A synthetic biology library for the Semantic Web

描述(申请人提供)：该项目的长期目标是改善合成生物学家的工程实践，从而加快合成生物学研究的步伐。合成生物学正准备通过建立从生产抗疟疾药物、到改进抗生素、到肿瘤跟踪细菌、到设计新的碳中性能源、到清理环境毒素和对抗污染的生物的系统，为健康、医学、能源和环境做出巨大贡献。我们的研究方法是将成熟的工程原理与语义网方法和技术相结合。更具体地说，我们将开发支持模块化、重用和版本控制的工程原则的工具，以配置完整的生物系统。我们应用于该领域的语义网技术包括本体开发、语义的形式化规范，以及用于执行验证、智能信息检索和配置任务的OWL推理系统。拟议研究的具体目标是开发一个原型工具，用于在合成生物学研究生命周期中管理信息。该工具的功能将包括版本控制、有关合成生物组件的智能信息检索和配置管理，以帮助将这些组件组装成工作的生物系统。我们将与Sauro博士实验室的合成生物学家直接合作，设计、开发和测试这个工具。我们将我们的研究工作分为三个具体目标：(1)分析合成生物学家的工作，并扩展我们的本体以包括合成生物学组件的配置约束和版本控制知识；(2)为合成生物学家开发版本管理能力；(3)为合成生物学家开发配置和部件检索能力。为了支持组件的协作工作和重用，我们的工具和我们的研究利用了合成生物学组件库的思想。我们的工作将使用现有的库，我们的工具将通过使用添加到这些库中。为了支持最广泛的系统重用，我们的工具将基于公共的语义网标准，并将被开发为开放的、现代的Web应用程序。我们设想在整个企业范围内使用我们的工具，这将允许更好地沟通、改进设计和更好地设计合成生物系统。反过来，这些工程改进将有助于加速合成生物学结构的广泛工业生产、采用和使用，从而导致生物工程治疗、能源和食品技术的新进展。

DESCRIPTION (provided by applicant): The long-term aims of this project are to improve the engineering practices of synthetic biologists, and thereby to hasten the pace of synthetic biology research. Synthetic biology is poised to make great contributions to health, medicine, energy, and the environment by building systems ranging from the production of anti-malarial drugs, to improved antibiotics, to tumor-tracking bacteria, to engineering new carbon-neutral energy sources, and to organisms that clean up environmental toxins and fight pollution. Our research approach is to combine well-established engineering principles with semantic web methods and technologies. More specifically, we will develop tools that support the engineering principles of modularity, reuse, and version control for the configuration of complete biological systems. The semantic web technologies that we apply to this domain include ontology development, the formal specification of semantics, and an OWL reasoning system to carry out validation, intelligent information retrieval, and configuration tasks. The specific goal of the proposed research is develop a prototype tool for the management of information throughout the synthetic biology research lifecycle. The capabilities of this tool will include version control, intelligent information retrieval about synthetic biology components, and configuration management to assist in assembling those components into working biological systems. We will design, develop, and test this tool in direct collaboration with working synthetic biologists from Dr. Sauro's laboratory. We divide our research work into three specific aims: (1) analyzing the work of synthetic biologists and extending our ontology to include configuration constraints and versioning knowledge for synthetic biology components; (2) developing version management capabilities for synthetic biologists; and (3) developing configuration and parts retrieval capabilities for synthetic biologists. To support both collaborative work and reuse of components, our tool and our research leverages the idea of an annotated library of synthetic biology components. Our work will use existing libraries, and our tool will add to these libraries through its use. To support the widest range of system reuse, our tool will be based on public, semantic web standards and will be developed as an open, modern web application. We envision an enterprise-wide use of our tool, which will allow for better communication, improved design, and better engineering of synthetic biological systems. In turn, these engineering improvements will help hasten the wide-scale industrial production, adoption, and use of synthetic biology constructs, leading to new advances in bioengineered therapeutic, energy, and food technologies.