Generation of unified data structure and data warehouse for protein data banks

Brookhaven Protein Data Bank (H.M Bermon et al., 2000); a database and format of files, which describe the 3D structure of a protein or nucleic acid, as determined by X-ray crystallography or nuclear magnetic resonance (NMR) imaging. Protein data banks are semi structured data A table contains collection of record. Record contains collection of fields. The data schema is inspired by a combination of graph based methods, generalized data structures, ontologies and meta-data. A data warehouse (S.A. Kirovl ea tal., 2005) is a subject oriented, integrated, time variant and nonvolatile collection of data in support of management´s decision making process. The present system formats the semi structured (D.P.P. Latha, 2007) data available in protein data bank into a structured database format. In the present work, the system is finding the data type of the field. The user need not specify the data type. We present a data warehouse (D. Yusuf, 2005) that locally stores and integrates different protein data bank files of a group. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development for the user. In the proposed system, the tables are generated automatically from the PDB file and different protein data banks tables were combined to unified structure and put it in a data warehouse (S. Pacifico et al., 2006) . The meta-data (S.P. Shab, 2006) is created to know the list of protein data bank tables that are combined. The system not only gets the information from the user specification such as protein data bank keyword, mode of display etc. but also displays the related information to the user as a text format or save the information in the file according to the display mode. By simply mentioning the table and columns name, the available data are made clear to the user. Hence the accesses of datum are made easy. Sialidases are taken for case studies.