The First Organ‐Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems ‐ OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions
The First Organ‐Based Ontology for Arthropods (Ontology of Arthropod Circulatory Systems ‐ OArCS) and its Integration into a Novel Formalization Scheme for Morphological Descriptions
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第一个基于器官的节肢动物本体（节肢动物循环系统本体 - OArCS）及其与形态描述的新型形式化方案的整合
DOI：
10.1093/sysbio/syw108
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发表时间：
2017
影响因子：
6.5
通讯作者：
S. Richter
中科院分区：
文献类型：
--
作者：
C.S. Wirkner;T. Göpel;J. Runge;J. Keiler;B.-J. Klussmann-Fricke;K. Huckstorf;S. Scholz;I. Mikó;M. Yoder;S. Richter
形态学是生物科学中最古老的学科，目前正在比较表型组学领域经历复兴。然而，形态学/表型研究仍然在各个层面上缺乏标准。这个缺点，首先强调为“形态学的语言学问题”，涉及术语的使用，也需要形式化的形态描述本身，至关重要的东西，不仅是形态学领域，而且当它涉及到使用表型数据在系统学和进化生物学。因此，我们认为，形态描述，所有系统和进化的解释的基础上，本体论需要被利用，这是完全基于结构的质量/属性，在任何情况下，包括有关同源性和/或功能的声明。关于同源性和功能的陈述构成了不同或更高层次上的解释。基于这些“解剖学本体”，进一步的本体维度（例如，指的是功能特性或同源性）可以在进化表型组学中广泛使用。为此，我们提出了第一个基于器官的本体论的物种最丰富的动物群，节肢动物。我们的节肢动物循环系统本体（OArCS）包含383个术语的综合集合（即，标签）绑定到296个概念（即，定义）收集自节肢动物循环器官特征的表型方面的文献。OArCS中使用的所有概念都完全基于结构特征，并且在本体论的上下文中独立于同源性和功能假设。我们不能排除在某些情况下，使用的术语在传统用法和以前的解释中可能暗示同源性和/或功能（例如心脏、胸骨动脉）。概念由描述性元素组成，用于将观察到的实例分类到本体的组织框架中。也就是说，本体中的描述仅仅是个体的描述，如果它们是针对个体（独立地）观察和记录的属性的必要和/或充分的表示。此外，我们在这里首次提出了一个全新的方法来正式化表型研究，一个语义模型的描述一个复杂的器官系统在一个高度不同的类群，节肢动物。我们证明了这一点与一个标本的欧洲花园蜘蛛Araneus diadematus的血淋巴血管系统的正式形态描述。我们的描述针对五类描述性陈述：“位置”，“空间关系”，“形状”，“成分”和“连接”，因为相应的形式化构成了不仅在谈论循环系统时有用的示例性模式，而且在一般描述中也有用。计算机可解析形态描述的下游应用是广泛的，其核心效用是，它们可以在计算时间内比较集体描述集，也就是说，非常快。除此之外，这有助于在比较单个个体时识别表型可塑性和变异，识别分类群之间和分类群内相关的那些性状，以及识别形态性状与遗传（使用GO，基因本体论）或环境（使用ENVO，环境本体论）因素之间的联系。[节肢动物;概念;功能;血淋巴血管系统;同源性;术语。]
Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the “linguistic problem of morphology”, concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology. We therefore argue, that for morphological descriptions, the basis of all systematic and evolutionary interpretations, ontologies need to be utilized which are based exclusively on structural qualities/properties and which in no case include statements about homology and/or function. Statements about homology and function constitute interpretations on a different or higher level. Based on these “anatomy ontologies”, further ontological dimensions (e.g., referring to functional properties or homology) may be exerted for a broad use in evolutionary phenomics. To this end we present the first organ-based ontology for the most species-rich animal group, the Arthropoda. Our Ontology of Arthropod Circulatory Systems (OArCS) contains a comprehensive collection of 383 terms (i.e., labels) tied to 296 concepts (i.e., definitions) collected from the literature on phenotypic aspects of circulatory organ features in arthropods. All of the concepts used in OArCS are based exclusively on structural features, and in the context of the ontology are independent of homology and functional assumptions. We cannot rule out that in some cases, terms are used which in traditional usage and previous accounts might have implied homology and/or function (e.g. heart, sternal artery). Concepts are composed of descriptive elements that are used to classify observed instances into the organizational framework of the ontology. That is, descriptions in ontologies are only descriptions of individuals if they are necessary/and or sufficient representations of attributes (independently) observed and recorded for an individual. In addition, we here present for the first time an entirely new approach to formalizing phenotypic research, a semantic model for the description of a complex organ system in a highly disparate taxon, the arthropods. We demonstrate this with a formalized morphological description of the hemolymph vascular system in one specimen of the European garden spiderAraneus diadematus. Our description targets five categories of descriptive statement: “position”, “spatial relationships”, “shape”, “constituents”, and “connections”, as the corresponding formalizations constitute exemplary patterns useful not only when talking about the circulatory system, but also in descriptions in general. The downstream applications of computer-parsable morphological descriptions are widespread, with their core utility being the fact that they make it possible to compare collective description sets in computational time, that is, very quickly. Among other things, this facilitates the identification of phenotypic plasticity and variation when single individuals are compared, the identification of those traits which correlate between and within taxa, and the identification of links between morphological traits and genetic (using GO, Gene Ontology) or environmental (using ENVO, Environmental Ontology) factors. [Arthropoda; concept; function; hemolymph vascular system; homology; terminology.]
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