Chemoinformatics and Metabolism, European Bioinformatics Institute, Hinxton, United Kingdom.
PLoS One. 2011;6(10):e25513. doi: 10.1371/journal.pone.0025513. Epub 2011 Oct 3.
Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).
cheminformatics 是将信息学技术应用于计算机化学领域以解决化学问题的一门学科。在生物学的许多领域中， cheminformatics 在计算研究中都起着重要的作用，包括代谢、蛋白质组学和系统生物学。在这些领域中应用 cheminformatics 的一个关键方面是准确地交换数据，这越来越多地通过使用本体论来完成。本体论是使用基于逻辑的本体语言对对象及其属性的一种正式表示。目前正在开发许多本体论来表示所有科学领域的对象。本体论可以定义、分类和支持对特定领域中的对象进行查询，从而构建智能计算机应用程序，支持该领域中的科学家以及相关领域的科学家的工作。现代化学研究依赖于计算技术来筛选和组织数据，以最大限度地提高研究效率。在这些算法和过程中操作的对象，以及算法和过程本身，在计算机中都享有一种虚拟的生命。我们将这些信息实体称为信息实体。在这里，我们描述了我们开发化学信息实体本体论的工作，主要重点是数据驱动的研究以及在语义网上下文中集成化学实体的计算性质（描述符）。我们的本体论区分算法或过程信息与声明或事实信息，并特别重视对计算数据来源的注释。化学信息本体论正在作为一个开放的协作项目进行开发。更多详细信息和可下载的 OWL 文件可在 http://code.google.com/p/semanticchemistry/ 获得（许可证：CC-BY-SA）。
