title: Temporal representation for gene networks: towards a qualitative temporal data mining.
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 timestamped gene relations found in texts.
authors.affiliation: French National Institute for Agricultural Research MIG, 78352 Jouy-en-Josas, France. nicolas.turenne@jouy.inra.fr
authors.forename: Nicolas
authors.initials: N
authors.lastname: Turenne
authors.forename: Sylviane R
authors.initials: SR
authors.lastname: Schwer
mesh_terms: D000465:Algorithms; D003628:Database Management Systems; D016247:Information Storage and Retrieval / Q000379:methods*; D016239:MEDLINE; D008954:Models, Biological; D009323:Natural Language Processing; D010506:Periodicals as Topic; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D020543:Proteome