Development of an Ontology for Periodontitis.
Development of an Ontology for Periodontitis.
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DOI：
10.1186/s13326-015-0028-y
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发表时间：
2015
影响因子：
1.9
通讯作者：
Tanaka H
中科院分区：
文献类型：
--
作者：
Suzuki A;Takai-Igarashi T;Nakaya J;Tanaka H
在临床牙医和牙周研究人员的社区，有一个明显的需求，系统模型能够连接牙周炎的临床表现，以潜在的分子知识。一个计算机可读的疾病发展过程的表示将给牙周研究人员阐明牙周炎的途径和机制的机会。牙周炎的本体可以是用于整合与复杂疾病相关的多种因素的模型，所述复杂疾病诸如不同器官中的慢性炎症，伴随有骨重建和免疫系统紊乱，其最近被称为骨免疫学。牙周病专家从194篇综述文章和PubMed摘要中手动提取与牙周炎发病和进展相关的描述特征术语。我们指定了所有提取的术语之间的关系，并将它们构建成牙周炎的本体。我们还研究了我们的本体和基因本体生物过程的类之间的匹配。我们开发了一个牙周炎的本体，称为牙周炎本体（PeriO）。牙周炎的病理进展是由复杂的、多因素的相互关系引起的。PeriO包括所有必需的概念，以代表牙周炎的病理进展和临床治疗。病理过程是参照基本形式本体和关系本体进行形式化的，其说明了由生物对象（例如分子和细胞）实现的过程的参与者。我们研究了在病理进展和疾病的医学治疗中观察到的生物过程的特殊性，并与基因本体生物过程（GO-BP）注释进行比较。结果表明，Perio的特殊性存在于1）粒度和上下文的依赖性的概念化，和2）因果关系的内在病理过程。PeriO定义了比GO-BP更具体的概念，因此可以作为GO-BP叶节点的后代添加。PeriO定义了过程概念之间的因果关系，这在GO-BP中没有显示。这种差异可以通过概念化的目标来解释：PeriO侧重于致病过程的机制，而GO-BP侧重于对实验中观察到的所有生物过程进行编目。在PeriO中概念化的目标可以反映领域知识，其中因果关系中的结果是主要兴趣。我们认为，当比较GO-BP疾病的过程时，这些特点可以在其他疾病中共享。这是第一个开放的牙周炎生物医学本体，能够为牙周炎相关的分子生物学和病理过程及其与全身性疾病的关系的基于本体的模型提供基础。PeriO可在http://bio-omix.tmd.ac.jp/periodontitis/上获得。本文的在线版本（doi：10.1186/s13326-015-0028-y）包含补充材料，可供授权用户使用。
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. 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. 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. 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/. The online version of this article (doi:10.1186/s13326-015-0028-y) contains supplementary material, which is available to authorized users.
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影响因子：
4.1
作者：
Jung SM;Kim KW;Yang CW;Park SH;Ju JH
通讯作者：
Ju JH
DOI：
10.1093/bioinformatics/btp193
发表时间：
2009-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
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通讯作者：
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影响因子：
1.9
作者：
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通讯作者：
Smith, Barry
影响因子：
2.6
作者：
Duan, Li;Ren, Yijin
通讯作者：
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影响因子：
12.3
作者：
Mungall CJ;Gkoutos GV;Smith CL;Haendel MA;Lewis SE;Ashburner M
通讯作者：
Ashburner M