Abstract There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery. [Homology; ontology; anatomy; morphology; evolution; knowledgebase; phenoscape.]

中文翻译：

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比较生物学同源性的逻辑模型

摘要 有越来越多的关于各种生物体解剖学进化的研究。计算方法和资源可以极大地加速该领域的发现，使这些发现能够在不同的研究和不同的生物体之间进行比较，并与负责解剖学修饰的基因相关联。同源性是比较解剖学中的一个关键概念；两种重要的类型是历史同源性（由于共同祖先而导致的生物体相似性）和序列同源性（生物体内重复结构的相似性）。我们探索了如何最有效地表示跨解剖结构的历史和序列同源性，以促进计算推理。我们从文献中收集了一组同源性断言，其中包含一组来自 Phenoscape 知识库的脊椎动物鳍和四肢骨骼元素的分类单元表型。使用七个能力问题，我们评估了两个逻辑模型的推理后果：互惠存在公理 (REA) 同源模型和祖先价值公理 (AVA) 同源模型。除了搜索词及其任何子类之外，AVA 模型还返回了所有用户预期的结果。AVA 模型还返回已断言同源关系的查询词的任何超类。REA 模型为七分之五的查询返回了用户预期的结果。由于 OWL 推理的局限性，我们确定了实现完整同源查询的一些挑战。这项工作为将同源推理纳入其他基于本体的工具奠定了基础，例如那些能够构建合成超矩阵和候选基因发现的工具。[同源性；本体论；解剖学; 形态学; 进化; 知识库; 现象。]