Moving the Ribosome Database Project (RDP) to a DBMS Foundation

将核糖体数据库项目 (RDP) 移至 DBMS 基金会

• 批准号: 9507552
• 负责人: Sakti Pramanik
• 金额: $ 32.14万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1995
• 资助国家: 美国
• 起止时间: 1995-08-15 至 1999-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9507552&HistoricalAwards=false
• 关键词: Moving; Ribosome; Database; Project; RDP

Ribosomal RNA (rRNA) sequences are central to biology from both the basic and the methodological perspectives. As the key elements in the cellular translation process they are subjects of detailed structure/function studies in their own right. In addition, their evolutionary characteristics make them extremely useful as tools in other areas, microbiology in particular. Comparative analysis of rRNA sequences has (i) provided the secondary structure of the rRNAs; (ii) led to the inference of the universal tree of life--a basis for a natural microbial classification--and the discovery of the Archaea, (iii) provided the basis for new and powerful approaches to microbial ecology; (iv) defined targets for much of the organism-specific probe development in medical diagnosis; and (v) provided new methods for environmental impact and bioremediation assessment. Such studies require large amounts of the rRNA data, and these can be used effectively only in the context of the appropriate database of rRNA sequences and related data. It is not sufficient to provide just the raw sequence data; many analyses require that the data be organized into alignments, that there be a phylogenetic overview, and that tools and (for many users) ser vices be available for data handling and analysis. In that an rRNA sequence database this useful, this versatile, did not exist, the Ribosome Database Project (RDP) has been established at the University of Illinois with support from the NSF. Through its E-mail ([e-mail]), ftp (rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and World Wide Web (http://rdpwww.life.uiuc.edu/index.html) servers, the RDP offers aligned and phylogenetically ordered rRNA sequences in a variety of user-selectable formats, as well as various software for handling and analysis of the data. In addition, services including automated sequence alignment, organism-specific (or group-specific) probe design checking, retrieval of user-selectable subsets of t he sequence data and phylogenetic trees, and rRNA secondary structure diagrams are provided. The RDP currently maintains its data in files with formats that are appropriate for the tools used by the RDP and by the researchers served. As the volume of data increases, the need for a more robust and structured system is clear. A properly designed and implemented version of the RDP on a database management system (DBMS) will: (i) ensure smooth growth of the RDP; (ii) provide a uniform and efficient interface to the RDP data for data accumulation, curation and querying; and (iii) facilitate the addition of new modes of access to the RDP data and services. The increased structuring of the data is being carried out with an eye toward linkage of the RDP's resources with other available data, facilitating the creation of a federated database. In addition to increasing the value of the RDP (and the data that will be linked to it), the proposed work will explore methods for efficient storage and retrieval of aligned sequence data (the largest component of the RDP), and for performing the kinds of complex queries that are used in curating and exploiting these data. Specific objectives of this proposal are: (i) complete a detailed design and implementation of a DBMSbased version of the RDP; (ii) provide the graphical user interfaces (GUIs) necessary for the efficient curation of the data; (iii) use the increased data structuring to further automate the RDP's data updating and management procedures; (iv) provide all existing user access modes through the DBMS implementation (v) improve and expand the access modes and query capabilities available to users of the RDP; and (v provide the necessary "hooks" for integration of the RDP with other data, initially the federation of microbial databases being proposed by the Center for Microbial Ecology (CME) at Michigan State University (MSU). Given the present volume of rRNA sequence data l approximately 3500 sequences) and the e stimated future level (tens of thousands of sequences, or more), the RDP has essential roles to play in biological, medical and environmental research in the future. To fill these roles, it is necessary to update its design without interfering with current services. This proposal addresses this need.

从基础和方法学的角度来看，核糖体RNA(RRNA)序列都是生物学的核心。作为细胞翻译过程中的关键要素，它们本身就是详细的结构/功能研究的对象。此外，它们的进化特性使它们在其他领域，特别是微生物学领域，成为非常有用的工具。对rRNA序列的比较分析(I)提供了rRNA的二级结构；(Ii)导致了宇宙生命树的推断--这是自然微生物分类的基础--以及古细菌的发现，(Iii)为研究微生物生态学的新的和强有力的方法提供了基础；(Iv)为医学诊断中的许多特定生物探针的开发确定了目标；(V)为环境影响和生物修复评估提供了新的方法。这种研究需要大量的rRNA数据，这些数据只有在rRNA序列和相关数据的适当数据库的背景下才能有效地使用。仅仅提供原始序列数据是不够的；许多分析要求将数据组织成比对，有一个系统发育概况，并提供工具和(对许多用户来说)可用于数据处理和分析的服务。由于不存在如此有用、如此通用的rRNA序列数据库，在国家科学基金会的支持下，伊利诺伊大学建立了核糖体数据库项目(RDP)。通过其电子邮件([e-mail])、ftp(rdp.life.uiuc.edu)、Gopher(rdpgopher.life.uiuc.edu)和万维网(http://rdpwww.life.uiuc.edu/index.html)服务器)，RDP以各种用户可选择的格式提供经过比对和系统发育排序的rRNA序列，以及用于处理和分析数据的各种软件。此外，还提供了包括自动序列比对、生物体特定(或组特定)探针设计检查、用户可选择的序列数据和系统发育树子集的检索以及rRNA二级结构图的服务。RDP目前以适合RDP和所服务的研究人员所使用的工具的格式保存其数据。随着数据量的增加，显然需要一个更强大和更结构化的系统。一个在数据库管理系统(DBMS)上适当设计和实施的RDP版本将：(1)确保RDP的顺利发展；(2)为RDP数据提供统一和有效的接口，以便进行数据积累、整理和查询；以及(3)促进增加RDP数据和服务的新访问模式。正在加强数据的结构化，着眼于将区域发展计划的资源与其他现有数据联系起来，促进建立一个联合数据库。除了增加RDP的价值(以及将链接到RDP的数据)外，拟议的工作还将探索有效存储和检索比对的序列数据(RDP的最大组成部分)的方法，以及执行用于管理和利用这些数据的各种复杂查询的方法。这项建议的具体目标是：(1)完成基于数据库管理系统的区域数据计划版本的详细设计和实施；(2)提供有效管理数据所需的图形用户界面；(3)利用改进的数据结构进一步使区域数据计划的数据更新和管理程序自动化；(4)通过实施数据库管理系统提供所有现有的用户访问模式；(5)改进和扩大区域数据计划用户可用的访问模式和查询能力；以及(V)为RDP与其他数据的整合提供必要的“挂钩”，最初是由密歇根州立大学微生物生态学中心(CME)提出的微生物数据库联盟。考虑到目前的rRNA序列数据量(约3,500个序列)和估计的未来水平(数以万计的序列或更多)，RDP在未来的生物、医学和环境研究中具有重要的作用。要填补这些角色，有必要在不干扰当前服务的情况下更新其设计。这项建议满足了这一需求。