Biological databases are the semi structured data. The search procedure in the semi structured data is hard. The proposed system is developed to make the search and the comparison of the protein data banks easy and it gives the data in a structured way. Analyzing the protein data banks are easy, because of the data warehouse creation. The table name and the columns name are entered by the user, the system itself find the data type of the columns. It is giving the user friendliness to the user. Since the meta-data is created, the datum can be easily found by the user. Also the system will give the information to user as a text file or it will display in the monitor according to the user choice. This is an added advantage to the system.