title: Development of an Ontology for Periodontitis.
abstract: BACKGROUND
  In the clinical dentists and periodontal researchers' community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. A computer-readable representation of processes on disease development will give periodontal researchers opportunities to elucidate pathways and mechanisms of periodontitis. An ontology for periodontitis can be a model for integration of large variety of factors relating to a complex disease such as chronic inflammation in different organs accompanied by bone remodeling and immune system disorders, which has recently been referred to as osteoimmunology.
  
  
  METHODS
  Terms characteristic of descriptions related to the onset and progression of periodontitis were manually extracted from 194 review articles and PubMed abstracts by experts in periodontology. We specified all the relations between the extracted terms and constructed them into an ontology for periodontitis. We also investigated matching between classes of our ontology and that of Gene Ontology Biological Process.
  
  
  RESULTS
  We developed an ontology for periodontitis called Periodontitis-Ontology (PeriO). The pathological progression of periodontitis is caused by complex, multi-factor interrelationships. PeriO consists of all the required concepts to represent the pathological progression and clinical treatment of periodontitis. The pathological processes were formalized with reference to Basic Formal Ontology and Relation Ontology, which accounts for participants in the processes realized by biological objects such as molecules and cells. We investigated the peculiarity of biological processes observed in pathological progression and medical treatments for the disease in comparison with Gene Ontology Biological Process (GO-BP) annotations. The results indicated that peculiarities of Perio existed in 1) granularity and context dependency of both the conceptualizations, and 2) causality intrinsic to the pathological processes. PeriO defines more specific concepts than GO-BP, and thus can be added as descendants of GO-BP leaf nodes. PeriO defines causal relationships between the process concepts, which are not shown in GO-BP. The difference can be explained by the goal of conceptualization: PeriO focuses on mechanisms of the pathogenic progress, while GO-BP focuses on cataloguing all of the biological processes observed in experiments. The goal of conceptualization in PeriO may reflect the domain knowledge where a consequence in the causal relationships is a primary interest. We believe the peculiarities can be shared among other diseases when comparing processes in disease against GO-BP.
  
  
  CONCLUSIONS
  This is the first open biomedical ontology of periodontitis capable of providing a foundation for an ontology-based model of aspects of molecular biology and pathological processes related to periodontitis, as well as its relations with systemic diseases. PeriO is available at http://bio-omix.tmd.ac.jp/periodontitis/.
authors.affiliation: Department of Computational Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Bunkyō, Japan ; General Dentistry, The Nippon Dental University Hospital at Tokyo, Tokyo, Japan.
authors.forename: Asami
authors.initials: A
authors.lastname: Suzuki
authors.affiliation: Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ; Department of Computational Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Bunkyō, Japan.
authors.forename: Takako
authors.initials: T
authors.lastname: Takai-Igarashi
authors.affiliation: Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ; School of Medicine, Tohoku University, Sendai, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Nakaya
authors.affiliation: Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ; Department of Computational Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Bunkyō, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Tanaka
keywords: Gene Ontology; biomedical process; bone remodeling; ontology; osteoimmunology; periodontitis