Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
Towards a GOannotation tool curation accelerator software
FlyBase Literature       Curators• Read papers• Extract information for FlyBase• Per paper, genes mentioned: per gene,  an...
Annotation with Gene     ontologies• How can we make this easy? or farm it  out to The Community (wikipedia  model)
About Gene Ontology -   GO -annotation• Each gene should have up to 3 GO terms  associated with it, describing  • molecula...
17 columns
GO annotation• Common problem: S.pombe, Zfin, Dictybase,  WormBase, Protein2GO, GO consortium• Changing format for GO annot...
The GO curation tools• Usually perl (java) front end. All directly input to database• Web-based• Combined ontology explora...
Strategy• User designed GUI (speed + accuracy)• Modular design of GO editor with xml  config• OOP with API for different GM...
Programming• Java - OOP - GUI - JSP/Tomcat• Our tool focus on reducing mouse-  work, tool switches, ‘manual’ editing  and ...
archive      Peeves                chado                      d                                                    records...
GO toolSoftware houses GO lines
GO toolSoftware houses GO lines
GO toolSoftware houses GO lines
GO toolSoftware houses GO lines
GO tool   Software houses GO linesClever editor .. makes GO lines
GO tool
Config XML          For each component, describes which          source filecomponents to use        database ids       API ...
Clever editor
Clever editorF
Clever editor F
Clever editor FlyBase
Clever editor F
Clever editor
Clever editor
Clever editor
Clever editor
Clever editor
Clever editor            def
Clever editor            def
GO Tool +
Other tools
Tab & Type
GO editor
GO editor
GO editor
GO editor
GO editor
GO editor
GO editor
GO editor
GO editor
GO editor
Add evidence gene
GO editor
GO editor
GO editor
GO editor
Information
Save work
Open curation record
Open curation record
Open curation record
edit existing
edit existing
edit existing
The end.
almost
details• Mac OS X (testing) 10.5 and 10.6 preAlpha_v002• 3.8GB RAM but may use less• Flat file input but also talks to post...
Future• chado queries• XML config/s for clever editor• API in collaboration• JSP or J2EE/SOAP web interface          • Hele...
Go curation sept2010
Go curation sept2010
Upcoming SlideShare
Loading in …5
×

Go curation sept2010

426 views

Published on

Published in: Design
  • Be the first to comment

  • Be the first to like this

Go curation sept2010

  1. 1. Towards a GOannotation tool curation accelerator software
  2. 2. FlyBase Literature Curators• Read papers• Extract information for FlyBase• Per paper, genes mentioned: per gene, any alleles: new constructs, phenotypes, controls
  3. 3. Annotation with Gene ontologies• How can we make this easy? or farm it out to The Community (wikipedia model)
  4. 4. About Gene Ontology - GO -annotation• Each gene should have up to 3 GO terms associated with it, describing • molecular function • biological process • cellular component• Common to GMOD databases: each GO term has a standard definition designed to have the same biological meaning across the entire living world, ie for all disciplines, any organism.• GO ontology terms designed to standardise the biology
  5. 5. 17 columns
  6. 6. GO annotation• Common problem: S.pombe, Zfin, Dictybase, WormBase, Protein2GO, GO consortium• Changing format for GO annotation lines (16, 17)• Production of GO lines in standard EDIT format eg for FlyBase• or in standard GO format required for data input to the GO consortium database (FB submits periodically)
  7. 7. The GO curation tools• Usually perl (java) front end. All directly input to database• Web-based• Combined ontology exploration tools - trees, graphical views, definitions - previously created ontology lines.• (FB does not have one) FB curators edit text files.• FB: curation process is independent of database parsing. Highly Recommended• Database can be developed without reference to the curation interface• Exploit this to design beautifully engineered GUI based tools
  8. 8. Strategy• User designed GUI (speed + accuracy)• Modular design of GO editor with xml config• OOP with API for different GMODs• Proof of concept: desktop GO tool to speed up curation > XML config > API for general use• Translate to web service
  9. 9. Programming• Java - OOP - GUI - JSP/Tomcat• Our tool focus on reducing mouse- work, tool switches, ‘manual’ editing and textual errors• One window, many tools
  10. 10. archive Peeves chado d records File names Google docs Blue scripts terminal book www Phenote TermLinkontologie s OBO Curator QuickGO PubMed Pubget PDF search Text editor tools Printe r curfiles Finder window Cur paper Rec
  11. 11. GO toolSoftware houses GO lines
  12. 12. GO toolSoftware houses GO lines
  13. 13. GO toolSoftware houses GO lines
  14. 14. GO toolSoftware houses GO lines
  15. 15. GO tool Software houses GO linesClever editor .. makes GO lines
  16. 16. GO tool
  17. 17. Config XML For each component, describes which source filecomponents to use database ids API source file parsingType of component database queries with display text output formats
  18. 18. Clever editor
  19. 19. Clever editorF
  20. 20. Clever editor F
  21. 21. Clever editor FlyBase
  22. 22. Clever editor F
  23. 23. Clever editor
  24. 24. Clever editor
  25. 25. Clever editor
  26. 26. Clever editor
  27. 27. Clever editor
  28. 28. Clever editor def
  29. 29. Clever editor def
  30. 30. GO Tool +
  31. 31. Other tools
  32. 32. Tab & Type
  33. 33. GO editor
  34. 34. GO editor
  35. 35. GO editor
  36. 36. GO editor
  37. 37. GO editor
  38. 38. GO editor
  39. 39. GO editor
  40. 40. GO editor
  41. 41. GO editor
  42. 42. GO editor
  43. 43. Add evidence gene
  44. 44. GO editor
  45. 45. GO editor
  46. 46. GO editor
  47. 47. GO editor
  48. 48. Information
  49. 49. Save work
  50. 50. Open curation record
  51. 51. Open curation record
  52. 52. Open curation record
  53. 53. edit existing
  54. 54. edit existing
  55. 55. edit existing
  56. 56. The end.
  57. 57. almost
  58. 58. details• Mac OS X (testing) 10.5 and 10.6 preAlpha_v002• 3.8GB RAM but may use less• Flat file input but also talks to postgres• Configurable (text file)• Designed by the CURATORS• Thanks to FlyBase Curators: Steve Marygold, Gillian Millburn, Steph Bunt, Simon Reeve, Pete McQuilton, Dave Osumi Sutherland, Ray Stefancsik, Nick Brown and Advisory Board members
  59. 59. Future• chado queries• XML config/s for clever editor• API in collaboration• JSP or J2EE/SOAP web interface • Helen Imogen Field • hif22 @ gen.cam.ac.uk

×