摘要
在最近兴起的生物医学大数据和精准医学研究中,本体正发挥着不可替代的作用。但一大部分人对本体的定义、类型与应用比较混淆。这篇综述对这些问题进行了回答。具体而言,本体使用人和计算机都可以理解的术语及关系集来表述各种实体/概念以及它们之间关系。根据本体的作用,本体可分为三类:具有多关系模型的增强版控制术语集,反映某知识域的本体知识系统,和对元数据在语义上的约束与标准化的元数据本体。基于这些作用,本体被广泛地应用于生物医学数据的标准化、整合、检索与分析,已经知识的挖掘。当代本体学的研究发展迅速,我国刚刚起步,机遇与挑战并存。广泛地开展国内与国际有关本体的合作研究,将促进国内生物医学本体领域研究水平的整体提升,提高生物与临床科研大数据整合与精准医学研究的能力。
Ontology plays an unreplaceable role in the recently emerging big data and precision medicine research.However,the definition,subtypes and applications of ontology remain unclear for the majority of researchers.The goal of this review is to address these issues.Specifically,an ontology is a set of human-and computer readable terms,or concepts,and the relations that represent entities and their relationships in a specific domain.Based on functions,ontologies can be classified into three types:as an enhanced controlled terminology with multiple relational types,as a knowledge base abstracted from a specific real-life domain,and as a metadata ontology for metadata standardization.These types of ontologies have been widely used in biomedical domains for data standardization,integration,query and analysis,as well as for information transformation and knowledge mining.Researches on biomedical ontology have witnessed a fast progress worldwide in the last decade.As a late starter,China faces both opportunities and challenges in its ontology researches and applications.A collaboration between Chinese and international biomedical ontology communities is strongly suggested to elevate China’s national capacity for biological and clinical big data integration,and to facilitate precision medicine research.
作者
HE Yongqun
余红
杨啸林
邵晨
周伟
朱彦
王海河
刘清平
谢江安
ZHENG Jie
朱伟民
HE Yongqun;YU Hong;YANG Xiaolin;SHAO Chen;ZHOU Wei;ZHU Yan;WANG Haihe;LIU Qingping;XIE Jiang an;ZHENG Jie;ZHU Weimin(Institute of Basic Medical Sciences,Chinese Academy of Medical Sciences,Beijing 100700,China;University of Michigan Medical School,Ann Arbor,MI 48109,USA;Guizhou University Medical College,Guizhou Province People’s Hospital, Guiyang 550002,China;National Scientific Data Sharing Platform for Population and Health,Beijing 100700,China;Institute of Information on Traditional Chinese Medicine,China Academy of Chinese Medical Sciences,Beijing 100700,China;Daqing Branch of Harbin Medical University,Daqing 163319,Chin;Guangzhou University of Chinese Medicine,Guangzhou,510000,China;Chongqing University of Posts and Telecommunications,Chongqing 400065,China;University of Pennsylvania Perelman School of Medicine,PA 19104,USA;The National Center for Protein Sciences,Beijing 102206,China)
出处
《生物信息学》
2018年第1期7-14,共8页
Chinese Journal of Bioinformatics
基金
美国NIH LINCS(U54HL127624)eDSR课题
贵阳市科技计划筑科合同(20151001社78号,20161001号)
北京市自然科学基金资助项目(7174328)
国家重点研发计划资助(2017YFC0908404)
国际科技合作专项(S2014ZR0005)
关键词
可控词表
本体
基因本体
生物医学大数据
精准医学
本体中国
Controlled terminology
Ontology
Gene ontology
Biomedical big data
Precision medicine
Onto-China
