TAIR: The Arabidopsis Information Resource

TAIR:拟南芥信息资源

基本信息

  • 批准号:
    0417062
  • 负责人:
  • 金额:
    --
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Cooperative Agreement
  • 财政年份:
    2004
  • 资助国家:
    美国
  • 起止时间:
    2004-09-01 至 2009-08-31
  • 项目状态:
    已结题

项目摘要

Recent technical advances in large scale sequencing and genomics methods have triggered a scientific revolution with immense potential for extending biological knowledge. They have also posed an immense challenge: how to make optimal use of vast quantities of biological data. Without long-term high quality mechanisms for accessing and analyzing the data, the resources used in generating the data are in danger of going to waste. It is essential that databases to house the data, tools and interfaces to provide access to the data, and curatorial efforts to organize data for maximum utility be established and supported for the long term. For the model plant Arabidopsis, the successful effort to sequence the genome and the current effort of the 2010 Functional Genomics Initiative to understand the function of every Arabidopsis gene have produced great quantities of valuable data which can only be put to maximal use if the information is stored, interrelated, updated and made accessible to researchers for the long term. TAIR (the Arabidopsis Information Resource, www.arabidopsis.org) has taken up the challenge posed by this flood of data in its first five years of funding, developing a data structure to house the diversity of available data along with tools and interfaces needed to access and analyze it. The aim of the second phase of this project is to maintain the data and tools currently existing in TAIR and add new efforts in key areas, including maintaining and improving the genome annotation, extracting phenotype and gene expression data from the literature, and improving accessibility of TAIR's resources to all biologists, teachers, students and the general public through development of tutorials and improved site navigation. TAIR will continue to develop controlled vocabularies and standardized data exchange mechanisms for maximal interoperability with other biological databases and will provide data in explicitly defined and structured formats to facilitate programmatic data retrieval. TAIR will also continue to play a central role within the 2010 Functional Genomics Initiative as the site where researchers can browse existing projects, view lists of genes already under investigation by other groups, and search for genes with no known function. TAIR will incorporate the resulting functional data and develop a tool that tracks progress toward the 2010 goal of complete functional annotation. Intellectual merit: Transformation of large quantities of data into useful knowledge is one of the biggest problems in today's post-sequencing era of biological research. Extraction of experimentally verified information from the corpus of research literature and encoding of the information using explicitly defined and computable ontologies representing biological concepts will facilitate the analysis and interpretation of large-scale data sets. In addition, creation and population of a data model for the complex relationships between biological objects will create a comprehensive computational framework for mining, exploring and retrieving the data. Development of standardized data curation methods also benefits the whole biological research community.Broader Impact: The Internet is a widely accessed source of information for researchers and students. Creation of interactive, on-line tutorials and user guides for students, plant researchers with no or little Arabidopsis knowledge and Arabidopsis experts will provide educational materials that can be used in classrooms, laboratories, workshops and for self-paced learning. Dissemination of research methods and data through TAIR will benefit scientists all over the world and foster international collaboration. Continuous integration and annotation of data by TAIR's curators will ensure that researchers have access to current, accurate data that would otherwise require significant time and effort to amass individually. Through collaborations with educators, college and pre-college students will access research materials to generate authentic data as they learn about scientific inquiry and plant biology, which will be disseminated to the research community through TAIR.
大规模测序和基因组学方法的最新技术进步引发了一场科学革命,具有扩展生物学知识的巨大潜力。它们还提出了一个巨大的挑战:如何最佳利用大量生物数据。如果没有长期的高质量机制来访问和分析数据,用于生成数据的资源就有浪费的危险。必须建立和长期支持存放数据的数据库、提供数据访问的工具和界面,以及组织数据以实现最大效用的策展工作。 对于模式植物拟南芥,基因组测序的成功努力和2010年功能基因组学计划目前为了解每个拟南芥基因的功能所做的努力产生了大量有价值的数据,这些数据只有在信息被存储,相互关联,更新并长期供研究人员访问时才能得到最大限度的利用。TAIR(the Arabidopsis Information Resource,www.arabidopsis.org)在其最初的五年资助中接受了这一数据洪流所带来的挑战,开发了一个数据结构,以容纳可用数据的多样性,沿着提供访问和分析数据所需的工具和接口。该项目的第二阶段旨在维护TAIR中现有的数据和工具,并在关键领域增加新的努力,包括维护和改进基因组注释,从文献中提取表型和基因表达数据,并通过开发教程和改进网站导航,提高所有生物学家、教师、学生和公众对TAIR资源的可访问性。 TAIR将继续开发受控词汇表和标准化数据交换机制,以实现与其他生物数据库的最大互操作性,并将以明确定义和结构化的格式提供数据,以便利程序化数据检索。TAIR还将继续在2010年功能基因组学倡议中发挥核心作用,研究人员可以在该网站浏览现有项目,查看其他小组正在研究的基因列表,并搜索未知功能的基因。 TAIR将整合由此产生的功能数据,并开发一种工具,跟踪实现2010年完整功能注释目标的进展。 智力优点:将大量数据转化为有用的知识是当今后测序时代生物研究的最大问题之一。从研究文献语料库中提取实验验证的信息,并使用明确定义的和可计算的生物概念本体对信息进行编码,将有助于分析和解释大规模数据集。此外,为生物对象之间的复杂关系创建和填充数据模型将创建用于挖掘、探索和检索数据的综合计算框架。 标准化数据管理方法的发展也有利于整个生物学研究社区。更广泛的影响:互联网是研究人员和学生广泛访问的信息来源。创建交互式,在线教程和用户指南的学生,植物研究人员没有或很少拟南芥知识和拟南芥专家将提供教育材料,可用于教室,实验室,研讨会和自定进度的学习。通过TAIR传播研究方法和数据将使全世界的科学家受益,并促进国际合作。TAIR策展人对数据的持续整合和注释将确保研究人员能够获得最新的准确数据,否则需要花费大量的时间和精力来单独收集这些数据。通过与教育工作者的合作,大学和大学预科学生将访问研究材料,以生成真实的数据,因为他们了解科学探究和植物生物学,这将通过TAIR传播给研究界。

