gene_variation ME gene_product gene_product_attribute molecular_function GO protein_family INTERPRO phenotype mutant phenotype
anatomy
For complete current draft see ftp://ftp.geneontology.org/pub/go/gobo/README
Some GOBO Ontologies
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• Not a way to unify biological databases
• Not a dictated standard
• Does not define evolutionary relationships
• Additional ontologies needed to model biology and experimentation
What GO is NOT:
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DAG Structure
Annotate to any level within DAG
mitosisS.c. NNF1
mitotic chromosome condensation
S.c. BRN1, D.m. barren
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Using GO Annotation: Example Workflow
text
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ID
definition
cross-reference
synonyms
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Using GO Annotation: Example Workflow