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PAG2008_partI

VIEWS: 2 PAGES: 38

									             TAIR Workshop
 Model Organism Databases and
    Community Annotation




Plant and Animal Genome XVI Conference, San Diego
                  January 13, 2008
Curator-User collaborations in various databases



                       Karen Yook

  Issak Yosief Tecle


                          Donghui Li
                          Philippe Lamesch




                                                   2
Community Annotation at TAIR


        Philippe Lamesch
            Donghui Li
     curator@arabidopsis.org
Outline




 • Introduction to TAIR
 • Community annotation at TAIR: an overview
 • Community annotation: process and examples (gene
   function annotation)
 • New initiative on encouraging community annotation:
   collaborations between Publisher and MODs
 • Phil: community involvement in genome annotation




                                                         4
Outline




 • Introduction to TAIR
 • Community annotation at TAIR: an overview
 • Community annotation: process and examples (gene
   function annotation)
 • New initiative on encouraging community annotation:
   collaborations between Publisher and MODs
 • Phil: community involvement in genome annotation




                                                         5
Who we are




 • The Arabidopsis Information Resource (TAIR)
   maintains a database of genetic and molecular
   biology data for the model plant Arabidopsis


 • Funded by NSF




                                                   6
TAIR website: www.arabidopsis.org




                                    7
TAIR is used worldwide

           Visits per month (source: Google Analytics)




                                                         8
What we do: (1) Arabidopsis genome annotation




                       Swarbreck et al, Nuclear Acids Research 2007
                                                                  9
What we do: (2) manual literature curation




 • Controlled vocabulary annotations
        Gene Ontology
        Plant Ontology
 • Gene name, symbol
 • Allele, phenotype
 • Summary statement composition




                                             10
What we do: (3) metabolic pathway curation




 AraCyc:

 A metabolic pathway database for Arabidopsis thaliana
 that contains information about both predicted and
 experimentally determined pathways, reactions,
 compounds, genes and enzymes.




                                                         11
What we do: (4) work with ABRC to distribute research materials




                                                           12
Outline




 • Introduction to TAIR
 • Community annotation at TAIR: an overview
 • Community annotation: process and examples (gene
   function annotation)
 • New initiative on encouraging community annotation:
   collaborations between Publisher and MODs
 • Phil: community involvement in genome annotation




                                                         13
          Why encourage community annotation?



                                     Arabidopsis literature
                2500



                2000
# of articles




                1500



                1000



                500



                  0
                       1999   2000    2001    2002   2003     2004   2005   2006



                                             Year

                                                                               14
Why encourage community annotation?


                   We need help!




                                      15
Why encourage community annotation?




Benefits for the community
   Increased data accessibility
       unpublished data
       data from publications that are not curated by us
   Up to date information
   Improved accuracy




                                                           16
Big issues in community annotation




Curators
                     How to get the community involved?

                     Meetings, workshops
                     Contact authors, project PIs
                     Invite experts for on-site annotation jamboree




Community


                                                                 17
Big issues in community annotation




Curators
                     Tools and methods for community annotation

                     Submission forms (gene function)
                     Post comments on TAIR website (comments
                     on individual gene/seed stock)
                     Customized submission for large datasets

                     Email helpdesk curator@arabidopsis.org
                     (questions, errors, omissions)
Community


                                                                18
Outline




 • Introduction to TAIR
 • Community annotation at TAIR: an overview
 • Community annotation: process and examples (gene
   function annotation)
 • New initiative on encouraging community annotation:
   collaborations between Publisher and MODs
 • Phil: community involvement in genome annotation




                                                         19
How to submit data to TAIR?




Submission method                    Example



Submission form                      Gene functional annotation



Direct submission on TAIR website    Add Comments on individual gene


                                     Large-scale datasets (e.g. Arabidopsis
Customized submission process
                                     2010 Project data submission)


