Semantic Web meets Integrative Biology: a survey
Semantic Web meets Integrative Biology: a survey
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DOI：
10.1093/bib/bbs014
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发表时间：
2013-01-01
影响因子：
9.5
通讯作者：
Chen, Jake Y.
中科院分区：
文献类型：
--
作者：
Chen, Huajun;Yu, Tong;Chen, Jake Y.
综合生物学（IB）使用实验或计算定量技术来表征分子、细胞、组织和群体水平的生物系统。 IB 通常涉及跨学科边界的数据、知识和能力的集成，以解决复杂的问题。我们确定了跨学科整合带来的一系列生物信息学问题：（i）将相关生物医学领域的结构化数据互连的数据集成； (ii) 本体集成，将不同学科的行话、术语和分类法纳入统一的本体网络中； (iii) 知识整合，整合来自多个来源的不同知识要素； (iv) 服务集成，利用不同供应商提供的服务构建应用程序。我们认为，IB 可以从语义网 (SW) 技术支持的集成解决方案中获益匪浅。软件使科学家能够超越应用程序和网站的界限共享内容，从而形成对任何计算机都有意义且可以理解的数据网络。在这篇评论中，我们深入探讨了如何使用软件技术为全球跨学科集成构建开放、标准化和可互操作的解决方案。我们在系统生物学、综合神经科学、生物制药和转化医学领域提供了丰富的案例研究，以突出 SW 应用在 IB 中的技术特点和优势。
Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems. We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration that brings jargons, terminologies and taxonomies from various disciplines into a unified network of ontologies; (iii) knowledge integration that integrates disparate knowledge elements from multiple sources; (iv) service integration that build applications out of services provided by different vendors. We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies. The SW enables scientists to share content beyond the boundaries of applications and websites, resulting into a web of data that is meaningful and understandable to any computers. In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis. We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB.