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

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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 (server@rdp.life.uiuc.edu), 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.