Bioinformatics web data and service integration - An experiemnt with Gene Regulatory Networks

Web data integration has been an active research topic for the last few years. Bioinformatics is a huge domain wealth of data. By reverse engineering web data, in this paper we report a Java based implementation of biologically relevant application of web data integration consisting of few sites such as Flybase, YMF and STAMP. We have developed a tool that can automate the finding of transcription factor binding sites for arbitrary gene regulatory networks. We employed vertical (i.e link) and horizontal (i.e combine) integration for the whole process. As a running example and proof of concept of our approach, we report here a real example motivated by the biological domain of Drosophila Melanogaster model organism database. For a given set of genes, we could find a set of sequences (800~1500 bp) from Flybase site, then we feed those into YMF site to get a motif of 6{~}8 bp. The result motifs were fed into STAMP site and by combining result from Fly curated by Bergman and by TRANSFAC, we were able to get a sample correct result for a Bicoid gene, namely bin. The lesson learned from the exercise can be applied in generic dynamic web form based data integration application like e-commerce, comparison shopping etc.