项目成果

期刊论文数量(0)
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Seung Rhee其他文献

MIAME/Plant – adding value to plant microarrray experiments
  • DOI:
    10.1186/1746-4811-2-1
  • 发表时间:
    2006-01-09
  • 期刊:
  • 影响因子:
    4.400
  • 作者:
    Philip Zimmermann;Beatrice Schildknecht;David Craigon;Margarita Garcia-Hernandez;Wilhelm Gruissem;Sean May;Gaurab Mukherjee;Helen Parkinson;Seung Rhee;Ulrich Wagner;Lars Hennig
  • 通讯作者:
    Lars Hennig

Seung Rhee的其他文献

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{{ truncateString('Seung Rhee', 18)}}的其他基金

TRTech-PGR: Establishing a one-stop-shop for plant metabolism annotations and launching a plant enzyme function consortium
TRTech-PGR:建立植物代谢注释一站式服务并启动植物酶功能联盟
  • 批准号:
    2312181
  • 财政年份:
    2023
  • 资助金额:
    --
  • 项目类别:
    Standard Grant
BII: Life without water: protecting macromolecules, cells, and organisms during desiccation and rehydration across kingdoms of life
BII:没有水的生命:在生命王国的干燥和补水过程中保护大分子、细胞和生物体
  • 批准号:
    2419923
  • 财政年份:
    2023
  • 资助金额:
    --
  • 项目类别:
    Cooperative Agreement
RCN: Creating and Fostering the Plant Cell Atlas Community
RCN:创建和培育植物细胞图谱社区
  • 批准号:
    2420360
  • 财政年份:
    2023
  • 资助金额:
    --
  • 项目类别:
    Continuing Grant
BII: Life without water: protecting macromolecules, cells, and organisms during desiccation and rehydration across kingdoms of life
BII:没有水的生命:在生命王国的干燥和补水过程中保护大分子、细胞和生物体
  • 批准号:
    2213983
  • 财政年份:
    2022
  • 资助金额:
    --
  • 项目类别:
    Cooperative Agreement
RCN: Creating and Fostering the Plant Cell Atlas Community
RCN:创建和培育植物细胞图谱社区
  • 批准号:
    2052590
  • 财政年份:
    2021
  • 资助金额:
    --
  • 项目类别:
    Continuing Grant
1st Workshop on the Plant Cell Atlas Initiative; January, 2020; Stanford, CA
第一届植物细胞图谱计划研讨会;
  • 批准号:
    1916797
  • 财政年份:
    2019
  • 资助金额:
    --
  • 项目类别:
    Standard Grant
TOOLS-PGR: Computational Infrastructure to Enable High-throughput, High-quality Annotations of Compartmentalized Metabolic Networks for Plant Genomes
TOOLS-PGR:计算基础设施可实现植物基因组分区代谢网络的高通量、高质量注释
  • 批准号:
    1546838
  • 财政年份:
    2016
  • 资助金额:
    --
  • 项目类别:
    Continuing Grant
Building a Highly Automated Metabolic Pathway Reconstruction Infrastructure for Plants
构建高度自动化的植物代谢途径重建基础设施
  • 批准号:
    1026003
  • 财政年份:
    2010
  • 资助金额:
    --
  • 项目类别:
    Continuing Grant
Building a Network of Plant Metabolic Pathway Databases and Communities
建立植物代谢途径数据库和社区网络
  • 批准号:
    0640769
  • 财政年份:
    2008
  • 资助金额:
    --
  • 项目类别:
    Continuing Grant
The First International Biocurator Meeting to be held on December 8-11, 2005 at the Asilomar Conference Grounds in Pacifice Grove, CA.
第一届国际生物策展人会议将于 2005 年 12 月 8 日至 11 日在加利福尼亚州 Pacifice Grove 的阿西洛玛会议场地举行。
  • 批准号:
    0551286
  • 财政年份:
    2006
  • 资助金额:
    --
  • 项目类别:
    Standard Grant

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Single cell level elucidation of local cell death-triggered regeneration mechanism in Arabidopsis
单细胞水平阐明拟南芥局部细胞死亡触发的再生机制
  • 批准号:
    24K17869
  • 财政年份:
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  • 批准号:
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  • 批准号:
    22KF0023
  • 财政年份:
    2023
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ELMOD家族蛋白及其遗传网络在拟南芥花粉表面特殊膜结构域发育中的作用
  • 批准号:
    2240972
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