The Gene Ontology Project: Content for the Semantic Web

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

GO provides two bodies of data: Terms with definitions and cross- references Gene product annotations with supporting data GO Data

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

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

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

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

ID Text string Definition with source Synonyms (optional) Cross-references (optional) GO Terms: Associated Data

Enzyme Commission (EC) Transport Commission (TC) University of Minnesota Biocatalysis/ Biodegradation Database (UM-BBD) MetaCyc GO Terms: Cross-References

Association between gene product and applicable GO terms Provided by member databases Made by manual or automated methods GO Annotation

Database object: gene or gene product GO term ID Reference publication or computational method Evidence supporting annotation GO Annotation: Data

DAG Structure Annotate to any level within DAG

Improve coverage: Developmental processes Physiological processes Relational database Support ontology development for additional domains of biology The Future of GO:

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

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.

Conference: Standards and Ontologies for Functional Genomics (SOFG) Towards unified ontologies for describing biology and biomedicine 17 – 20 November 2002 Hinxton Hall Conference Centre Hinxton, Cambridge, UK

First Standards and Ontologies for Functional Genomics (SOFG) Keynote Speakers Ken Buetow, NCI, USA Win Hide, SANBI, South Africa Peter Karp, SRI International, USA November 2002, Hinxton, UK

Aims and Objectives Bring together scientists developing standards and ontologies, both biologists, bioinformaticians and computer scientists

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

Structure 3 keynote speakers ~20 invited talks 10 short talks selected from poster abstracts Panel discussion Parallel working groups/tutorials

Programme Committee Michael 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, UK Victor Markowitz, Gene Logic, USA Helen Parkinson, EMBL-EBI, UK John Quackenbush, TIGR, USA Martin Ringwald, The Jackson Laboratories, USA Steffen 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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chitin metabolism: before revision The True Path Rule chitin biosynthesis cuticle synthesis chitin catabolism cell wall biosynthesis chitin metabolism

chitin metabolism: after revision The True Path Rule

chitin metabolism: after revision The True Path Rule cuticle synthesischitin metabolism cuticle chitin biosynthesis chitin biosynthesiscuticle chitin metabolism

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

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:

DAG Structure Annotate to any level within DAG mitosis S.c. NNF1 mitotic chromosome condensation S.c. BRN1, D.m. barren

Using GO Annotation: Example Workflow text

ID definition cross-reference synonyms

Using GO Annotation: Example Workflow