Title: Temporal representation for gene networks: towards a qualitative temporal data mining

Authors: Nicolas Turenne, Sylviane R. Schwer

Addresses: INRA MIG, 78352 Jouy-en-Josas, France. ' LIPN UMR 7030 (CNRS Universite Paris Nord), 99 Avenue Jean-Baptiste Clement, 93230 Villetaneuse, France

Abstract: Processing literature (i.e., text corpora) to capture gene regulation events is not easy and can be driven by the final data representation. We propose to build, manually, an example of temporal representation (whole gene networks for coat formation in Bacillus Subtilis). Our temporal representation is based on a generalised formal language theory (S-languages). We propose an algorithm to link bags of relations with representation, by ordering interactions. In this paper, starting from the network made manually from text data, we show that S-languages are quite relevant to encapsulate gene properties, and infer knowledge across time-stamped gene relations found in texts.

Keywords: temporal representation; qualitative data mining; database; gene networks; data mining; bioinformatics.

DOI: 10.1504/IJDMB.2008.016755

International Journal of Data Mining and Bioinformatics, 2008 Vol.2 No.1, pp.36 - 53

Published online: 21 Jan 2008 *

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