BioPW+:基于Linked Data的生物途径数据可视化系统

doi:10.11896/j.issn.1002-137X.2019.02.003

计算机科学 ›› 2019, Vol. 46 ›› Issue (2): 18-23.doi: 10.11896/j.issn.1002-137X.2019.02.003

所属专题：生物信息学

BioPW+:基于Linked Data的生物途径数据可视化系统

刘源^1,2, 王鑫^1,2, 甘瀛¹, 杨朝洲¹, 李维熙¹

天津大学计算机科学与技术学院天津300050¹
天津大学国际工程师学院天津300072²

收稿日期:2017-12-04 出版日期:2019-02-25 发布日期:2019-02-25
通讯作者: 王鑫(1981-),男,博士,副教授,CCF高级会员,主要研究方向为图数据库、知识图谱数据管理、大数据管理,E-mail:wangx@tju.edu.cn
作者简介:刘源(1992-),男,硕士生,CCF会员,主要研究方向为生物途径数据集成;甘瀛(1994-),男,硕士生,主要研究方向为图数据库;杨朝洲(1995-),男,主要研究方向为知识图谱;李维熙(1995-),男,主要研究方向为知识图谱。
基金资助:
本文受国家自然科学基金项目(61572353),天津市自然科学基金项目(17JCYBJC15400)资助。

BioPW+:Biological Pathway Data Visualization System Based on Linked Data

LIU Yuan^1,2, WANG Xin^1,2GAN Ying¹, YANG Chao-zhou¹LI Wei-xi¹

School of Computer Science and Technology,Tianjin University,Tianjin 300050,China¹
Tianjin International Engineering Institute,Tianjin 300072,China²

Received:2017-12-04 Online:2019-02-25 Published:2019-02-25

摘要/Abstract

摘要： 自Linked Data项目被提出以来,大量的开放关联数据被发布到语义Web上,这其中就包含了许多的生物途径数据集。为了使生物学家能够有效地利用这些开放的数据集,对基于Linked Data的生物途径数据可视化系统进行研究,提出了生物途径可视化模型和展示布局方案,并且采用标识符动态映射实现了多源生物途径数据的浏览,最终开发了基于Linked Data的生物途径数据查询可视化系统——BioPW+。该系统应用语义Web技术,依靠SPARQL查询来定位生物途径的基本信息,然后基于Open PHACTS平台获取生物途径元素的详细信息,最终Web界面采用力导向图布局、Sankey图布局对生物途径数据进行展示并提供多种交互操作。与已有的仅仅基于某一特定数据库的生物途径工具相比,BioPW+系统基于Linked Data,可以同时一次性展示多个数据集中的生物途径数据及与其相关的其他生物化学数据,极大节省了时间并增强了数据的完整性。

关键词: Linked Data, 可视化, 生物途径, 语义Web

Abstract: Since the Linked Data project arises,abundant open linked data have been published on the semantic Web,which contain plentiful biological pathway datasets.To make these data be utilized effectively for the biological scientists,this paper conducted the research on heterogeneous biological pathway data visualization system based on Linked Data,proposed a biological pathway visualization model,and then designed visualization layout strategies.After that,this paper utilized the dynamic mapping of identifiers to implement the browsing of heterogeneous biological pathway data,and finally developed a biological pathway visualization system called BioPW+.Primarily,BioPW+ retrieves the essential information with respect to the biological pathway by means of the semantic Web technologies and SPARQL queries.Then,through the Open PHACTS platform,it acquires the detailed information of the pathway.Finally,it illustrates the biological pathway on the Web page by employing the force-directed layout and Sankey layout,and furnishes various interoperable functions.Not like the existing tools that only retrieve data from single data source,BioPW+ is based on the Linked Data,and can elaborate the biological pathways with their relevant biochemical information from multiple datasets,saving large amounts of time and improving the data integrity.

Key words: Biological pathway, Linked Data, Semantic Web, Visualization

中图分类号:

TP311.13

刘源, 王鑫, 甘瀛, 杨朝洲, 李维熙. BioPW+:基于Linked Data的生物途径数据可视化系统[J]. 计算机科学, 2019, 46(2): 18-23. https://doi.org/10.11896/j.issn.1002-137X.2019.02.003

LIU Yuan, WANG XinGAN Ying, YANG Chao-zhouLI Wei-xi. BioPW+:Biological Pathway Data Visualization System Based on Linked Data[J]. Computer Science, 2019, 46(2): 18-23. https://doi.org/10.11896/j.issn.1002-137X.2019.02.003

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BioPW+:基于Linked Data的生物途径数据可视化系统

BioPW+:Biological Pathway Data Visualization System Based on Linked Data

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