TAIR: The Arabidopsis Information Resource

TAIR：拟南芥信息资源

• 批准号: 0417062
• 负责人: Seung Rhee
• 金额: --
• 依托单位: Carnegie Institution of Washington
• 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
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0417062&HistoricalAwards=false
• 关键词: TAIR; Arabidopsis; Information; Resource

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。他们还提出了巨大的挑战：如何最佳利用大量生物学数据。如果没有长期访问和分析数据的长期高质量机制，用于生成数据的资源就有浪费的危险。重要的是要容纳数据，工具和界面以提供对数据的访问，并且长期建立和支持策展以组织数据以最大程度地支持数据。 对于模型植物拟南芥，为了了解每个拟南芥基因的功能而进行的基因组和当前努力的成功努力和当前的努力产生了大量有价值的数据，只有在长期存储，相互关联，更新和使研究人员可以访问该信息的情况下，这些数据才能最大程度地使用。 Tair（拟南芥信息资源，www.arabidopsis.org）在其前五年的资金中，这一数据泛滥成灾，开发了一个数据结构，以容纳可用数据的多样性以及访问和分析所需的工具和接口。该项目的第二阶段的目的是维护当前在Tair中存在的数据和工具，并在关键领域增加工作，包括维持和改善基因组注释，从文献中从文献中提取表型和基因表达数据，并通过通过改善教程和改进的站点导航的开发来提高Tair资源的可访问性，并将Tair资源的可访问性提高到所有生物学家，老师，学生和一般公众。 Tair将继续开发受控的词汇和标准化数据交换机制，以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，以促进程序化数据检索。 Tair还将继续在2010年功能基因组学计划中发挥核心作用，作为研究人员可以浏览现有项目的网站，查看其他群体已经调查的基因清单，以及搜索没有已知功能的基因。 Tair将合并所得的功能数据，并开发一种工具，该工具跟踪朝着2010年全功能注释目标的进度。 智力优点：将大量数据转化为有用的知识是当今生物学后时代的最大问题之一。从研究文献的语料库中提取经过实验验证的信息，并使用代表生物学概念的明确定义且可计算的本体来编码信息，将促进大规模数据集的分析和解释。此外，生物学对象之间复杂关系的数据模型的创建和人口将创建一个全面的计算框架，用于采矿，探索和检索数据。 标准化数据策展方法的开发也使整个生物学研究社区受益。Boader的影响：互联网是研究人员和学生的广泛访问的信息来源。创建互动性，在线教程和用户指南，为学生，没有或小拟南芥知识的植物研究人员和拟南芥专家提供教育材料，这些材料可用于教室，实验室，讲习班和自定进度学习。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的策展人对数据的持续集成和注释将确保研究人员能够访问当前的准确数据，否则这些数据将需要大量的时间和精力来单独积累。通过与教育工作者的合作，大学和大学前的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传播给研究社区。