Research Group Ontologies in Medicine, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany.
BMC Bioinformatics. 2009 Nov 18;10:377. doi: 10.1186/1471-2105-10-377.
Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike.
We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving.
Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.
生物序列在分子和计算生物学中起着重要作用。它们被作为包含信息的实体进行研究，这些实体构成了 DNA、RNA 或蛋白质。作为 OBO 基金会的一部分，序列本体论包含了对序列及其属性的描述和定义。然而，关于序列的最基本问题仍然没有答案：生物序列是一种什么样的实体？这个问题的答案不仅有利于使用生物序列概念的形式化本体，也有利于计算生物学中的分析。
我们提供了生物序列的本体分析和正式表示，可以用于基于知识的应用和其他本体。我们区分了三种可以被称为“生物序列”的不同实体：分子链、生物数据库中的句法表示，以及承载抽象信息的实体。为了在基于知识的应用中使用，并包含在生物医学本体中，我们为自动化定理证明实现了所开发的公理系统。
公理对于实现本体的主要目标是必要的：即正式指定在一个领域内使用的术语的含义。生物序列本体的公理系统是 OBO 基金会本体的第一个详细的公理系统，它可以作为开发更正式的本体和最终基于知识的应用的起点。
