TrOn: An Anatomical Ontology for the Beetle Tribolium castaneum
TrOn: An Anatomical Ontology for the Beetle Tribolium castaneum
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DOI：
10.1371/journal.pone.0070695
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发表时间：
2013-07-30
期刊：
影响因子：
3.7
通讯作者：
Bucher, Gregor
中科院分区：
文献类型：
--
作者：
Doenitz, Juergen;Grossmann, Daniela;Bucher, Gregor
在形态本体中，专家的知识用术语表示，术语描述形态结构以及这些结构如何相互关联。在本体论的帮助下，通过术语及其相互关系的正式和标准化表示，使这种专家知识可由机器处理。赤拟谷盗Tribolium castaneum是鞘翅目昆虫中物种最丰富的类群之一，是研究昆虫发育、进化、生理和害虫防治的模式生物。为了促进Tribolium研究，我们启动了Tribolium Ontology（Tron），它描述了红粉甲虫的形态。这种本体论的内容包括迄今为止大多数外部形态结构以及一些内部形态结构。所有建模的结构一致注释的发育阶段幼虫，蛹和成人。在Tron中，所有术语被分为三类：通用术语代表形态结构，独立于发育阶段。相反，这些术语的下游是具体术语，代表甲虫在特定生命阶段的可解剖结构。最后，有混合术语描述仅在一个发育阶段发现的结构。这些术语联合收割机结合了一般术语和具体术语的特点，并兼有两者的特点。这些注释原则考虑了甲虫在开发过程中不断变化的形态，并提供了在应用程序中使用或与其他本体和数据资源交叉链接的通用术语。我们使用本体论在电子iBeetle-Base上实现直观的搜索功能，该电子iBeetle-Base存储在全基因组RNA干扰（RNAi）屏幕中发现的形态缺陷。本体可在http://ibeetle-base.uni-goettingen.de下载。
In a morphological ontology the expert's knowledge is represented in terms, which describe morphological structures and how these structures relate to each other. With the assistance of ontologies this expert knowledge is made processable by machines, through a formal and standardized representation of terms and their relations to each other. The red flour beetle Tribolium castaneum, a representative of the most species rich animal taxon on earth (the Coleoptera), is an emerging model organism for development, evolution, physiology, and pest control. In order to foster Tribolium research, we have initiated the Tribolium Ontology (TrOn), which describes the morphology of the red flour beetle. The content of this ontology comprises so far most external morphological structures as well as some internal ones. All modeled structures are consistently annotated for the developmental stages larva, pupa and adult. In TrOn all terms are grouped into three categories: Generic terms represent morphological structures, which are independent of a developmental stage. In contrast, downstream of such terms are concrete terms which stand for a dissectible structure of a beetle at a specific life stage. Finally, there are mixed terms describing structures that are only found at one developmental stage. These terms combine the characteristics of generic and concrete terms with features of both. These annotation principles take into account the changing morphology of the beetle during development and provide generic terms to be used in applications or for cross linking with other ontologies and data resources. We use the ontology for implementing an intuitive search function at the electronic iBeetle-Base, which stores morphological defects found in a genome wide RNA interference (RNAi) screen. The ontology is available for download at http://ibeetle-base.uni-goettingen.de.