1. Gene Ontology Project http://www.geneontology.org/

2. There is a lot of biological research output.

3. Search on mesoderm development…

4. You get 6752 results! How will you ever find what you want? Another example…

5. attacked time control Puparial adhesion Molting cycle hemocyanin Defense response Immune response Response to stimulus Toll regulated genes JAK-STAT regulated genes Immune response Toll regulated genes Amino acid catabolism Lipid metobolism Peptidase activity Protein catabloism Immune response Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI. Microarray data shows changed expression of thousands of genes. How will you spot the patterns?

6. Scientists work hard. http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg

7. There are lots of papers to read. http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg

8. More papers… http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg

9. more and more and more! http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg

10. Aiuto!Help! more and more and more! http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif http://www.teamtechnology.co.uk/f-scientist.jpg

11. Can the computer geeks help? http://www.newberntg.com/images/Computer-Geek-2.gif They are trying! With ontologies!

12. Ontology is a way to capture knowledge in a written and computable form.

13. computable The computer finds patterns so we don’t have to.

14. The Gene Ontology

15. This is our browser.

16. Search on mesoderm development.

17. Here is mesoderm development.

18. Definition of mesoderm development. Gene products involved in mesoderm development.

19. There are many gene products involved in mesoderm development. You can read papers describing what is known about them. But fewer gene products than papers.

21. attacked time control Puparial adhesion Molting cycle hemocyanin Defense response Immune response Response to stimulus Toll regulated genes JAK-STAT regulated genes Immune response Toll regulated genes Amino acid catabolism Lipid metobolism Peptidase activity Protein catabloism Immune response Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI. Gene Ontology can help with Microarray data.

22. attacked time control Puparial adhesion Molting cycle hemocyanin Defense response Immune response Response to stimulus Toll regulated genes JAK-STAT regulated genes Immune response Toll regulated genes Amino acid catabolism Lipid metobolism Peptidase activity Protein catabloism Immune response See which processes are upregulated or downregulated. Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

23. Whole genome analysis (J. D. Munkvold et al., 2004)

24. How does the Gene Ontology work?

25. Clark et al., 2005 part_of is_a A diagram of the whole system.

26. The Gene Ontology is like a dictionary a name term: transcription initiation definition: Processes involved in the assembly of the RNA polymerase complex at the promoter region of a DNA template resulting in the subsequent synthesis of RNA from that promoter. a definition id: GO:0006352 an ID number Each concept has:

27. Biological process ontology Which process is a gene product involved in? Molecular function ontology Which molecular function does a gene product have? Cellular component ontology Where does a gene product act? The ontologies are used to categorize gene products.

28. Mitochondrial P450 ( CC24 PR01238; MITP450CC24) An example…

29. GO cellular component term: GO:0005743 Where is it? Mitochondrial p450 mitochondrial inner membrane

30. GO molecular function term: GO:0004497 What does it do? substrate + O 2 = CO 2 +H 2 0 product monooxygenase activity

31. http://ntri.tamuk.edu/cell/ mitochondrion/krebpic.html GO biological process term: GO:0006118 Which process is this? electron transport

32. is_a DNA binding is a type of nucleic acid binding. Nucleic acid binding is a type of binding. Molecular function ontology

33. Biological process ontology is_a part_of Adaxial/abaxial pattern formation is a type of pattern specification. Adaxial/abaxial pattern specification is a part of adaxial/abaxial pattern formation.

34. part_of is_a nucleus is part of the intracellular domain membrane- bound organelle is a type of organelle Cellular component ontology

35. process function component The gene product inner no outer is involved in adaxial/abaxial axis specification. Categorizing gene products is called ‘annotation’.

36. process function component The gene product inner no outer has transcription factor activity.

37. process function component The gene product inner no outer is active in the nucleus.

38. Clark et al., 2005 part_of is_a A diagram of the whole system.

39. Clark et al., 2005 Many species groups annotate. We see the research of one function across all species.

40. The Gene Ontology is for all species and that means we have to *bridge* some language barriers.

41. http://www.darknessandlight.co.uk/cambridge_photographs.html http://www.lockeheemstra.com/italy/bridge-of-sighs-venice.html Ponte dei Sospiri, Venice. Bridge of Sighs, Cambridge. Same name, same thing?

42. Tactition Tactile sense Taction ? In biology…

43. Tactition Tactile sense Taction perception of touch ; GO:0050975

44. Bud initiation? An imaginary example.

45. tooth bud initiation broad_synonym: bud initiation reproductive bud initiation broad_synonym: bud initiation shoot bud initiation broad_synonym: bud initiation

46. Categorization of gene products using GO is called annotation. So how does that happen?

47. P05147 Choose your favourite gene.

48. P05147 PMID: 2976880 Find a paper about it.

49. P05147 PMID: 2976880 GO:0047519 Find the GO term describing its function, process or location of action.

50. P05147 PMID: 2976880 IDA GO:0047519 What evidence do they show?

51. P05147 PMID: 2976880 GO:0047519 IDA P05147GO:0047519 IDA PMID:2976880 Write these down…

52. Send to the GO Consortium.

53. Annotation appears in AmiGO.

54. GO slims

55. Clark et al., 2005 part_of is_a

56. Clark et al., 2005 part_of is_a

57. Whole genome analysis (J. D. Munkvold et al., 2004)

58. attacked time control Puparial adhesion Molting cycle hemocyanin Defense response Immune response Response to stimulus Toll regulated genes JAK-STAT regulated genes Immune response Toll regulated genes Amino acid catabolism Lipid metobolism Peptidase activity Protein catabloism Immune response Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI. …analysis of high-throughput data according to GO MicroArray data analysis

59. Adding terms to the GO.

66. 2006 Consortium Meeting, St. Croix, U.S. Virgin Islands, March 30 - April 3, 2006

67. Contributors dictyBase FlyBaseGeneDB Gramene ReactomeWormBase The GO Editorial Office Berkeley Bioinformatics and Ontology Project (BBOP) Gene Ontology Annotation @ EBI (GOA) Mouse Genome Database (MGD) and Gene Expression Database (GXD) Rat Genome Database (RGD) Saccharomyces Genome Database (SGD) The Arabidopsis Information Resource (TAIR) The Institute for Genomic Research (TIGR) Zebrafish Information Network (ZFIN)