Literature DB >> 18629167

Design, implementation and maintenance of a model organism database for Arabidopsis thaliana.

Danforth Weems1, Neil Miller, Margarita Garcia-Hernandez, Eva Huala, Seung Y Rhee.   

Abstract

The Arabidopsis Information Resource (TAIR) is a web-based community database for the model plant Arabidopsis thaliana. It provides an integrated view of genes, sequences, proteins, germplasms, clones, metabolic pathways, gene expression, ecotypes, polymorphisms, publications, maps and community information. TAIR is developed and maintained by collaboration between software developers and biologists. Biologists provide specification and use cases for the system, acquire, analyse and curate data, interact with users and test the software. Software developers design, implement and test the database and software. In this review, we briefly describe how TAIR was built and is being maintained.

Entities:  

Year:  2004        PMID： 18629167      PMCID： PMC2447457          DOI： 10.1002/cfg.408

Source DB:  PubMed          Journal:  Comp Funct Genomics        ISSN： 1531-6912


  12 in total

1.  Seed and molecular resources for Arabidopsis.

Authors:  R L Scholl; S T May; D H Ware
Journal:  Plant Physiol       Date:  2000-12       Impact factor: 8.340

2.  Genomics. Plant biology in 2010.

Authors:  C Somerville
Journal:  Science       Date:  2000-12-15       Impact factor: 47.728

Review 3.  Legume genomes: more than peas in a pod.

Authors:  Nevin Dale Young; Joann Mudge; T H Noel Ellis
Journal:  Curr Opin Plant Biol       Date:  2003-04       Impact factor: 7.834

4.  The Pathway Tools software.

Authors:  Peter D Karp; Suzanne Paley; Pedro Romero
Journal:  Bioinformatics       Date:  2002       Impact factor: 6.937

Review 5.  Arabidopsis map-based cloning in the post-genome era.

Authors:  Georg Jander; Susan R Norris; Steven D Rounsley; David F Bush; Irena M Levin; Robert L Last
Journal:  Plant Physiol       Date:  2002-06       Impact factor: 8.340

Review 6.  Donor management and selection for heart transplantation.

Authors:  Ranjit John
Journal:  Semin Thorac Cardiovasc Surg       Date:  2004

7.  A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

Authors:  Jun Yu; Songnian Hu; Jun Wang; Gane Ka-Shu Wong; Songgang Li; Bin Liu; Yajun Deng; Li Dai; Yan Zhou; Xiuqing Zhang; Mengliang Cao; Jing Liu; Jiandong Sun; Jiabin Tang; Yanjiong Chen; Xiaobing Huang; Wei Lin; Chen Ye; Wei Tong; Lijuan Cong; Jianing Geng; Yujun Han; Lin Li; Wei Li; Guangqiang Hu; Xiangang Huang; Wenjie Li; Jian Li; Zhanwei Liu; Long Li; Jianping Liu; Qiuhui Qi; Jinsong Liu; Li Li; Tao Li; Xuegang Wang; Hong Lu; Tingting Wu; Miao Zhu; Peixiang Ni; Hua Han; Wei Dong; Xiaoyu Ren; Xiaoli Feng; Peng Cui; Xianran Li; Hao Wang; Xin Xu; Wenxue Zhai; Zhao Xu; Jinsong Zhang; Sijie He; Jianguo Zhang; Jichen Xu; Kunlin Zhang; Xianwu Zheng; Jianhai Dong; Wanyong Zeng; Lin Tao; Jia Ye; Jun Tan; Xide Ren; Xuewei Chen; Jun He; Daofeng Liu; Wei Tian; Chaoguang Tian; Hongai Xia; Qiyu Bao; Gang Li; Hui Gao; Ting Cao; Juan Wang; Wenming Zhao; Ping Li; Wei Chen; Xudong Wang; Yong Zhang; Jianfei Hu; Jing Wang; Song Liu; Jian Yang; Guangyu Zhang; Yuqing Xiong; Zhijie Li; Long Mao; Chengshu Zhou; Zhen Zhu; Runsheng Chen; Bailin Hao; Weimou Zheng; Shouyi Chen; Wei Guo; Guojie Li; Siqi Liu; Ming Tao; Jian Wang; Lihuang Zhu; Longping Yuan; Huanming Yang
Journal:  Science       Date:  2002-04-05       Impact factor: 47.728

8.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).

