Synthetic biology open language (SBOL) version 3.0.0.
Synthetic biology open language (SBOL) version 3.0.0.
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DOI：
10.1515/jib-2020-0017
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发表时间：
2020-06-25
影响因子：
1.9
通讯作者：
Myers CJ
中科院分区：
文献类型：
--
作者：
Baig H;Fontanarrosa P;Kulkarni V;McLaughlin JA;Vaidyanathan P;Bartley B;Beal J;Crowther M;Gorochowski TE;Grünberg R;Misirli G;Scott-Brown J;Oberortner E;Wipat A;Myers CJ
合成生物学建立在遗传学，分子生物学和代谢工程的基础上，将工程原理应用于生物系统的设计。在设计合成系统时，合成生物学家需要交换有关多种类型分子、系统预期行为和实际实验测量的信息。合成生物学开放语言（SBOL）已被开发为标准，以支持合成生物学中生物设计信息的规范和交换，遵循开放社区过程，涉及学术界，工业界和其他机构的湿台科学家和干科学建模师和软件开发人员。本文档描述了SBOL 3.0.0，它基于在各种科学和工业环境中部署的经验，压缩和简化了SBOL的先前版本。特别地，SBOL 3.0.0，（1）将序列特征与部分/子部分关系分离，（2）将组件定义/组件重命名为组件/子组件，（3）合并组件和模块类，（4）确保数据模型和本体术语之间的一致性，（5）扩展定义和引用子组件的方法，（6）细化对对象URI的要求，（7）启用基于图的序列化，（8）移动组件类型的系统生物学本体（SBO），（9）使所有序列关联显式化，（10）使接口显式化，（11）将序列约束推广到一般结构约束类，以及（12）扩展允许的约束集合。
Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints.
影响因子：
1.8
作者：
Hucka M
通讯作者：
Hucka M