The document summarizes TAIR, a resource for Arabidopsis thaliana genome annotation, and its transition to institutional subscription funding after losing grant funding. It provides statistics on TAIR's curation of experimental gene function data from publications. Over the past 10 months, TAIR curated annotations for 940 new genes from 3,835 new publications. It promotes TAIR's value in its long history of high-quality, reliable data integration and community involvement. TAIR is working with other resources like AIP to provide more comprehensive plant genomics data.

1. 15 Years of Arabidopsis thaliana
Genome Annotation at TAIR:
Looking Back and Looking Ahead
Tanya Berardini, Ph.D

2. www.arabidopsis.org

3. TAIR and Subscription Funding
• Grant funding has ceased.
• TAIR staff wanted to continue providing this
resource to the research community.
• No other projects are currently funded to
provide the literature-derived data that is
TAIR’s specialty.

4. Institutional Subscribers
The Australian National
University
Centre for Cellular & Molecular Biology
Hyderabad (CCMB)
University of Leeds St. Louis University
University of Melbourne Jawaharlal Nehru University University of Leicester Stanford University
University of Queensland Weizmann Institute Auburn University
Stony Brook University, The State
University of New York
University of Western Australia Kazusa DNA Research Institute Brown University Texas A&M University
Gregor Mendel Institute Nagoya University Cold Spring Harbor Laboratory University of Arizona
IST Austria Nara Institute of Science and Technology Cornell University University of California Berkeley
Ghent University National Institute for Environmental Studies Dartmouth College University of California Davis
Agriculture and Agri-Food
Canada (AAFC)
RIKEN
Donald Danforth Plant Science
Center
University of California Irvine
McGill University
Korea Advanced Institute of Science and
Technology (KAIST)
Duke University
University of California Los Angeles
University of Montreal
Universidad Nacional Autonoma de Mexico Fralin Life Science Institute,
Virginia Tech University
University of California Merced
Chinese National Science and
Technology Library (NSTL)
University of Amsterdam
Indiana University, Bloomington
University of California Riverside
Copenhagen University
Institute of Biochemistry and Biophysics,
Polish Academy of Sciences
Iowa State University
University of California San Diego
Tartu University
King Abdullah University of Science and
Technology (KAUST)
Kansas State University
University of California Santa
Barbara

5. Institutional Subscribers
Helsinki University
Pohang University of Science and Technology
(POSTECH)
South Korea
Kenyon College
University of California Santa Cruz
University of Turku
Center for Research in Agricultural Genomics
(CRAG)
Michigan State University
University of Illinois at Urbana
Champaign
CNRS (Centre National de la
Recherche Scientifique)
Umea University New York University
University of Maryland, College Park
INRA (Institut National de la
Recherche Agronomique)
Swedish University of Agricultural Sciences
North Carolina State
University
University of Michigan
Helmholtz Zentrum Muenchen University of Lausanne The Ohio State University University of Minnesota
Leibniz Institute of Plant
Biochemistry
Academia Sinica Oklahoma State University
University of Nebraska-Lincoln
University of Cologne Edinburgh University Oregon State University University of Nevada, Reno
University of Erlangen-
Nuremberg
James Hutton Institute/SCRI Rockefeller University
University of North Carolina,
Charlotte
University of Goettingen
Norwich Bioscience Institutes - John Innes Centre
and The Sainsbury Laboratory
Rutgers, The State University
of New Jersey
University of North Texas
University of Hamburg University of Cambridge
The Samuel Roberts Noble
Foundation
University of Tennessee at Knoxville
University of Heidelberg University of Durham South Dakota State University University of Texas, Austin
University of Regensburg University of Exeter
Southern Illinois University,
Carbondale
University of Washington

7. 0
500
1000
1500
2000
2500
3000
3500
4000
4500
2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
Number of Arabidopsis Publications per Year

8. Data Generation/Extraction
• Gene function data
– Experimental data extracted from 8,929 articles
– 56,976 experimental GO annotations from articles
– 11,595 genes annotated with GO using experimental data
• Several thousand articles with gene data still uncurated

9. What’s new?
Since Sept. 1, 2013: (10 months)
• New publications: 3835
• New annotations: 940
• New gene symbols: 573
• Genes with new annotations: 459
• Genes with new publications: 2476

10. Total: 33,602 genes
• >10K labs all over the world, grant $$$$
• Lots of experiments, lots of papers
• New gene and gene function predictions
• Predictions must be based on experimental
results

11. Other Resources

12. Other Resources

13. Other Resources

14. Other Resources

15. Other Resources

16. Other Resources

17. The Future
• Works with complementary digital resources
to provide a complete set of data/tools for the
user community
• Working on making updated TAIR data
available to authenticated subscribers within
AIP
• New tools, services, data types, genomes

18. Come see us!
• Poster # P41007-A
• Booth # 415: Plant Genome Resources
Outreach
– Monday, 7/14, 12:30 – 1:30 pm and 3:30 – 4:30
pm
– Tuesday, 7/15, 10:30 – 11:30 am and 12-1 pm
• curator@arabidopsis.org
• info@phoenixbioinformatics.org

20. Special Minisymposium: Bioinformatic Resources for Plant Biology Research
This workshop will provide overviews of a variety of tools and resources likely to be of interest to plant biology
researchers. In addition to this workshop, the presenters will also be co-hosting two booths in the Exhibitors Area
and will be present to answer questions, etc.
7.45 pm Opening Remarks
7:50 pm 15 Years of Arabidopsis thaliana Genome Annotation at TAIR: Looking Back and Looking Ahead,Tanya
Berardini, TAIR
8:05 pm The First Release of the Arabidopsis Information Portal, Chris Town, JCVI
8:20 pm The iPlant Collaborative–Scalable Cyberinfrastructure for Life Science, Jason Williams, CSHL/iPlant
8:35 pm Gramene:A Resource for Comparative Plant Genomics, Pankaj Jaiswal, Oregon State University
8.50 pm PMN: metabolic pathway databases of 17 viridiplantae species, an introduction and demo of use cases,
Peifen Zhang, Carnegie Institution for Science
9:05 pm Medicago truncatula genome resources at JCVI, Chris Town, JCVI
9:20 pm Data Sets, Webservices and Visualization Apps from the Bio-Analytic Resource for use in the Arabidopsis
Information Portal and other Cyberinfrastructure Assets, Asher Pasha, University of Toronto
9:35 pm The DOE Systems Biology Knowledgebase: An integrated knowledgebase for biofuel research, Doreen
Ware and Sunita Kumari, Cold Spring Harbor Laboratory

21. EntrezGene
GO Ensembl
SIGNaL UniProt
AIPothers

22. EntrezGene
GO Ensembl
SIGNaL UniProt
AIPothers

23. Journals and Community

24. Community Input
Since Feb. 2008:
• Over 120334* Gene Ontology and Plant
Ontology annotations
• Over 670 papers
• 48 journals
• Over 560 authors
*4 submissions, >18K each

25. The Value of TAIR
• 15 year history
– Quality
– Immediacy
– Reliability (longevity, availability, stability)
– High visibility
– Familiarity and ease of use
• Integrated data and data analysis tools
– Organized, computationally accessible
• Community ownership
– Community annotation
– Help desk responsiveness
– Meeting/conference presence
Links
Publications
Phenotypes
Alleles
GO/PO Terms
Expression
Domains
Structure
Names

26. EntrezGene
GO Ensembl
SIGNaL UniProt
AIPothers

27. TAIR and AIP
• Complementary resources
• Working on providing TAIR subscriber only
information within AIP