Authors:  Stephen A Goff; Darrell Ricke; Tien-Hung Lan; Gernot Presting; Ronglin Wang; Molly Dunn; Jane Glazebrook; Allen Sessions; Paul Oeller; Hemant Varma; David Hadley; Don Hutchison; Chris Martin; Fumiaki Katagiri; B Markus Lange; Todd Moughamer; Yu Xia; Paul Budworth; Jingping Zhong; Trini Miguel; Uta Paszkowski; Shiping Zhang; Michelle Colbert; Wei-lin Sun; Lili Chen; Bret Cooper; Sylvia Park; Todd Charles Wood; Long Mao; Peter Quail; Rod Wing; Ralph Dean; Yeisoo Yu; Andrey Zharkikh; Richard Shen; Sudhir Sahasrabudhe; Alun Thomas; Rob Cannings; Alexander Gutin; Dmitry Pruss; Julia Reid; Sean Tavtigian; Jeff Mitchell; Glenn Eldredge; Terri Scholl; Rose Mary Miller; Satish Bhatnagar; Nils Adey; Todd Rubano; Nadeem Tusneem; Rosann Robinson; Jane Feldhaus; Teresita Macalma; Arnold Oliphant; Steven Briggs
Journal:  Science       Date:  2002-04-05       Impact factor: 47.728

9.  Maize genome sequencing by methylation filtration.

Authors:  Lance E Palmer; Pablo D Rabinowicz; Andrew L O'Shaughnessy; Vivekanand S Balija; Lidia U Nascimento; Sujit Dike; Melissa de la Bastide; Robert A Martienssen; W Richard McCombie
Journal:  Science       Date:  2003-12-19       Impact factor: 47.728

10.  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.

Authors:  Seung Yon Rhee; William Beavis; Tanya Z Berardini; Guanghong Chen; David Dixon; Aisling Doyle; Margarita Garcia-Hernandez; Eva Huala; Gabriel Lander; Mary Montoya; Neil Miller; Lukas A Mueller; Suparna Mundodi; Leonore Reiser; Julie Tacklind; Dan C Weems; Yihe Wu; Iris Xu; Daniel Yoo; Jungwon Yoon; Peifen Zhang
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971
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  4 in total

1.  Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.

Authors:  Johannes Griss; María Martín; Claire O'Donovan; Rolf Apweiler; Henning Hermjakob; Juan Antonio Vizcaíno
Journal:  Proteomics       Date:  2011-10-17       Impact factor: 3.984

2.  Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.

Authors:  Johannes Griss; Richard G Côté; Christopher Gerner; Henning Hermjakob; Juan Antonio Vizcaíno
Journal:  Mol Cell Proteomics       Date:  2011-06-23       Impact factor: 5.911

Review 3.  It's Hard to Avoid Avoidance: Uncoupling the Evolutionary Connection between Plant Growth, Productivity and Stress "Tolerance".

Authors:  Albino Maggio; Ray A Bressan; Yang Zhao; Junghoon Park; Dae-Jin Yun
Journal:  Int J Mol Sci       Date:  2018-11-20       Impact factor: 5.923

4.  MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools.

Authors:  Chun Liang; Feng Sun; Haiming Wang; Junfeng Qu; Robert M Freeman; Lee H Pratt; Marie-Michèle Cordonnier-Pratt
Journal:  BMC Bioinformatics       Date:  2006-03-07       Impact factor: 3.169
  4 in total

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