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Scope of the Gene Ontology Vocabularies

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

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Scope of the Gene Ontology Vocabularies

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  1. Scope of the Gene Ontology Vocabularies

  2. 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

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

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

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

  6. 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

  7. 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

  8. 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

  9. Terms outside the Scope of GO • Names of gene products • Protein domains • Protein sequence features • Phenotypes; diseases • Anatomical terms (except as part of terms generated by cross-products)

  10. 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

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

  12. DAG Cross-Products hexose glucose fructose metabolism biosynthesis catabolism hexosemetabolism hexosebiosynthesis glucosebiosynthesis fructosebiosynthesis hexosecatabolism glucosecatabolism fructosecatabolism glucosemetabolism ... etc.

  13. 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

  14. www.geneontology.org • 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.

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