1. A Common Language for Annotation of Genes from Yeast, Flies and Mice The Gene Ontologies …and Plants and Worms …and Humans …and anything else!

2. Gene Ontology Objectives GO represents concepts used to classify specific parts of our biological knowledge: –Biological Process –Molecular Function –Cellular Component GO develops a common language applicable to any organism GO terms can be used to annotate gene products from any species, allowing comparison of information across species

3. Expansion of Sequence Info

4. Eukaryotic Genome Sequences YearGenome# Genes Size (Mb) Yeast ( S. cerevisiae )1996 12 6,000 Worm ( C. elegans )1998 97 19,100 Fly ( D. melanogaster )2000 120 13,600 Plant ( A. thaliana )2001 125 25,500 Human ( H. sapiens, 1st Draft )2001 ~3000~35,000 Entering the Genome Sequencing Era

5. Baldauf et al. (2000) Science 290:972

6. MCM3 MCM2 CDC46/MCM5 CDC47/MCM7 CDC54/MCM4 MCM6 These proteins form a hexamer in the species that have been examined Comparison of sequences from 4 organisms

7. http://www.geneontology.org/

8. Outline of Topics Introduction to the Gene Ontologies (GO) Annotations to GO terms GO Tools Applications of GO

9. What is an Ontology? (from OED) 1721 B AILEY, Ontology, an Account of being in the Abstract. 1733 (title) A Brief Scheme of Ontology or the Science of Being in General. a1832 B ENTHAM Fragm. Ontol. Wks. 1843 VIII. 195 The field of ontology, or as it may otherwise be termed, the field of supremely abstract entities, is a yet untrodden labyrinth. 1884 B OSANQUET tr. Lotze's Metaph. 22 Ontology..as a doctrine of the being and relations of all reality, had precedence given to it over Cosmology and Psychology, the two branches of enquiry which follow the reality into its opposite distinctive forms.

10. Sriniga Srinivasan, Chief Ontologist, Yahoo! The ontology. Dividing human knowledge into a clean set of categories is a lot like trying to figure out where to find that suspenseful black comedy at your corner video store. Questions inevitably come up, like are Movies part of Art or Entertainment? (Yahoo! lists them under the latter.) -Wired Magazine, May 1996

11. Molecular Function = elemental activity/task –the tasks performed by individual gene products; examples are carbohydrate binding and ATPase activity Biological Process = biological goal or objective –broad biological goals, such as mitosis or purine metabolism, that are accomplished by ordered assemblies of molecular functions Cellular Component = location or complex –subcellular structures, locations, and macromolecular complexes; examples include nucleus, telomere, and RNA polymerase II holoenzyme The 3 Gene Ontologies

12. Function (what) Process (why) Drive nail (into wood) Carpentry Drive stake (into soil) Gardening Smash roach Pest Control Clown’s juggling object Entertainment Example: Gene Product = hammer

13. Biological Examples Molecular Function Biological Process Cellular Component

14. term: MAPKKK cascade (mating sensu Saccharomyces) goid: GO:0007244 definition: OBSOLETE. MAPKKK cascade involved in transduction of mating pheromone signal, as described in Saccharomyces. definition_reference: PMID:9561267 comment: This term was made obsolete because it is a gene product specific term. To update annotations, use the biological process term 'signal transduction during conjugation with cellular fusion ; GO:0000750'. Terms, Definitions, IDs definition: MAPKKK cascade involved in transduction of mating pheromone signal, as described in Saccharomyces

15. Directed Cyclic Graph Figure 4.1. Life cycles of heterothallic and homothallic strains of S. cerevisiae. Heterothallic strains can be stably maintained as diploids and haploids, whereas homothallic strains are stable only as diploids, because the transient haploid cells switch their mating type, and mate. An Introduction to the Genetics and Molecular Biology of the Yeast Saccharomyces cerevisiae Fred Sherman 2000; Modified from: F. Sherman, Yeast genetics. The Encyclopedia of Molecular Biology and Molecular Medicine, pp. 302-325, Vol. 6. Edited by R. A. Meyers, VCH Pub., Weinheim, Germany,1997.

16. Nucleus Nucleoplasm Nuclear envelope ChromosomePerinuclear spaceNucleolus A child is a subset of a parent’s elements The cell component term Nucleus has 5 children Parent-Child Relationships

17. Derivation of Romance languages from Latin. From R.A. Hall Jr., Introductory Linguistics; originally published by Chilton Books, now distributed by Rand McNally & Co. “Tree” Relationships

18. Ontology Relationships Directed Acyclic Graph http://www.ebi.ac.uk/ego

19. Evidence Codes for GO Annotations http://www.geneontology.org/doc/GO.evidence.html

20. IEAInferred from Electronic Annotation ISSInferred from Sequence Similarity IEPInferred from Expression Pattern IMPInferred from Mutant Phenotype IGIInferred from Genetic Interaction IPIInferred from Physical Interaction IDAInferred from Direct Assay RCAInferred from Reviewed Computational Analysis TASTraceable Author Statement NASNon-traceable Author Statement ICInferred by Curator NDNo biological Data available

21. IEA Inferred from Electronic Annotation Sequence Similarity (BLAST) Automatic transfer from mappings (InterPro2GO, EC2GO etc.) -> Not manually reviewed

22. ISS Inferred from Sequence or Structural Similarity Sequence similarity Recognized domains Structural similarity ->Use of ‘with’ column recommended

23. IEP Inferred from Expression Pattern Transcript levels (Northerns, microarrays) Protein levels (Western blots) ->Timing or localization of expression ->Biological process annotations

24. IMP Inferred from Mutant Phenotype Gene mutation/knockout Overexpression/ectopic expression Anti-sense experiments RNAi experiments Specific protein inhibitors

25. IGI Inferred from Genetic Interaction Suppressors, synthetic lethals… Functional complementation Rescue experiments ->Use of ‘with’ column recommended

26. IPI Inferred from Physical Interaction 2-hybrid interactions Co-purification Co-immunoprecipitation Ion/complex/protein binding experiments ->Use of ‘with’ column recommended

27. IDA Inferred from Direct Assay Enzyme assays In vitro reconstitution (e.g. transcription) Immunofluorescence (for cell. comp.) Cell fractionation (for cell. comp.) Physical interaction/binding assay

28. RCA Inferred from Reviewed Computational Analysis Non-sequence-based computational methods Genome-wide analyses (e.g. 2-hybrid) Combinations of large-scale experiments

29. TAS Traceable Author Statement Support from review article Textbook ‘common knowledge’ ->Data that can be ‘traced’ back

30. NAS Non-traceable Author Statement Database entries that don't cite a paper ->Data that cannot be ‘traced’ back

31. IC Inferred by Curator Not supported by any direct evidence Inferred from other GO annotations -> GO term in ‘with/from’ column required

32. ND No biological Data available molecular function unknown GO:0005554 biological process unknown GO:0000004 cellular component unknown GO:0008372 Curator found no information supporting any annotation

33. TAS/IDA IMP/IGI/IPI ISS/IEP NAS IEA Term Hierarchy

34. Qualifiers NOT: explicit note that a gene product is not associated with a GO term colocalizes_with: only transient localization, or low resolution of an assay contributes_to: gene product that is part of a complex can be annotated to the process/function of the complex http://www.geneontology.org/GO.annotation.shtml#qual The qualifier modifies the interpretation of a GO term

35. http://www.geneontology.org/doc/GO.evidence.html