A synthetic biology library for the Semantic Web

描述（由申请人提供）：拟议研究的目标是确定的可行性，并创建原型软件，使用语义Web技术OWL，RDF，SPARQL和SWRL的可重用合成生物学组件库。该库将大大增加合成生物学可重用组件信息的可用性，包括组件语义的机器可读描述。这些信息，适合自动推理，智能检索和其他服务，将增加合成生物学图书馆的研究人员以及从事设计合成生物学产品的商业供应商的效用。这样一个图书馆将加速合成生物学的产业化，从而为公共卫生带来一系列好处，包括更快、更有效地设计和制造更好的“活机器”。 为了实现这些结果，在第一阶段，我们将扩展BioBricks标准的生物组件描述语义丰富的描述，使用OWL本体，以支持更好的集成，无论是与其他组件，通过模型检查和验证式的分析服务，以及与丰富的生物背景知识，目前存在于OWL本体的形式。我们将扩展OWL推理系统来解释这些语义丰富的BioBrick描述，包括通过SPARQL的语义Web查询支持和通过SWRL的规则支持。第一阶段可交付成果包括生物工程的用例和需求;这些需求与现有技术之间的差距分析;详细介绍第二阶段的经验教训和初步设计的最终报告;包含OWL扩展的BioBrick描述和OWL，SPARQL和SWRL推理和查询服务的原型库;以及用于与库条目进行直观交互的分面BioBrick浏览器。简而言之，更好的信息共享和分析基础设施将为合成生物学研究人员和从业者提供生产力的提高，这反过来又将加速合成生物学技术的大规模工业采用和使用，从而导致生物工程治疗，能源和食品技术的新进展。 公共卫生相关性：拟议中的研究与公共卫生的相关性是，语义Web支持的合成生物学图书馆将通过计算机辅助决策支持和无缝信息共享来提高合成生物学研发和工业活动的设计质量和效率，从而加速工业规模合成生物学的出现。这一发明将通过更好的“活机器”直接造福于公共卫生，以解决治疗、能源、食品和其他重要领域的问题。

DESCRIPTION (provided by applicant): The goal of the proposed research is to determine the feasibility of, and create prototype software for, a library of reusable synthetic biology components using Semantic Web technologies OWL, RDF, SPARQL and SWRL. This library will dramatically increase the availability of information about reusable components for synthetic biology, including machine-readable descriptions of the semantic meaning of the components. Such information, amenable to automated reasoning, intelligent retrieval, and other services, will increase the utility of the synthetic biology library for researchers as well as for commercial vendors engaged in designing synthetic biology products. Such a library will hasten the industrialization of synthetic biology, with a host of resulting benefits to public health, including better "living machines" designed and manufactured more quickly and efficiently. In order to achieve these results, in Phase I we will extend BioBricks standard biological component descriptions with semantically-rich descriptions, using OWL ontologies, to support better integration, both with other components, via model checking and verification-style analysis services, as well as with the wealth of biological background knowledge that presently exists in OWL ontology form. We will extend OWL reasoning systems to interpret these semantically rich BioBrick descriptions, including Semantic Web query support via SPARQL and rule support via SWRL. Phase I deliverables include use case and requirements from bioengineering; gap analysis between these requirements and existing technologies; a final report detailing lessons learning and preliminary designs for Phase II; and a prototype library containing OWL-extended BioBrick descriptions and OWL, SPARQL, and SWRL reasoning and query services; and a faceted BioBrick browser for intuitive interaction with the library's entries. In short, better information sharing and analysis infrastructure will provide productivity increases for synthetic biology researchers and practitioners, which will in turn hasten the widescale industrial adoption and use of synthetic biology techniques, leading to new advances in bioengineered therapeutic, energy, and food technologies. PUBLIC HEALTH RELEVANCE: The relevance of the proposed research to public health is that a Semantic Web-enabled library for synthetic biology will increase the design quality and efficiency-via computer-aided decision support and seamless information sharing-of synthetic biology R&D and industrial activity, thus hastening the advent of industrialscale synthetic biology. That advent will directly benefit public health by way of better "living machines" to address therapeutics, energy, food, and other vital areas.