Literature DB >> 22751211

Taking the next step: building an Arabidopsis information portal.

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Abstract

The Arabidopsis information portal (AIP), a resource expected to provide access to all community data and combine outputs into a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics Consortium (IAIC). The design of the AIP will provide core functionality while remaining flexible to encourage multiple contributors and constant innovation. An IAIC-hosted Design Workshop in December 2011 proposed a structure for the AIP to provide a framework for the minimal components of a functional community portal while retaining flexibility to rapidly extend the resource to other species. We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner.

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Year:  2012        PMID: 22751211      PMCID: PMC3406920          DOI: 10.1105/tpc.112.100669

Source DB:  PubMed          Journal:  Plant Cell        ISSN: 1040-4651            Impact factor:   11.277


  36 in total

1.  MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data.

Authors:  Hiren J Joshi; Matthias Hirsch-Hoffmann; Katja Baerenfaller; Wilhelm Gruissem; Sacha Baginsky; Robert Schmidt; Waltraud X Schulze; Qi Sun; Klaas J van Wijk; Volker Egelhofer; Stefanie Wienkoop; Wolfram Weckwerth; Christophe Bruley; Norbert Rolland; Tetsuro Toyoda; Hirofumi Nakagami; Alexandra M Jones; Steven P Briggs; Ian Castleden; Sandra K Tanz; A Harvey Millar; Joshua L Heazlewood
Journal:  Plant Physiol       Date:  2010-11-12       Impact factor: 8.340

2.  Gramene: a resource for comparative grass genomics.

Authors:  Doreen Ware; Pankaj Jaiswal; Junjian Ni; Xiaokang Pan; Kuan Chang; Kenneth Clark; Leonid Teytelman; Steve Schmidt; Wei Zhao; Samuel Cartinhour; Susan McCouch; Lincoln Stein
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  MetaCyc and AraCyc. Metabolic pathway databases for plant research.

Authors:  Peifen Zhang; Hartmut Foerster; Christophe P Tissier; Lukas Mueller; Suzanne Paley; Peter D Karp; Seung Y Rhee
Journal:  Plant Physiol       Date:  2005-05       Impact factor: 8.340

4.  The 1001 genomes project for Arabidopsis thaliana.

Authors:  Detlef Weigel; Richard Mott
Journal:  Genome Biol       Date:  2009-05-27       Impact factor: 13.583

5.  agriGO: a GO analysis toolkit for the agricultural community.

Authors:  Zhou Du; Xin Zhou; Yi Ling; Zhenhai Zhang; Zhen Su
Journal:  Nucleic Acids Res       Date:  2010-04-30       Impact factor: 16.971

6.  Cytoscape 2.8: new features for data integration and network visualization.

Authors:  Michael E Smoot; Keiichiro Ono; Johannes Ruscheinski; Peng-Liang Wang; Trey Ideker
Journal:  Bioinformatics       Date:  2010-12-12       Impact factor: 6.937

7.  AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.

Authors:  Jian Cui; Peng Li; Guang Li; Feng Xu; Chen Zhao; Yuhua Li; Zhongnan Yang; Guang Wang; Qingbo Yu; Yixue Li; Tieliu Shi
Journal:  Nucleic Acids Res       Date:  2007-10-25       Impact factor: 16.971

8.  GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.

Authors:  Eran Eden; Roy Navon; Israel Steinfeld; Doron Lipson; Zohar Yakhini
Journal:  BMC Bioinformatics       Date:  2009-02-03       Impact factor: 3.169

9.  ATTED-II provides coexpressed gene networks for Arabidopsis.

Authors:  Takeshi Obayashi; Shinpei Hayashi; Motoshi Saeki; Hiroyuki Ohta; Kengo Kinoshita
Journal:  Nucleic Acids Res       Date:  2008-10-25       Impact factor: 16.971

10.  An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets.

Authors:  Debbie Winter; Ben Vinegar; Hardeep Nahal; Ron Ammar; Greg V Wilson; Nicholas J Provart
Journal:  PLoS One       Date:  2007-08-08       Impact factor: 3.240

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  16 in total

1.  ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology.

Authors:  Jamie Waese; Jim Fan; Asher Pasha; Hans Yu; Geoffrey Fucile; Ruian Shi; Matthew Cumming; Lawrence A Kelley; Michael J Sternberg; Vivek Krishnakumar; Erik Ferlanti; Jason Miller; Chris Town; Wolfgang Stuerzlinger; Nicholas J Provart
Journal:  Plant Cell       Date:  2017-08-14       Impact factor: 11.277

2.  Araport Lives: An Updated Framework for Arabidopsis Bioinformatics.

Authors:  Asher Pasha; Shabari Subramaniam; Alan Cleary; Xingguo Chen; Tanya Berardini; Andrew Farmer; Christopher Town; Nicholas Provart
Journal:  Plant Cell       Date:  2020-07-22       Impact factor: 11.277

3.  RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing.

Authors:  Ann E Loraine; Sheila McCormick; April Estrada; Ketan Patel; Peng Qin
Journal:  Plant Physiol       Date:  2013-04-16       Impact factor: 8.340

4.  From bench to bountiful harvests: a road map for the next decade of Arabidopsis research.

Authors:  Irene Lavagi; Mark Estelle; Wolfram Weckwerth; Jim Beynon; Ruth M Bastow
Journal:  Plant Cell       Date:  2012-06-29       Impact factor: 11.277

5.  Mobile small RNAs regulate genome-wide DNA methylation.

Authors:  Mathew G Lewsey; Thomas J Hardcastle; Charles W Melnyk; Attila Molnar; Adrián Valli; Mark A Urich; Joseph R Nery; David C Baulcombe; Joseph R Ecker
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-19       Impact factor: 11.205

6.  UniProtKB amid the turmoil of plant proteomics research.

Authors:  Michel Schneider; Sylvain Poux
Journal:  Front Plant Sci       Date:  2012-12-06       Impact factor: 5.753

7.  Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.

Authors:  Anna Flis; Aurora Piñas Fernández; Tomasz Zielinski; Virginie Mengin; Ronan Sulpice; Kevin Stratford; Alastair Hume; Alexandra Pokhilko; Megan M Southern; Daniel D Seaton; Harriet G McWatters; Mark Stitt; Karen J Halliday; Andrew J Millar
Journal:  Open Biol       Date:  2015-10       Impact factor: 6.411

8.  Correlation networks visualization.

Authors:  Nicholas Provart
Journal:  Front Plant Sci       Date:  2012-10-29       Impact factor: 5.753

9.  PhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt.

Authors:  Monika Zulawski; Rostyslav Braginets; Waltraud X Schulze
Journal:  Nucleic Acids Res       Date:  2012-11-20       Impact factor: 16.971

Review 10.  MASCP gator: an overview of the Arabidopsis proteomic aggregation portal.

Authors:  Gregory W Mann; Paul C Calley; Hiren J Joshi; Joshua L Heazlewood
Journal:  Front Plant Sci       Date:  2013-10-23       Impact factor: 5.753

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