COEUS: "semantic web in a box" for biomedical applications.
COEUS: "semantic web in a box" for biomedical applications.
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DOI：
10.1186/2041-1480-3-11
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发表时间：
2012-12-17
影响因子：
1.9
通讯作者：
Oliveira JL
中科院分区：
文献类型：
--
作者：
Lopes P;Oliveira JL
随着“组学”革命的展开，数据量和多样性的增长带来了对开创性生物信息学软件的需求，能够显著改善研究工作流程。为了应对这些计算机科学需求，生物医学软件工程师正在采用更适合生命科学领域的新兴语义网技术。后者的复杂关系很容易映射到语义网络图中，从而能够更好地理解收集的知识。尽管人们对生物信息学中的语义网技术的认识有所提高，但它们的使用仍然有限。COEUS是一个新的语义网框架，旨在简化应用程序开发周期，并遵循“盒子里的语义网”的方法。该框架提供了一个单一的包，包括高级数据集成和三元化工具、基本本体、面向Web的引擎和灵活的探索API。可以集成来自不同来源的资源，包括CSV和XML文件或SQL和SPARQL查询结果，并直接映射到一个或多个本体。高级互操作性特性包括REST服务、SPARQL端点和LinkedData发布。这些支持为Web、桌面或移动环境创建多个应用程序，并支持新的知识联盟层。该平台面向生物医学应用程序开发人员，为快速应用程序部署提供了一个完整的框架，增强了新语义信息系统的创建。COEUS可以在http://bioinformatics.ua.pt/coeus/.上以开源形式获得
As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter’s complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a “semantic web in a box” approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.
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