A pathway editor for literature-based knowledge curation

Authors:
Ken Ichiro Fukuda;Toshihisa Takagi
Affiliations:
University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan;University of Tokyo, Kashiwanoha, Kashiwa-shi, Chiba, Japan
Venue:
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
Year:
2004

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Abstract

As functional-genomics data become available in an ever increasing rate, proper accumulation and dis-semination of background knowledge about biological functions of higher order, such as signal transduction pathways, become indispensable. While a graphanalogical representation is typically observed in biological literatures, due to the diversity of topics that the term "signal" covers, the kind of biological entities that constitutes pathways are highly diverse and mixed-up even in a single diagram. As signal transduction pathway describes the underlying molecular mechanisms of phenotypes, biological processes, its component are hierarchically structured and can be decomposed to sub-processes of arbitral granularities. To support the accumulation processes of this type of knowledge, a pathway editor that displays and manipulates pathway knowledge in a strongly structured manner, such as hierarchical recursive structures is necessary.This paper describes a fully operational implementation of a pathway editor for signal transduction pathways. The system is designed to support curation task for signal transduction pathway knowledge that is buried in biological literatures. The system supports manipulation of attributed compound graphs. An XML format for recursive pathway representation is also presented. The software should be available to the open public from www.ontology.jp/GEST/.