0
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

285

Published on

Published in: Design
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
285
On Slideshare
0
From Embeds
0
Number of Embeds
0
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • \n
  • Transcript of "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
    1. A particular slide catching your eye?

      Clipping is a handy way to collect important slides you want to go back to later.

    ×