Scope of the Gene Ontology Vocabularies GO Project

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_attribute gene_structure SO gene_variation ME 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 • Fly. Base & Berkeley Drosophila Genome Project • Saccharomyces Genome Database • Mouse Genome Informatics • The Arabidopsis Information Resource • Swiss-Prot/Tr. EMBL/Inter. Pro • Worm. Base • Dicty. Base • Compugen, Inc • Pathogen Sequencing Unit (Sanger Institute) • Pom. Base (Sanger Institute) • Rat Genome Database • Genome Knowledge Base (CSHL) • The Institute for Genomic Research The Gene Ontology Consortium is supported by NHGRI grant HG 02273 (R 01). The Gene Ontology project thanks Astra. Zeneca for financial support. The Stanford group acknowledges a gift from Incyte Genomics.