By email (curator@arabidopsis.org)   Errors, corrections, omissions




                                                                              20
Community annotation process: an example




                                           21
Submission page




                  22
1. User: download, fill in and send back the
submission form

61 gene products, 204 annotations




                                               23
2. Curator: review and curate data




                phloem = PO:0005417




                                      24
3. Curator: data loading




                           25
Community annotation on TAIR




                               26
How to submit data to TAIR?




Submission method                    Example



Submission form                      Gene functional annotation



Direct submission on TAIR website    Add Comments on individual gene


                                     Large-scale datasets (e.g. Arabidopsis
Customized submission process
                                     2010 Project data submission)


By email (curator@arabidopsis.org)   Errors, corrections, omissions




                                                                              27
User comments on TAIR website




                                28
User comments on TAIR website




                                29
How to submit data to TAIR?




Submission method                    Example



Submission form                      Gene functional annotation



Direct submission on TAIR website    Add Comments on individual gene


                                     Large-scale datasets (e.g. Arabidopsis
Customized submission process
                                     2010 Project data submission)


By email (curator@arabidopsis.org)   Errors, corrections, omissions




                                                                              30
NSF Arabidopsis 2010 Project


    To determine the function of each Arabidopsis gene by 2010

 Year      Funded                               Data           Data       Contact but
                             Contacted
 funded    projects (*)                         submitted      promised   did not reply

 2005      16                15                 8              6          1

 2004      14                14                 5              9          -

 2003      14                13                 7              5          -

 2002      16                15                 6              6          2

 2001      27                25                 13             9          2

 Total     87                80                 39             35         5

 *Source: National Science Foundation; numbers updated 01/08



                                                                                      31
Processing time



             From TAIR users:

             “Fabulous news! I should have thought of submitting it
             earlier. And thank you for such an informative and
             organized website. It was THE mainstay of my thesis
             research, which featured 22k microarrays.” [Donna
             Lindsay, University of Saskatchewan, Canada]

             “Its perfect! Thank you very much for you rapidity.”
             [Fabienne Granierg, Institut Jean-Pierre Bourgin - INRA,
             France]

             “Thanks for your rapid response.” [Qunfeng Dong, China]

             “Thanks for your good work.” [Sabeeha Merchant, UCLA]


                                                                        32
Outline




 • Introduction to TAIR
 • Community annotation at TAIR: an overview
 • Community annotation: process and examples (gene
   function annotation)
 • New initiative on encouraging community annotation:
   collaborations between Publisher and MODs
 • Phil: community involvement in genome annotation




                                                         33
2006 high priority journals



CELL                      FEBS LETTERS
CURRENT BIOLOGY           GENETICS
DEVELOPMENT               JOURNAL OF BIOLOGICAL CHEMISTRY
GENES AND DEVELOPMENT     MOLECULAR PLANT-MICROBE INTERACTIONS
NATURE                    PLANT MOLECULAR BIOLOGY
NATURE CELL BIOLOGY       PLANT PHYSIOLOGY
NATURE GENETICS
NUCLEIC ACIDS RESEARCH
PLoS biology
PNAS
SCIENCE
THE EMBO JOURNAL
THE PLANT CELL
THE PLANT JOURNAL
TRENDS IN PLANT SCIENCE


                                                         34
Collaboration between Publishers and TAIR



Editorial board meeting in July 2007

Our proposal: request the following additional
information from authors after paper is accepted:

• AGI Locus identifier/s (e.g. At1g01040)
    Provides clarity, avoid nomenclature conflicts

• Gene function annotation linked to AGI Loci with
method
    Up-to-date information about Arabidopsis genes
    from Plant Physiology is available at TAIR




                                                     35
Collaboration between Publishers and TAIR




              • Launch of new feature via Benchpress

              • Authors fill in an online form in TAIR-
                suggested format

              • Data sent to TAIR for processing




                                                          36
Outline




 • Introduction to TAIR
 • Community annotation at TAIR: an overview
 • Community annotation: process and examples (gene
   function annotation)
 • New initiative on encouraging community annotation:
   collaborations between Publisher and MODs
 • Phil: community involvement in genome annotation




                                                         37
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