A synthetic biology library for the Semantic Web

描述（由申请人提供）：该项目的长期目标是提高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。合成生物学将为健康、医学、能源和环境做出巨大贡献，因为它构建了一系列系统，从生产抗疟疾药物，到改进抗生素，到肿瘤追踪细菌，再到设计新的碳中性能源，再到清除环境毒素和对抗污染的生物体。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，我们将为完整生物系统的配置开发支持模块化、重用和版本控制的工程原则的工具。我们应用于该领域的语义web技术包括本体开发、语义的形式化规范以及执行验证、智能信息检索和配置任务的OWL推理系统。该研究的具体目标是开发一个原型工具，用于在整个合成生物学研究生命周期中管理信息。这个工具的功能将包括版本控制，关于合成生物学组件的智能信息检索，以及配置管理，以帮助将这些组件组装成工作的生物系统。我们将与索罗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)开发合成生物学家的版本管理能力；(3)开发合成生物学家的构型和部件检索能力。为了支持协同工作和组件的重用，我们的工具和研究利用了合成生物学组件的注释库的想法。我们的工作将使用现有的库，我们的工具将通过它的使用来添加这些库。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web标准，并将作为一个开放的现代web应用程序开发。我们设想在企业范围内使用我们的工具，这将允许更好的沟通，改进的设计，以及更好的合成生物系统的工程。反过来，这些工程改进将有助于加速合成生物学结构的大规模工业生产、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.