Department of Medicine, University of Chicago, Chicago, Illinois, United States of America.
PLoS Comput Biol. 2011 Sep;7(9):e1002191. doi: 10.1371/journal.pcbi.1002191. Epub 2011 Sep 29.
The use of structured knowledge representations-ontologies and terminologies-has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies.
在生物医学领域，使用结构化知识表示（本体和术语）已经成为标准。本体的定义差异很大，其背后的价值观和理念也各不相同。为了明确这些观点，我们对十几位领先的本体论者进行了采访并总结了他们的观点。这些观点可以分为三个广泛的视角，我们将其概括为数学、计算机代码和世界语。本体论作为数学将最终重视严谨性和逻辑性、代表科学子领域的对称性和一致性，以及只包含已建立的、非矛盾的知识。本体论作为计算机代码专注于实用性和多样性，使本体适合其目的。就像计算机语言 C++、Prolog 和 HTML 一样，代码视角认为，不同的应用程序需要定制设计的本体。作为世界语的本体论侧重于促进跨学科交流、知识交叉引用以及来自不同社区的数据集的计算。我们展示了这些观点如何与科学中的经典分歧相一致，并提出了如何综合它们的关注点，以加强下一代生物医学本体的观点。
