1. Annotation of Gene Function …and how thats useful to you

2. What is TAIR*? NSF-funded project begun in 1999 Web resource for Arabidopsis data and stocks Literature-based manual annotation of gene function Genome annotation (gene structure, computational gene function) * URL

3. Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

4. Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

5. What is an annotation? An annotation is a statement that a gene product … …has a particular molecular function …is involved in a particular biological process …is located within a certain cellular component …based on a particular method …and described in a particular reference. Adapted from Harold J Drabkin, The Jackson Laboratory Smith et al. (2006) determined by a direct assay that Abc2 has protein kinase activity, is involved in the process of protein phosphorylation, and is located in the cytoplasm. Reference Method Controlled vocabularies Gene product

6. Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

7. Controlled vocabularies (CV) Non-controlled vocabularies Different names, same concept Same name, different concepts A standardized restricted set of defined terms designed to reduce ambiguity in describing a concept

8. Different names, same concept The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol glucose biosynthesis glucose synthesis glucose formation glucose anabolism gluconeogenesis

9. Same name, different concepts

10. Controlled vocabularies (CV) Non-controlled vocabularies Different names, same concept Same name, different concepts A standardized restricted set of defined terms designed to reduce ambiguity in describing a concept Controlled vocabularies Clearly defined Extensive use of synonyms Can be used to perform complex cross-species cross-database queries.

11. Controlled vocabularies used at TAIR The Gene Ontology (GO) vocabularies by the Gene Ontology Consortium The Plant Ontology (PO) vocabularies by the Plant Ontology Consortium

12. Gene Ontology molecular function: catalytic / binding activities kinase activity, DNA binding activity biological process: biological goal or objective signal transduction mitosis, purine metabolism cellular component: location or complex nucleus ribosome, proteasome

13. is-a protein complex organelle mitochondrion fatty acid beta-oxidation multienzyme complex part-of is-a Relationships: is_a and part_of

14. Plant Ontology Plant structure stamen, petal, guard cell Growth and developmental stages seedling growth, rosette growth, leaf development stages, embryo development stages.

15. Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

16. How are annotations made? Sources - Primary literature - Computational analyses of the genome sequence - Contributions from the research community

17. How are annotations made? What result? Fig. 1: At5g27620 has protein kinase activity What term?[Molecular Function] Protein kinase activity Evidence?Kinase assay PublicationThe Plant Journal (2006) 47:701 Which gene?At5g27620 Annotation

18. How are annotations made?

19. Experimental evidence codes -IMP - Inferred from Mutant Phenotype (mutant analysis) -IDA (enzyme assay) - Inferred from Direct Assay (enzyme assay) - IGI - Inferred from Genetic Interaction (double mutant analysis) -IPI - Inferred from Physical Interaction (yeast 2-H) -IEP (Northern blot) - Inferred from Expression Pattern (Northern blot) Computational analysis Author statement Curatorial statement Evidence codes

20. Summary of functional annotation of the Arabidopsis genome Based on annotation data as of May 3, 2007. More information can be found on TAIR: Portals: Genome Annotation: Genome Snapshot. Molecular Function Biological Process Cellular Component

21. Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

22. GO at TAIR Gene search Keyword search GO annotation search Bulk download Community annotations

23. Gene Search Finding genes based on controlled vocabulary annotations

24. Gene search Search by AGI identifier

25. Gene search results page

26. Search by gene name Gene search Search by gene name Plant U-box17

27. Gene search results page

28. Locus detail page

29. Annotation detail page

30. Keyword Search Finding all types of data associated with a given keyword

31. Select keyword search

32. Keyword search page

33. Keyword search result page

34. Keyword search page

35. GO Annotation Search Finding GO annotations for sets of genes and grouping them by function, location and biological roles

36. Select GO annotations

37. GO annotation search page

38. Functional categorization

39. Pie chart for functional annotations

40. GO annotation search page

41. Accessing Whole Genome Files When you want it all

42. Bulk download

43. GO annotation user submission

44. curator@arabidopsis.org GO annotation user submission

45. External links GOhttp://www.geneontology.org/ AmiGOhttp://www.godatabase.org/ POhttp://www.plantontology.org/ Questionscurator@arabidopsis.org