利用语义网技术实现的分布式异构食品微生物数据整合

doi:10.13523/j.cb.20170317

中国生物工程杂志

2017, Vol. 37

Issue (3): 124-132 DOI: 10.13523/j.cb.20170317

专题

利用语义网技术实现的分布式异构食品微生物数据整合

吴林寰, 陆震鸣, 龚劲松, 史劲松, 许正宏

江南大学工业生物技术教育部重点实验室药学院无锡 214122

Integrating Distributed Heterogeneous Food Microorganism Data by Semantic Web Technology

WU Lin-huan, LU Zhen-ming, GONG Jin-song, SHI Jin-song, XU Zheng-hong

Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, China

全文: PDF(2105 KB) HTML

摘要：

随着高通量测序技术的迅速发展和食品微生物研究的逐步深入，产生了大量的数据和知识，且以不同的数据格式分布在各种数据库中。为了更好地支持食品微生物的相关研究，从各种分布式、异构的数据和知识中，进行数据提取与转换，并形成一个整合的数据平台显得尤为重要。FoodMicrobes数据库利用语义网技术，建立了一个食品微生物的整合型数据平台。该平台从各种开放的公共数据库，提取了与食品微生物相关的基因、基因组、基因功能、蛋白质序列与结构、代谢途径、文献、专利等信息，利用RDF的方法，对数据进行转换，并建立了数据之间的关联，实现了数据整合，是目前在食品微生物领域以语义网方式建立的第一个数据库。在该平台中，实现了将食品微生物的物种、菌株层面的宏观信息与基因组、蛋白质、代谢与功能等微观层面信息的贯通，并通过友好的数据检索界面，为用户进行食品微生物研究提供了重要的工具。

关键词： 语义网; 关联数据; 食品微生物

Abstract:

With the rapid development of next generation sequencing technology and the researches on fermentation mechanism of food microorganism, data and knowledge of food microorganisms increased enormously, including genomic, metagenomics, metabolic and phylogenetic information. These data are distributed from different resources with various data formats. An integrated data platform is necessary for better understanding of biological knowledge from such growing heterogeneous data. As a result, we construct a food microorganism database using semantic web technology. We describe information of gene, genome sequences, gene ontology, protein sequences and structures, pathway and enzyme in the form of Resource Description Framework (RDF) from a wide range of open data resources. In this database, physiological information of microbes from culture collections could be linked to the genomic information and further linked to the metabolic information which allows flexible queries across different domains. User-friendly interfaces of the database provide the ability to answer a number of food microorganisms research related questions based on the linked data.

Key words: Food microorganisms Linked data Semantic web

收稿日期: 2016-09-19 出版日期: 2017-03-25

ZTFLH:

Q811.4

基金资助:

国家自然科学基金（31271922），国家"863"计划（2012AA021301，2014AA021501，2013AA102106）资助项目

通讯作者: 许正宏 E-mail: zhenghxu@jiangnan.edu.cn

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引用本文:

吴林寰, 陆震鸣, 龚劲松, 史劲松, 许正宏. 利用语义网技术实现的分布式异构食品微生物数据整合[J]. 中国生物工程杂志, 2017, 37(3): 124-132.

WU Lin-huan, LU Zhen-ming, GONG Jin-song, SHI Jin-song, XU Zheng-hong. Integrating Distributed Heterogeneous Food Microorganism Data by Semantic Web Technology. China Biotechnology, 2017, 37(3): 124-132.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20170317 或 https://manu60.magtech.com.cn/biotech/CN/Y2017/V37/I3/124

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