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The Gene Ontology Project:

The Gene Ontology Project:. Content for the Semantic Web. 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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The Gene Ontology Project:

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  1. The Gene Ontology Project: Content for the Semantic Web

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

  4. 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

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

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

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

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

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

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

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

  12. DAG Structure Annotate to any level within DAG

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

  14. 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)

  15. 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

  16. 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.

  17. 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 www.ebi.ac.uk/SOFG/

  18. First Standards and Ontologies for Functional Genomics (SOFG) Keynote Speakers Ken Buetow, NCI, USA Win Hide, SANBI, South Africa Peter Karp, SRI International, USA 17-20 November 2002, Hinxton, UK

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

  20. 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

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

  22. 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

  23. URL http://www.ebi.ac.uk/microarray/General/Events/SOFG/SOFG.html

  24. The True Path Rule cell wall biosynthesis cuticle synthesis chitin metabolism chitin biosynthesis chitin catabolism chitin metabolism: before revision

  25. The True Path Rule chitin metabolism: after revision

  26. The True Path Rule chitin metabolism cuticle synthesis chitin biosynthesis cuticle chitin metabolism cuticle chitin biosynthesis chitin metabolism: after revision

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

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

  29. 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

  30. 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

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

  32. Using GO Annotation: Example Workflow text

  33. ID synonyms cross-reference definition

  34. Using GO Annotation: Example Workflow

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