Development of a database and ontology for pathogenic pathways in periodontitis.
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/.
Suzuki
Asami
A
General Dentistry, The Nippon Dental University Hospital at Tokyo, Tokyo, Japan.
Takai-Igarashi
Takako
T
Numabe
Yukihiro
Y
Tanaka
Hiroshi
H
D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D010518:Periodontitis / Q000150:complications / Q000209:etiology / Q000378:metabolism* / Q000473:pathology; D016966:Porphyromonas gingivalis / Q000378:metabolism / Q000472:pathogenicity*; D015398:Signal Transduction / Q000502:physiology*; D014584:User-Computer Interface; D018875:Vocabulary, Controlled