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Development of an Ontology for Periodontitis.

Suzuki A, Takai-Igarashi T, Nakaya J, Tanaka H - J Biomed Semantics (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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/.

No MeSH data available.


Related in: MedlinePlus

Relationships in Process between PeriO and GO. This figure illustrates relationships between classes of ‘medical treatment for periodontitis’, ‘molecular pathogenesis of periodontitis’, and GO-BP. ‘Bone remodeling’ (GO:0046849) is referred not only by ‘pathogenic shift of bone remodeling’ and ‘destruction of alveolar bone’, but also by ‘keep balance between bone resorption and bone formation’ and ‘maintenance of structural integrity of bone’
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Fig5: Relationships in Process between PeriO and GO. This figure illustrates relationships between classes of ‘medical treatment for periodontitis’, ‘molecular pathogenesis of periodontitis’, and GO-BP. ‘Bone remodeling’ (GO:0046849) is referred not only by ‘pathogenic shift of bone remodeling’ and ‘destruction of alveolar bone’, but also by ‘keep balance between bone resorption and bone formation’ and ‘maintenance of structural integrity of bone’

Mentions: In order to investigate the symmetrical relationships between ‘medical treatment for periodontitis’ and ‘molecular pathogenesis of periodontitis’, we again mapped the terms to GO-BP. As Additional file 3 shows, most of all the classes under ‘medical treatment for periodontitis’ were mapped to the classes in GO-BP, with the exception of ‘laboratory tests for periodontitis’. When mapping to GO-BP, both the corresponding classes of ‘medical treatment for periodontitis’ and ‘molecular pathogenesis of periodontitis’ linked to the same or closely related GO-BP classes. For example (Fig. 5), ‘bone remodeling’ (GO:0046849) was referred not only by ‘pathogenic shift of bone remodeling’ and ‘destruction of alveolar bone’, but also by ‘keep balance between bone resorption and bone formation’ and ‘maintenance of structural integrity of bone’. The same was true for ‘osteoblast development’ (GO:0002076).Fig. 5


Development of an Ontology for Periodontitis.

Suzuki A, Takai-Igarashi T, Nakaya J, Tanaka H - J Biomed Semantics (2015)

Relationships in Process between PeriO and GO. This figure illustrates relationships between classes of ‘medical treatment for periodontitis’, ‘molecular pathogenesis of periodontitis’, and GO-BP. ‘Bone remodeling’ (GO:0046849) is referred not only by ‘pathogenic shift of bone remodeling’ and ‘destruction of alveolar bone’, but also by ‘keep balance between bone resorption and bone formation’ and ‘maintenance of structural integrity of bone’
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4488034&req=5

Fig5: Relationships in Process between PeriO and GO. This figure illustrates relationships between classes of ‘medical treatment for periodontitis’, ‘molecular pathogenesis of periodontitis’, and GO-BP. ‘Bone remodeling’ (GO:0046849) is referred not only by ‘pathogenic shift of bone remodeling’ and ‘destruction of alveolar bone’, but also by ‘keep balance between bone resorption and bone formation’ and ‘maintenance of structural integrity of bone’
Mentions: In order to investigate the symmetrical relationships between ‘medical treatment for periodontitis’ and ‘molecular pathogenesis of periodontitis’, we again mapped the terms to GO-BP. As Additional file 3 shows, most of all the classes under ‘medical treatment for periodontitis’ were mapped to the classes in GO-BP, with the exception of ‘laboratory tests for periodontitis’. When mapping to GO-BP, both the corresponding classes of ‘medical treatment for periodontitis’ and ‘molecular pathogenesis of periodontitis’ linked to the same or closely related GO-BP classes. For example (Fig. 5), ‘bone remodeling’ (GO:0046849) was referred not only by ‘pathogenic shift of bone remodeling’ and ‘destruction of alveolar bone’, but also by ‘keep balance between bone resorption and bone formation’ and ‘maintenance of structural integrity of bone’. The same was true for ‘osteoblast development’ (GO:0002076).Fig. 5

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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/.

No MeSH data available.


Related in: MedlinePlus