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.

从基础和方法论的角度来看，核糖体 RNA (rRNA) 序列对于生物学来说都是至关重要的。作为细胞翻译过程中的关键要素，它们本身就是详细结构/功能研究的主题。此外，它们的进化特征使其成为其他领域（尤其是微生物学）中极其有用的工具。 rRNA 序列的比较分析 (i) 提供了 rRNA 的二级结构； (ii) 导致了普遍生命树的推论——自然微生物分类的基础——以及古菌的发现，(iii) 为微生物生态学的新的、强​​有力的方法提供了基础； (iv) 为医学诊断中的许多生物体特异性探针开发确定目标； (v) 提供了环境影响和生物修复评估的新方法。此类研究需要大量的 rRNA 数据，并且只有在适当的 rRNA 序列和相关数据数据库的背景下才能有效地使用这些数据。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，有系统发育概述，并且需要可用于数据处理和分析的工具和（对于许多用户）服务。 由于当时还不存在如此有用、如此通用的 rRNA 序列数据库，因此伊利诺伊大学在 NSF 的支持下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 提供多种用户可选格式的对齐和系统发育排序的 rRNA 序列，以及用于处理和分析数据的各种软件。此外，还提供包括自动序列比对、生物体特异性（或群体特异性）探针设计检查、序列数据和系统发育树的用户可选择子集的检索以及rRNA二级结构图等服务。 RDP 目前将其数据保存在文件中，其格式适合 RDP 和所服务的研究人员使用的工具。随着数据量的增加，显然需要一个更强大、更结构化的系统。在数据库管理系统 (DBMS) 上正确设计和实施的 RDP 版本将： (i) 确保 RDP 的平稳增长； (ii) 为 RDP 数据提供统一且高效的接口，以进行数据积累、管理和查询； (iii) 促进添加访问 RDP 数据和服务的新模式。 正在加强数据结构化，着眼于将 RDP 资源与其他可用数据链接起来，从而促进联合数据库的创建。除了增加 RDP（以及与其链接的数据）的价值之外，拟议的工作还将探索有效存储和检索比对序列数据（RDP 的最大组成部分）以及执行分类的方法。用于管理和利用这些数据的复杂查询。 该提案的具体目标是： (i) 完成基于 DBMS 版本的 RDP 的详细设计和实现； (ii) 提供有效管理数据所需的图形用户界面（GUI）； (iii) 使用增强的数据结构进一步实现 RDP 数据更新和管理程序的自动化； (iv) 通过 DBMS 实现提供所有现有的用户访问模式 (v) 改进和扩展 RDP 用户可用的访问模式和查询功能； (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 (MSU) 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 序列量根据数据（约 3500 个序列）和预计的未来水平（数万个序列或更多），RDP 在未来的生物、医学和环境研究中发挥着重要作用。为了填补这些角色，有必要在不干扰当前服务的情况下更新其设计。本提案解决了这一需求。