Donnelly Maureen, Bittner Thomas, Rosse Cornelius
Department of Philosophy, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, 135 Park Hall, Buffalo, NY 14260, USA.
Artif Intell Med. 2006 Jan;36(1):1-27. doi: 10.1016/j.artmed.2005.07.004. Epub 2005 Oct 24.
The objective of this paper is to demonstrate how a formal spatial theory can be used as an important tool for disambiguating the spatial information embodied in biomedical ontologies and for enhancing their automatic reasoning capabilities.
This paper presents a formal theory of parthood and location relations among individuals, called Basic Inclusion Theory (BIT). Since biomedical ontologies are comprised of assertions about classes of individuals (rather than assertions about individuals), we define parthood and location relations among classes in the extended theory Basic Inclusion Theory for Classes (BIT+Cl). We then demonstrate the usefulness of this formal theory for making the logical structure of spatial information more precise in two ontologies concerned with human anatomy: the Foundational Model of Anatomy (FMA) and GALEN.
We find that in both the FMA and GALEN, class-level spatial relations with different logical properties are not always explicitly distinguished. As a result, the spatial information included in these biomedical ontologies is often ambiguous and the possibilities for implementing consistent automatic reasoning within or across ontologies are limited.
Precise formal characterizations of all spatial relations assumed by a biomedical ontology are necessary to ensure that the information embodied in the ontology can be fully and coherently utilized in a computational environment. This paper can be seen as an important beginning step toward achieving this goal, but much more work along these lines is required.
本文的目的是展示一种形式化空间理论如何能够作为一种重要工具，用于消除生物医学本体中所包含的空间信息的歧义，并增强其自动推理能力。
本文提出了一种关于个体之间部分与位置关系的形式化理论，称为基本包含理论（BIT）。由于生物医学本体由关于个体类别的断言（而非关于个体的断言）组成，我们在扩展理论“类的基本包含理论”（BIT+Cl）中定义了类之间的部分与位置关系。然后，我们在涉及人体解剖学的两个本体——解剖学基础模型（FMA）和盖伦本体（GALEN）中，展示了这种形式化理论对于使空间信息的逻辑结构更加精确的有用性。
我们发现，在FMA和GALEN中，具有不同逻辑属性的类级空间关系并非总是被明确区分。因此，这些生物医学本体中所包含的空间信息常常模糊不清，并且在本体内或跨本体实现一致的自动推理的可能性有限。
生物医学本体所假定的所有空间关系的精确形式化表征对于确保本体中所包含的信息能够在计算环境中得到充分且连贯的利用是必要的。本文可被视为朝着实现这一目标迈出的重要第一步，但沿着这些思路还需要开展更多工作。
