Scope of the Gene Ontology Vocabularies. Compile structured vocabularies describing aspects of molecular biology Describe gene products using vocabulary.

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Presentation transcript:

Scope of the Gene Ontology Vocabularies

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:

DAG Structure Directed acyclic graph: each child may have one or more parents

Every path from a node back to the root must be biologically accurate The True Path Rule

is-a subclass; a is a type of b part-of physical part of (component) subprocess of (process) Relationship Types

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 The Three Ontologies

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:

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

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

Open source Can be instantiated in DAML+OIL or GO syntax Orthogonal Shared ID space Defined terms GOBO Criteria

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.

gene gene_attribute gene_structureSO gene_variationME gene_product gene_product_attribute molecular_functionGO protein_familyINTERPRO phenotype mutant phenotype anatomy For complete current draft see ftp://ftp.geneontology.org/pub/go/gobo/README Some GOBO Ontologies

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 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.