Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics
Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics
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DOI：
10.1093/sysbio/syad025
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发表时间：
2023-04-24
影响因子：
6.5
通讯作者：
Miko，Istvan
中科院分区：
文献类型：
--
作者：
Giron，Jennifer C.;Tarasov，Sergei;Miko，Istvan
昆虫的惊人辐射产生了惊人的表型多样性。在过去的250年里，昆虫系统学的研究已经产生了数百个术语来命名和比较它们。在其目前的形式，这种术语的多样性是在自然语言和缺乏形式化，这禁止使用语义网技术的计算机辅助比较。在这里，我们提出了一个模型描述表皮解剖结构（MoDCAS），它结合了结构特性和位置关系的标准化，一致性和可重复的描述节肢动物表型。我们应用MoDCAS框架创建昆虫骨骼-肌肉系统（AISM）解剖学的本体。AISM是第一个通用的昆虫本体论，旨在通过为每个术语提供广义的、完全逻辑的和可查询的定义来覆盖所有分类群。它是使用本体开发工具包（ODK）构建的，该工具包最大限度地提高了与Uberon（Uberon多物种解剖本体）和其他基本本体的互操作性，增强了昆虫解剖学与更广泛的生物科学的整合。还介绍了一个模板系统，用于添加新的术语，扩展和链接AISM到其他解剖，表型，遗传和化学本体。AISM被提议作为分类特异性昆虫本体的主干，并且具有跨越系统生物学和生物多样性信息学的潜在应用，允许用户：1）使用受控词汇并创建半自动化的计算机可解析的昆虫形态描述; 2）将昆虫形态学纳入更广泛的研究领域，包括基于本体的系统发育方法，逻辑同源性假设检验，进化-发育研究，和基因型到表型映射;和3）通过促进能够提取、链接、注释和处理形态学数据的信息学工具的产生和测试，使从文献中提取形态学数据自动化，从而能够产生大规模的表型数据。这种描述性的模型和它的本体论的应用程序将允许明确的和语义上可互操作的整合节肢动物表型生物多样性研究。
The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multispecies anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to: 1) use controlled vocabularies and create semiautomated computer-parsable insect morphological descriptions; 2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and 3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.