- Article -
| In Silico Biology 9, 0020 (2009); ©2009, Bioinformation Systems e.V. |
Development of a database and ontology for pathogenic pathways in periodontitis
Asami Suzuki1, 2, Takako Takai-Igarashi2, 3,*, Yukihiro Numabe4 and Hiroshi Tanaka2, 3
1 General Dentistry, The Nippon Dental University Hospital at Tokyo and Biomedical Clinical Omics Educational Program, Tokyo Medical and Dental University
2 Biomedical Clinical Omics Educational Program, Tokyo Medical and Dental University
3 Department of Bioinformatics, School of Biomedical Science, Tokyo Medical and Dental University
4 Department of Periodontology, The Nippon Dental University School of Life Dentistry at Tokyo
* Corresponding author
Email: bio-omix-perio@bioinfo.tmd.ac.jp
Edited by E. Wingender; received February 18, 2009; revised May 07, 2009; accepted April 25, 2009; published May 18, 2009
Abstract
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/.
Keywords: pathway database, ontology, pathogenic pathway, periodontitis, alveolar bone resorption