Standard biological parts knowledgebase.
Standard biological parts knowledgebase.
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DOI：
10.1371/journal.pone.0017005
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发表时间：
2011-02-24
期刊：
影响因子：
3.7
通讯作者：
Gennari JH
中科院分区：
文献类型：
--
作者：
Galdzicki M;Rodriguez C;Chandran D;Sauro HM;Gennari JH
我们已经创建了标准生物学部件的知识库（SBPkb）作为合成生物学（sbolstandard.org）的可访问语义Web资源。SBPkb允许研究人员查询和检索用于合成生物学研究和使用的标准生物部件。其初始版本包括标准生物部件注册表（partsregistry.org）中存储的所有部件信息。SBPkb使用我们的合成生物学部分语义框架转换这些信息，使其可计算。这个框架被称为SBOL语义，是合成生物学开放语言（SBOL）的一部分，SBOL是合成生物学数据交换组的一个项目。SBOL-语义表示常用的合成生物学实体，其目的是改善生物部分描述的分布和交换。在本文中，我们描述的数据，我们的方法转换到SBPkb，最后，我们证明了我们的知识库的价值与一组示例查询。我们使用RDF技术和SPARQL查询检索候选人的“启动子”部分，已知是负调控和正调控。该方法提供了新的基于Web的数据访问，以执行当前不可能的零件搜索。
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.