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The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

E. Huala
2001 Nucleic Acids Research  
In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis  ...  This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).  ...  ACKNOWLEDGEMENTS TAIR is supported by NSF Grant DBI-9978564. This is Carnegie Institution of Washington Department of Plant Biology publication 1460.  ... 
doi:10.1093/nar/29.1.102 pmid:11125061 pmcid:PMC29827 fatcat:iueebr53jnbbdmvjfbsct5sjn4

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

S. Y. Rhee
2003 Nucleic Acids Research  
This information is made available through a comprehensive on-line resource called the Arabidopsis Information Resource (TAIR) (http://arabidopsis.org), which is accessible via commonly used web browsers  ...  Finally, we have recently incorporated seed and DNA stock information from the Arabidopsis Biological Resource Center (ABRC) and implemented a shopping-cart style on-line ordering system.  ...  ACKNOWLEDGEMENTS We thank the TAIR users and the Arabidopsis research community for their continuing support, feedback, and particularly for sharing their data and expertise.  ... 
doi:10.1093/nar/gkg076 pmid:12519987 pmcid:PMC165523 fatcat:wuwswvhywzei7kkkbozv3p6bfu

TAIR: a resource for integrated Arabidopsis data

Margarita Garcia-Hernandez, Tanya Berardini, Guanghong Chen, Debbie Crist, Aisling Doyle, Eva Huala, Emma Knee, Mark Lambrecht, Neil Miller, Lukas Mueller, Suparna Mundodi, Leonore Reiser (+9 others)
2002 Functional & Integrative Genomics  
The Arabidopsis Information Resource (TAIR; http://arabidopsis.org) provides an integrated view of genomic data for Arabidopsis thaliana.  ...  A significant new feature is the integration of the ABRC database functions and stock ordering system, which allows users to place orders for seed and DNA stocks directly from the TAIR site.  ...  Acknowledgements We would like to thank the TAIR users and the Arabidopsis research community for their continuing support, feedback, and particularly for sharing their data and expertise.  ... 
doi:10.1007/s10142-002-0077-z pmid:12444417 fatcat:tolsqcyr6rfudawr6ozmlxcely

The arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome

Tanya Z. Berardini, Leonore Reiser, Donghui Li, Yarik Mezheritsky, Robert Muller, Emily Strait, Eva Huala
2015 Genesis  
The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community  ...  TAIR provides tools for data visualization and analysis, and enables ordering of seed and DNA stocks, protein chips and other experimental resources.  ...  Acknowledgments TAIR is supported by national, academic institutional, corporate, and individual subscriptions (see, https://goo.gl/ NYY6cf for a list of institutional subscribers).  ... 
doi:10.1002/dvg.22877 pmid:26201819 pmcid:PMC4545719 fatcat:o4jldjd7lzfilomkzp7bvk4tay

Web-Based Arabidopsis Functional and Structural Genomics Resources

Yan Lu, Robert L. Last
2008 The Arabidopsis Book  
ACKNOWLEDGMENTS The Chloroplast 2010 Project was supported by the National Science Foundation (grant no. MCB-0519740).  ...  Resources are being developed to investigate the function, regulation and evolution of small-RNA-based silencing pathways in plants using Arabidopsis as the model system ( This project uses MPSS technology  ...  databases (for example, TAIR) and projectspecific databases (for example, Purdue Ionomics Information Management System).  ... 
doi:10.1199/tab.0118 pmid:22303243 pmcid:PMC3243351 fatcat:swsrfjpxszaobflnda7udjizwa

Design, Implementation and Maintenance of a Model Organism Database forArabidopsis thaliana

Danforth Weems, Neil Miller, Margarita Garcia-Hernandez, Eva Huala, Seung Y. Rhee
2004 Comparative and Functional Genomics  
TheArabidopsisInformation Resource (TAIR) is a web-based community database for the model plantArabidopsis thaliana.  ...  Biologists provide specification and use cases for the system, acquire, analyse and curate data, interact with users and test the software.  ...  Acknowledgements We are grateful to all of the members of the former and current TAIR team. The current members are Leonore  ... 
doi:10.1002/cfg.408 pmid:18629167 pmcid:PMC2447457 fatcat:k5s2k6zstjatvii76zynbjw45y

Bioinformatic Resources, Challenges, and Opportunities Using Arabidopsis As a Model Organism in a Post-Genomic Era

Seung Yon Rhee
2000 Plant Physiology  
For the research community to benefit from the vast pool of information, there is a need for comprehensive databases, information retrieval and analysis systems that are easily accessible to researchers  ...  I will also briefly discuss other resources such as the Arabidopsis Genome Resource (AGR) and a few genome annotation databases. Table I provides addresses for these and other relevant web sites.  ... 
doi:10.1104/pp.124.4.1460 pmid:11115859 fatcat:slhguk7feje57kske2jylgr3cm

Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

K. Mochida, K. Shinozaki
2011 Plant and Cell Physiology  
From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances  ...  Omics and bioinformatics are essential to understanding the molecular systems that underlie various plant functions.  ...  Acknowledgments The authors thank Tetsuya Sakurai, Takuhiro Yoshida, Lam-Son Phan Tran and Yuji Sawada of the RIKEN Plant Science Center, and Kei Iida of RIKEN BASE for their valuable suggestions and comments  ... 
doi:10.1093/pcp/pcr153 pmid:22156726 pmcid:PMC3233218 fatcat:5p4m7xlrknflrfbjfb4pwdug4u

PMRD: a curated database for genes and mutants involved in plant male reproduction

Xiao Cui, Qiudao Wang, Wenzhe Yin, Huayong Xu, Zoe A Wilson, Chaochun Wei, Shenyuan Pan, Dabing Zhang
2012 BMC Plant Biology  
Description: Plant Male Reproduction Database (PMRD) is a comprehensive resource for browsing and retrieving knowledge on genes and mutants related to plant male reproduction.  ...  The aim of this study is to manually curate such gene and mutant information and provide a web-accessible resource to facilitate the effective study of plant male reproduction.  ...  Plant Male Reproduction Database (PMRD) is a comprehensive resource for browsing and retrieving knowledge about genes and mutants related to plant male reproduction.  ... 
doi:10.1186/1471-2229-12-215 pmid:23153247 pmcid:PMC3607949 fatcat:gdg5ee3xcjg6lhwdcz4c62ofi4

Omics databases in plant science: key to systems biology

Keita Suwabe, Kentaro Yano
2008 Plant Biotechnology  
Here, we review the current state of web databases and bioinformatics tools for plant biosciences and systems biology.  ...  This wealth of comprehensive online resources and web databases allow us to extract essential new biological information beyond a dataset obtained from an individual study.  ...  Acknowledgements This work was supported in part by Grants-in-Aid for Special Research on Priority Areas (19043015) to KY from the Ministry of Education, Culture, Sports, Science and Technology of Japan  ... 
doi:10.5511/plantbiotechnology.25.413 fatcat:becq535uhrhblmxw5qe6vllcre

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics

H. Schoof
2004 Nucleic Acids Research  
The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer  ...  This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications.  ...  MAtDB is funded by the GABI (http://www. gabi.de, BMBF FKZ 0312270/4) and PlaNet (http://www. eu-plant-genome.net, EU Framework V; QLRI-CT-2001-00006) projects.  ... 
doi:10.1093/nar/gkh068 pmid:14681437 pmcid:PMC308802 fatcat:ibbu7g46szfpppwuurtk2pdmve

Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems [chapter]

Leonore Reiser, Lukas A. Mueller, Seung Yon Rhee
2002 Functional Genomics  
We cite examples of resources available in the public domain and describe some of the software for data management systems currently available for plant research.  ...  In addition, we discuss a few concepts of data management from the perspective of an individual or group that wishes to provide data to the public databases, to use the information in the public databases  ...  Acknowledgments We thank Drs David Flanders and Angela Baldo for their contributions to the text and Eva Huala and Chris Somerville for their comments on the manuscript.  ... 
doi:10.1007/978-94-010-0448-0_5 fatcat:346nflg7cnh3rotodtz6f4sfwq

Preliminary Study on the Impact of Literature Curation in a Model Organism Database on Article Citation Rates

Tanya Berardini, Ron Daniel, Amanda Clare, Michael Lauruhn, Leonore Reiser
2016 D-Lib Magazine  
The Arabidopsis Information Resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Research 29:102-105.  ...  Leonore Reiser is a Scientific Curator for The Arabidopsis Information Resource and Phoenix Bioinformatics where she curates research literature about the model plant Arabidopsis thaliana and helps develop  ... 
doi:10.1045/september2016-berardini fatcat:udzvw2d3pneoddv2vkhtveiv2q

AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks

S. K. Palaniswamy, S. James, H. Sun, R. S. Lamb, R. V. Davuluri, E. Grotewold
2006 Plant Physiology  
To integrate this information into a Webbased knowledgebase, we have developed the Arabidopsis Gene Regulatory Information Server (AGRIS).  ...  AGRIS can be accessed at Curators for AGRIS Currently, there are curators for some families; based on our request and their expertise, the curators help us validate data through cross-verification approach  ...  ACKNOWLEDGMENTS We thank Sarat Subramanian for his help in AtTFDB, and Twyla Pohar for her comments and header design for the Web site.  ... 
doi:10.1104/pp.105.072280 pmid:16524982 pmcid:PMC1400579 fatcat:nozjjocitnbm5ilyfdfsjasyei

PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction

M. Krallinger, C. Rodriguez-Penagos, A. Tendulkar, A. Valencia
2009 Nucleic Acids Research  
molecular aspects of the plant model organism Arabidopsis thaliana.  ...  Here we present PLAN2L, a web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and  ...  Another system primarily used for literature curation by model organism databases is Textpresso (9) , now integrated at TAIR to facilitate a better access to information relevant for Arabidopsis.  ... 
doi:10.1093/nar/gkp484 pmid:19520768 pmcid:PMC2703909 fatcat:2jjdk7efzrcwdowjgqbdhxwctm
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