Data from: The Teleost Anatomy Ontology: anatomical representation for the genomics age

The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.

系统分类学文献中记载的各类生物体形态变异的丰富知识，长期以来仅以自由文本形式存在，难以应用于大规模综合系统发育研究工作。这种非可计算格式也使得该类知识无法与模式生物数据库中庞大的基因组、遗传、发育与表型知识库建立关联。为此，我们着手开发一个经人工编审、基于本体论的进化形态学数据库原型（http://kb.phenoscape.org），该数据库可与上述遗传数据库建立映射，以助力对表型多样性的机制基础与演化过程开展研究。构建该数据库的首要任务之一，是开发一种多物种解剖本体（multispecies anatomy ontology），旨在以系统化、可计算的方式收录解剖学数据。本体（ontology）是对一组概念及其间明确关系的形式化表征。多物种解剖本体尤其可高效表征某一演化支内生物体的形态结构多样性，但相较于单物种解剖本体，其开发过程面临诸多挑战。本文中，我们将介绍硬骨鱼解剖本体（Teleost Anatomy Ontology, TAO）——一种基于斑马鱼解剖本体（Zebrafish Anatomical Ontology, ZFA）开发的多物种解剖本体，用于跨物种标注不同的形态学特征。为便于与其他解剖本体实现互操作性，TAO以通用解剖参考本体（Common Anatomy Reference Ontology）作为其顶层节点的模板，同时TAO与ZFA保持同步，斑马鱼相关术语被定义为硬骨鱼术语的子类型。我们发现，本体架构的细节会对查询操作产生影响；同时本文还探讨了开发多物种解剖本体过程中普遍存在的各类挑战，包括术语定义的精细化、物种特异性的术语间关系，以及具有类群特异性的发育路径的表征问题。