Suzuki Asami, Takai-Igarashi Takako, Numabe Yukihiro, Tanaka Hiroshi
General Dentistry, The Nippon Dental University Hospital at Tokyo, Tokyo, Japan.
In Silico Biol. 2009;9(4):233-43.
It is getting familiar that pathway information greatly contributes to elucidate the molecular basis of human disease with large-scale biological data. We developed a pathway database for molecular pathology in periodontitis named 'Pathogenic Pathway Database for Periodontitis'. Periodontitis is an inflammation disease in periodontal tissue and associated with an increased health risk of angina, myocardial infarction, and fetal cardiovascular events. Despite accumulation of biomedical research on periodontitis pathology at the molecular level, there has been no systematization for biological pathways in periodontitis. We checked 185 reference papers and extracted causal relationships among molecules as well as pathways representing molecular etiology. We also built an ontology that systematizes conceptual terms associated with the pathways. Besides pathways, our ontology provides cellular and tissue specific contextual information that is required to represent pathology at the cellular and tissue specific levels. We implemented in our database an integrated viewer for the association between pathways and ontology. Pathogenic Pathway Database for Periodontitis is freely available at http://bio-omix.tmd.ac.jp/disease/perio/.
随着大规模生物数据的出现，利用通路信息来阐明人类疾病的分子基础已逐渐为人所熟知。我们开发了一个用于牙周炎分子病理学的通路数据库，名为“牙周炎致病通路数据库”。牙周炎是牙周组织的炎症性疾病，与心绞痛、心肌梗死和胎儿心血管事件等健康风险增加有关。尽管在分子水平上对牙周炎病理学的生物医学研究不断积累，但牙周炎的生物通路尚未系统化。我们查阅了185篇参考文献，提取了分子之间的因果关系以及代表分子病因的通路。我们还构建了一个本体，将与这些通路相关的概念术语系统化。除了通路，我们的本体还提供了在细胞和组织特异性水平上描述病理学所需的细胞和组织特异性上下文信息。我们在数据库中实现了一个用于通路与本体之间关联的集成查看器。牙周炎致病通路数据库可在http://bio-omix.tmd.ac.jp/disease/perio/上免费获取。
