TAIR: The Arabidopsis Information Resource

最近大规模测序和基因组学方法的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。它们也提出了一个巨大的挑战：如何最佳地利用大量的生物数据。如果没有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被浪费的危险。必须建立并长期支持存储数据的数据库、提供访问数据的工具和接口以及组织数据以获得最大效用的管理工作。对于模式植物拟南芥来说，基因组测序的成功以及2010年功能基因组学计划（Functional Genomics Initiative）了解每个拟南芥基因功能的努力已经产生了大量有价值的数据，只有这些信息被存储、相互关联、更新并长期供研究人员使用，才能最大限度地利用这些数据。TAIR（拟南芥信息资源，www.arabidopsis.org）在前五年的资助中接受了数据洪流带来的挑战，开发了一种数据结构，以容纳可用数据的多样性，以及访问和分析数据所需的工具和接口。该项目的第二阶段的目标是维护TAIR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，以及通过开发教程和改进网站导航来提高所有生物学家、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格式提供数据，以促进程序化数据检索。TAIR也将继续在2010年功能基因组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，查看其他小组已经在研究的基因列表，并搜索未知功能的基因。TAIR将合并得到的功能数据，并开发一个工具来跟踪实现2010年完整功能注释目标的进展。知识价值：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。从研究文献的语料库中提取实验验证的信息，并使用明确定义和可计算的本体对信息进行编码，表示生物概念，这将有助于大规模数据集的分析和解释。此外，为生物对象之间的复杂关系创建和填充数据模型将为挖掘、探索和检索数据创建一个全面的计算框架。标准化数据管理方法的发展也有利于整个生物研究界。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。为没有或很少了解拟南芥知识的学生、植物研究人员和拟南芥专家创建交互式在线教程和用户指南，将提供可用于教室、实验室、研讨会和自学的教育材料。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管理员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、准确的数据，否则这些数据将需要大量的时间和精力来收集。通过与教育工作者的合作，大学生和大学预科生将在学习科学探究和植物生物学的过程中获取研究材料，生成真实的数据，这些数据将通过TAIR传播给研究界。

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.