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Bioinformatics Vol. 18 no. 10 2002
Pages 1283-1288
© 2002 Oxford University Press

SAC 2002 Paper

An intelligent biological information management system

Mathew Palakal 1,*, Snehasis Mukhopadhyay 1, Javed Mostafa 2, Rajeev Raje 1, Mathias N'Cho 3 and Santosh Mishra 3

1 Computer Science Department, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
2 School of Library and Information Science, Indiana University, Bloomington, IN 47405, USA
3 Bioinformatics Group, Eli Lilly & Co., Indianapolis, IN 46285, USA

Received on August 31, 2001 ; accepted on October 24, 2001

Motivation: As biomedical researchers are amassing a plethora of information in a variety of forms resulting from the advancements in biomedical research, there is a critical need for innovative information management and knowledge discovery tools to sift through these vast volumes of heterogeneous data and analysis tools. In this paper we present a general model for an information management system that is adaptable and scalable, followed by a detailed design and implementation of one component of the model. The prototype, called BioSifter, was applied to problems in the bioinformatics area.

Results: BioSifter was tested using 500 documents obtained from PubMed database on two biological problems related to genetic polymorphism and extracorporal shockwave lithotripsy. The results indicate that BioSifter is a powerful tool for biological researchers to automatically retrieve relevant text documents from biological literature based on their interest profile. The results also indicate that the first stage of information management process, i.e. data to information transformation, significantly reduces the size of the information space. The filtered data obtained through BioSifter is relevant as well as much smaller in dimension compared to all the retrieved data. This would in turn significantly reduce the complexity associated with the next level transformation, i.e. information to knowledge.

Contact: mpalakal{at}cs.iupui.edu

* To whom correspondence should be addressed.


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