2014 ASPB Presentation- Berardini
- 1. 15 Years of Arabidopsis thaliana Genome Annotation at TAIR: Looking Back and Looking Ahead Tanya Berardini, Ph.D
- 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
- 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
- 27. TAIR and AIP • Complementary resources • Working on providing TAIR subscriber only information within AIP