Biomedical & Health Informatics, University of Washington, Seattle, Washington, United States of America.
PLoS One. 2011 Feb 24;6(2):e17005. doi: 10.1371/journal.pone.0017005.
We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.
我们创建了标准生物部件知识库（SBPkb），作为合成生物学的公共可访问语义网资源（sbolstandard.org）。SBPkb 允许研究人员查询和检索标准生物部件，以便在合成生物学中进行研究和使用。它的初始版本包括存储在标准生物部件注册中心（partsregistry.org）中的所有部件信息。SBPkb 通过使用我们的合成生物学部件语义框架来转换这些信息，使其具有计算能力。这个框架被称为 SBOL-semantic，是合成生物学开放语言（SBOL）的一部分，是合成生物学数据交换小组的一个项目。SBOL-semantic 表示常用的合成生物学实体，其目的是提高生物部件描述的分布和交换。在本文中，我们描述了数据、将其转换为 SBPkb 的方法，最后，我们通过一组示例查询展示了我们知识库的价值。我们使用 RDF 技术和 SPARQL 查询来检索已知受负调控和正调控的候选“启动子”部件。这种方法提供了新的基于网络的数据访问方法，以执行目前不可能的部件搜索。
