Temporal Representation for Gene Networks: Towards a Qualitative Temporal Data Mining

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