Ontological realism: A methodology for coordinated evolution of scientific ontologies.

IF 2.5 4区计算机科学 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE

Applied Ontology Pub Date : 2010-11-15 DOI:10.3233/AO-2010-0079

Barry Smith, Werner Ceusters

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引用次数: 0

Abstract

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill's critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.

查看原文本刊更多论文

本体论现实主义：科学本体论协调演化的方法论。

自2002年以来，我们一直在测试和改进一种本体开发方法，目前该方法已被不同生命科学领域的多个研究小组采用。加里-梅里尔（Gary Merrill）在本刊最近发表的一篇论文中，描述了这种方法论被生物和生物医学科学研究人员视为具有吸引力的一些原因。与此同时，他还从哲学的角度对这种方法论提出了质疑，特别是针对我们的建议，即为科学目的而开发的本体论在构建时，其术语应被视为是指我们所说的现实中的普遍性或类型。正如我们所展示的，梅里尔的批评与我们现实主义项目的成功关系不大，因为它不仅没有揭示我们工作中的实际错误，而且还批评了我们事实上并不持有的关于普遍性的观点。尽管如此，它还是为我们提供了一个宝贵的机会来澄清现实主义方法论，并展示其某些原则是如何被应用的，尤其是在OBO（开放生物医学本体论）基金会计划的框架内。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Applied Ontology COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE-COMPUTER SCIENCE, INFORMATION SYSTEMS

CiteScore

4.80

自引率

30.00%

发文量

审稿时长

>12 weeks

期刊介绍： Applied Ontology focuses on information content in its broadest sense. As the subtitle makes clear, two broad kinds of content-based research activities are envisioned: ontological analysis and conceptual modeling. The former includes any attempt to investigate the nature and structure of a domain of interest using rigorous philosophical or logical tools; the latter concerns the cognitive and linguistic structures we use to model the world, as well as the various analysis tools and methodologies we adopt for producing useful computational models, such as information systems schemes or knowledge structures. Applied Ontology is the first journal with explicit and exclusive focus on ontological analysis and conceptual modeling under an interdisciplinary view. It aims to establish a unique niche in the realm of scientific journals by carefully avoiding unnecessary duplication with discipline-oriented journals. For this reason, authors will be encouraged to use language that will be intelligible also to those outside their specific sector of expertise, and the review process will be tailored to this end. For example, authors of theoretical contributions will be encouraged to show the relevance of their theory for applications, while authors of more technological papers will be encouraged to show the relevance of a well-founded theoretical perspective. Moreover, the journal will publish papers focusing on representation languages or algorithms only where these address relevant content issues, whether at the level of practical application or of theoretical understanding. Similarly, it will publish descriptions of tools or implemented systems only where a contribution to the practice of ontological analysis and conceptual modeling is clearly established.