Title: Biological data cleaning: a case study

Authors: Katherine G. Herbert, Jason T.L. Wang

Addresses: Department of Computer Science, Montclair State University, Montclair, New Jersey, 07043, USA. ' Bioinformatics Center and Department of Computer Science, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA

Abstract: As databases become more pervasive through the biological sciences, various data quality concerns are emerging. Biological databases tend to develop data quality issues regarding data legacy, data uniformity and data duplication. Due to the nature of this data, each of these problems is non-trivial and can cause many problems for the database. For biological data to be corrected and standardised, methods and frameworks must be developed to handle both structural and traditional data. This paper discusses issues concerning biological data quality with respect to data cleaning. It presents BIO-AJAX, a framework developed to address these issues. It finally describes BIO-JAX for TreeBASE and BIO-AJAX for Lineage Path, two implementations of BIO-AJAX on phylogenetic data sets.

Keywords: bioinformatics; biological data quality; data quality; data cleaning; information quality; phylogenetic data; data legacy; data uniformity; data duplication; biological databases.

DOI: 10.1504/IJIQ.2007.013376

International Journal of Information Quality, 2007 Vol.1 No.1, pp.60 - 82

Published online: 23 Apr 2007 *

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