Worm: Biological data miner and personal relational database management system

Abstract

Today, ever growing and changing nature of the genetic information has caused a serious problem. Where is the information, you are looking for, in the internet? How could you get that information? After getting it how would you store it? How would you keep that stored information up-to-date? In view of the monstrous structure of the genetic information space, there is no doubt that answering those questions will be very difficult. Our solution, even if it is a partial one, to the questions related to these topics is a new software that we called as the Worm (Solucan in Turkish). The Worm, let researchers fill the database model they prepare according to their desires and priorities, by running in line with series of their principles, forming information groups from row databases of their interests. Dynamic nature of row data sources and relational databases and the fact that the rules of information gathering are determined by the user marks the Worm as an effective tool. For a total of 32.004 genes, it took the Worm approximately 18 minutes and 46 seconds to gather from row data sources the accession numbers for these genes and associate them relationally as we wish. © 2009 OMÜ Tüm Haklari Saklidir.