Formalization of mouse embryo anatomy
Formalization of mouse embryo anatomy
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DOI：
10.1093/bioinformatics/btg400
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发表时间：
2004-01-22
期刊：
影响因子：
5.8
通讯作者：
Baldock, R
中科院分区：
文献类型：
--
作者：
Burger, A;Davidson, D;Baldock, R
动机：爱丁堡小鼠图谱和基因表达数据库项目开发了小鼠发育的数字图谱，为空间映射数据（例如原位基因表达和细胞谱系）提供时空框架。作为该数据库的一部分，小鼠胚胎解剖学本体已经创建。需要对该解剖学进行形式化，以记录其精确的语义以及如何在鼠标图谱的上下文中使用它。结果：本文描述了现有的解剖学本体，并使用基于谓词逻辑的方法将其各个方面形式化。因此，它为当前版本本体的用户提供了指南，以及使用本体语言（例如 OWL）描述解剖结构的基础，从而使未来能够在智能基因表达生物信息学工作流程系统的背景下推理小鼠图谱。该逻辑已在 Prolog 原型中实现。
Motivation: The Edinburgh Mouse Atlas and Gene Expression Database project has developed a digital atlas of mouse development to provide a spatio-temporal framework for spatially mapped data such as in situ gene expression and cell lineage. As part of this database, a mouse embryo anatomy ontology has been created. A formalization of this anatomy is required to document its precise semantics and how it is used in the context of the Mouse Atlas.Results: The paper describes the existing anatomy ontology and formalizes aspects of it using a predicate logic based approach. It therefore provides a guide for users of the current version of the ontology, as well as the basis for a description of the anatomy using an ontology language, such as OWL, thus enabling future work on reasoning about the Mouse Atlas in the context of an intelligent gene expression bioinformatics workflow system. The logic has been implemented in a Prolog prototype.