TAIR Workshop Model Organism Databases and Community Annotation Plant and Animal Genome XVI Conference, San Diego January 13, 2008

2 Curator-User collaborations in various databases Karen Yook Issak Yosief Tecle Donghui Li Philippe Lamesch

Community Annotation at TAIR Philippe Lamesch Donghui Li

4 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 Outline

5 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 Outline

6 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

7 TAIR website:

8 TAIR is used worldwide Visits per month (source: Google Analytics)

9 What we do: (1) Arabidopsis genome annotation Swarbreck et al, Nuclear Acids Research 2007

10 What we do: (2) manual literature curation Controlled vocabulary annotations Gene Ontology Plant Ontology Gene name, symbol Allele, phenotype Summary statement composition

11 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.

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

13 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 Outline

14 Why encourage community annotation? Year # of articles Arabidopsis literature

15 Why encourage community annotation? We need help!

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 Benefits for the community  Increased data accessibility unpublished data data from publications that are not curated by us  Up to date information  Improved accuracy

17 Big issues in community annotation Curators Community Meetings, workshops Contact authors, project PIs Invite experts for on-site annotation jamboree How to get the community involved?

18 Big issues in community annotation Curators Community Submission forms (gene function) Post comments on TAIR website (comments on individual gene/seed stock) Customized submission for large datasets helpdesk (questions, errors, omissions) Tools and methods for community annotation

19 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 Outline

20 How to submit data to TAIR? Submission methodExample Submission formGene functional annotation Direct submission on TAIR websiteAdd Comments on individual gene Customized submission process Large-scale datasets (e.g. Arabidopsis 2010 Project data submission) By corrections, omissions

21 Community annotation process: an example

22 Submission page

23 61 gene products, 204 annotations 1. User: download, fill in and send back the submission form

24 2. Curator: review and curate data phloem = PO:

25 3. Curator: data loading

26 Community annotation on TAIR

27 How to submit data to TAIR? Submission methodExample Submission formGene functional annotation Direct submission on TAIR websiteAdd Comments on individual gene Customized submission process Large-scale datasets (e.g. Arabidopsis 2010 Project data submission) By corrections, omissions

28 User comments on TAIR website

29 User comments on TAIR website

30 How to submit data to TAIR? Submission methodExample Submission formGene functional annotation Direct submission on TAIR websiteAdd Comments on individual gene Customized submission process Large-scale datasets (e.g. Arabidopsis 2010 Project data submission) By corrections, omissions

31 NSF Arabidopsis 2010 Project Year funded Funded projects (*) Contacted Data submitted Data promised Contact but did not reply Total *Source: National Science Foundation; numbers updated 01/08 To determine the function of each Arabidopsis gene by 2010

32 Processing time “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] From TAIR users:

33 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 Outline

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

35 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

36 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

37 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 Outline

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