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Scope of the Gene Ontology
Vocabularies
GO Project Goals:
• 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
DAG Structure
Directed acyclic graph: each child
may have one or more parents
The True Path Rule
Every path from a node back to the
root must be biologically accurate
Relationship Types
• is-a
subclass; a is a type of b
• part-of
physical part of (component)
subprocess of (process)
The Three Ontologies
•Molecular Function — elemental activity or task
nuclease, DNA binding, transcription factor
•Biological Process — broad objective or goal
mitosis, signal transduction, metabolism
•Cellular Component — location or complex
nucleus, ribosome, origin recognition complex
The Three Ontologies
•Molecular Function — elemental activity or task
nuclease, DNA binding, transcription factor
•Biological Process — broad objective or goal
mitosis, signal transduction, metabolism
•Cellular Component — location or complex
nucleus, ribosome, origin recognition complex
What GO is NOT:
• Not a way to unify biological databases
• Not a dictated standard
• Does not define evolutionary relationships
• Additional ontologies needed to model
biology and experimentation
Terms outside the Scope of GO
• Names of gene products
• Protein domains
• Protein sequence features
• Phenotypes; diseases
• Anatomical terms
generated by cross-products)
(except as part of terms
The GOBO Proposal
• 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
GOBO Criteria
• Open source
• Can be instantiated in DAML+OIL
or GO syntax
• Orthogonal
• Shared ID space
• Defined terms
DAG Cross-Products
hexose
glucose
fructose
metabolism
biosynthesis
catabolism
hexose metabolism
hexose biosynthesis
glucose biosynthesis
fructose biosynthesis
hexose catabolism
glucose catabolism
fructose catabolism
glucose metabolism
... etc.
Some GOBO Ontologies
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
www.geneontology.org
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FlyBase & Berkeley Drosophila Genome Project
Saccharomyces Genome Database
Mouse Genome Informatics
The Arabidopsis Information Resource
Swiss-Prot/TrEMBL/InterPro
• WormBase
• DictyBase
• Compugen, Inc
• Pathogen Sequencing Unit (Sanger Institute)
• PomBase (Sanger Institute)
• Rat Genome Database
• Genome Knowledge Base (CSHL)
• The Institute for Genomic Research
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.