Implementation of linked data in the life sciences at BioHackathon 2011.
Implementation of linked data in the life sciences at BioHackathon 2011.
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在2011年Biohackathon生命科学中实施链接数据。
DOI：
10.1186/2041-1480-6-3
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发表时间：
2015
影响因子：
1.9
通讯作者：
Ogishima S
中科院分区：
文献类型：
--
作者：
Aoki-Kinoshita KF;Kinjo AR;Morita M;Igarashi Y;Chen YA;Shigemoto Y;Fujisawa T;Akune Y;Katoda T;Kokubu A;Mori T;Nakao M;Kawashima S;Okamoto S;Katayama T;Ogishima S
关联数据最近在生命科学领域获得了一些关注，作为提供和共享数据的有效方式。作为语义Web的一部分，数据被链接起来，以便人或机器可以探索数据网络。资源描述框架（RDF）是实现关联数据的标准方法。在生成RDF数据的过程中，不仅数据简单地彼此链接，链接本身也由本体来表征，从而允许区分链接的类型。虽然为数据提供者定义本体的劳动力成本很高，但其优点在于与数据分析和可视化软件的互操作性更高。这种互操作性的提高促进了数据的多方面检索，并且可以快速提取和可视化适当的数据。这种检索通常使用SPARQL（SPARQL协议和RDF查询语言）查询语言来执行，该语言用于查询RDF数据存储。对于数据库提供商来说，这种互操作性肯定会导致用户数量的增加。本文描述了为期一周的BioHacking2011的参与者之间分享的经验和讨论，他们经历了自己数据的RDF表示的开发，并开发了特定的RDF和SPARQL用例。为生物信息学家提供了关于在开发其数据的RDF表示时应考虑的事项的建议，这些建议考虑使数据可用和可互操作。2011年生物黑客大会的参与者能够在短短五天的时间内生成其数据的RDF表示，并更好地了解生成此类数据的要求。我们总结了所完成的工作，希望它将有助于参与开发实验室数据库或数据分析的研究人员，以及那些正在考虑RDF和关联数据等技术的人。
Linked Data has gained some attention recently in the life sciences as an effective way to provide and share data. As a part of the Semantic Web, data are linked so that a person or machine can explore the web of data. Resource Description Framework (RDF) is the standard means of implementing Linked Data. In the process of generating RDF data, not only are data simply linked to one another, the links themselves are characterized by ontologies, thereby allowing the types of links to be distinguished. Although there is a high labor cost to define an ontology for data providers, the merit lies in the higher level of interoperability with data analysis and visualization software. This increase in interoperability facilitates the multi-faceted retrieval of data, and the appropriate data can be quickly extracted and visualized. Such retrieval is usually performed using the SPARQL (SPARQL Protocol and RDF Query Language) query language, which is used to query RDF data stores. For the database provider, such interoperability will surely lead to an increase in the number of users. This manuscript describes the experiences and discussions shared among participants of the week-long BioHackathon 2011 who went through the development of RDF representations of their own data and developed specific RDF and SPARQL use cases. Advice regarding considerations to take when developing RDF representations of their data are provided for bioinformaticians considering making data available and interoperable. Participants of the BioHackathon 2011 were able to produce RDF representations of their data and gain a better understanding of the requirements for producing such data in a period of just five days. We summarize the work accomplished with the hope that it will be useful for researchers involved in developing laboratory databases or data analysis, and those who are considering such technologies as RDF and Linked Data.
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Miriam Resources：生成和解决系统生物学中强大的交叉引用的工具。
影响因子：
--
作者：
Laibe, Camille;Le Novere, Nicolas
通讯作者：
Le Novere, Nicolas
DOI：
10.1093/bioinformatics/btt765
发表时间：
2014-05-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Jupp S;Malone J;Bolleman J;Brandizi M;Davies M;Garcia L;Gaulton A;Gehant S;Laibe C;Redaschi N;Wimalaratne SM;Martin M;Le Novère N;Parkinson H;Birney E;Jenkinson AM
通讯作者：
Jenkinson AM
影响因子：
46.9
作者：
Smith, Barry;Ashburner, Michael;Lewis, Suzanna
通讯作者：
Lewis, Suzanna
影响因子：
14.9
作者：
Noy NF;Shah NH;Whetzel PL;Dai B;Dorf M;Griffith N;Jonquet C;Rubin DL;Storey MA;Chute CG;Musen MA
通讯作者：
Musen MA
影响因子：
1.9
作者：
Jonquet C;Musen MA;Shah NH
通讯作者：
Shah NH