Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL

The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge about techniques and best practice on ontology development. In the bio-ontology domain, these two camps have often come into conflict, especially where pragmatism comes into conflict with perceived best practice. One of these areas is the insistence of computer scientists on a well-defined semantic basis for the Knowledge Representation language being used. In this article, we will first describe why this community is so insistent. Second, we will illustrate this by examining the semantics of the Web Ontology Language and the semantics placed on the Directed Acyclic Graph as used by the Gene Ontology. Finally we will reconcile the two representations, including the broader Open Biomedical Ontologies format. The ability to exchange between the two representations means that we can capitalise on the features of both languages. Such utility can only arise by the understanding of the semantics of the languages being used. By this illustration of the usefulness of a clear, well-defined language semantics, we wish to promote a wider understanding of the computer science perspective amongst potential users within the biological community.生物本体论（bio-ontology）领域分为两大阵营：其一为生物学领域专家，他们掌握着我们期望通过本体论（ontology）加以收录的专业知识；其二为本体论专家，他们精通本体论开发的相关技术与最佳实践规范。在生物本体论领域，这两大阵营时常产生分歧，尤其是当实用主义与公认的最佳实践发生冲突之时。其中一个典型分歧点在于，计算机科学家坚持要求所用的知识表示语言（Knowledge Representation Language）必须具备明确界定的语义基础。本文将首先阐释该群体为何持此坚持态度；其次，通过剖析网络本体论语言（Web Ontology Language）的语义，以及基因本体论（Gene Ontology）所采用的有向无环图（Directed Acyclic Graph）所设定的语义，对此加以说明；最后对两种表示形式进行协调，其中也涵盖适用范围更广的开放式生物医学本体论（Open Biomedical Ontologies）格式。两种表示形式之间的互转能力，使得我们可以充分利用两种语言的特性优势。唯有充分理解所用语言的语义，方能实现此类应用价值。本文通过阐释清晰明确的语言语义所具备的应用价值，旨在推动生物学领域的潜在用户更全面地理解计算机科学视角下的本体论开发思路。