libSBOLj 2.0: A Java Library to Support SBOL 2.0
libSBOLj 2.0: A Java Library to Support SBOL 2.0
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libSBOLj 2.0：支持 SBOL 2.0 的 Java 库
DOI：
10.1109/lls.2016.2546546
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
C. Myers
中科院分区：
文献类型：
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作者：
Zhen Zhang;Tramy Nguyen;Nicholas Roehner;Goksel Misirli;M. Pocock;Ernst Oberortner;Meher Samineni;Z. Zundel;J. Beal;Kevin Clancy;A. Wipat;C. Myers
合成生物学开放语言(SBOL)是一种用于表示合成生物学设计的新兴数据标准。SBOL的目标是改善这些设计的重现性，以及研究人员和/或基因设计自动化工具之间的电子交流。该标准的最新版本SBOL 2.0允许对多种生物成分(例如DNA、RNA、蛋白质、复合体、小分子等)进行注释。以及它们之间的相互作用。SBOL 2.0还允许研究人员将组件组织成分层模块，指定其预期功能，并将模块链接到以数学方式描述其行为的模型。为了支持SBOL 2.0的使用，我们开发了libSBOLj 2.0 Java库，它为开发人员提供了一个易于使用的应用程序编程接口(API)，包括操作SBOL构造、与RDF/XML文件格式的串行化以及从先前的SBOL 1.1标准到SBOL 2.0的转换形式的迁移支持。这封信描述了libSBOLj2.0库及其设计中涉及的关键工程决策。
The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic design automation tools. The latest version of the standard, SBOL 2.0, enables the annotation of a large variety of biological components (e.g., DNA, RNA, proteins, complexes, small molecules, etc.) and their interactions. SBOL 2.0 also allows researchers to organize components into hierarchical modules, to specify their intended functions, and to link modules to models that describe their behavior mathematically. To support the use of SBOL 2.0, we have developed the libSBOLj 2.0 Java library, which provides an easy to use Application Programming Interface (API) for developers, including manipulation of SBOL constructs, serialization to and from an RDF/XML file format, and migration support in the form of conversion from the prior SBOL 1.1 standard to SBOL 2.0. This letter describes the libSBOLj 2.0 library and key engineering decisions involved in its design.