Since the boom of biomedical big data studies,various big data processing technologies have been developed rapidly.As an important form of knowledge representation,ontology has become an important means for the utiliz...Since the boom of biomedical big data studies,various big data processing technologies have been developed rapidly.As an important form of knowledge representation,ontology has become an important means for the utilization and integration of biomedical big data.The emergence of new technologies for ontology development has resulted in the generation of many biomedical ontologies by many ontology development communities.The Open Biological and Biomedical Ontology Foundry,an academic organization for bio-ontology developers,has provided a set of principles to guide community-based open ontology construction.The Open Biological and Biomedical Ontology Foundry have also built many widely used ontologies,such as Gene Ontology,Human Phenotype Ontology,and Chemical Entities of Biological Interest.Other various ontology repositories have also been created and used to support ontology reuse.Many efficient tools for ontology applications,such as data annotation and terms mapping,have also been developed.High quality ontologies are also being used to develop new methods and tools for biomedical data analysis.The applications of Gene Ontology and Human Phenotype Ontology for data analysis and integration in recent years are reviewed here.To promote the development and applications of biomedical ontologies in China,a research community,OntoChina,was founded recently.OntoChina aims to support the development of reference ontologies,especially bilingual and Chinese translated ontologies.OntoChina also encourages ontology developers to follow the Open Biological and Biomedical Ontology Foundry principles.展开更多
基金国家自然科学基金青年基金项目“基于本体方法的我国上市甲乙肝疫苗相关不良反应数据挖掘与建模分析”(61801067)重庆市教育委员会科学技术研究重点项目“卡介苗两种用途下相应不良反应信息的本体化表征与建模分析”(KJZD-K202000603)+4 种基金中国医学科学院中央级公益性科研院所基本科研业务费专项资金资助,“国家卫生健康委员会肺脏免疫性疾病诊治重点实验室”建设项目(2019PT320003)University of Michigan Medical School Global Reach FundMichigan Medicine-Peking University Health Sciences Center Joint Institute for Clinical and Translational Research“Systemic Investigation of the Microbiome-host interactions in H.pylori-associated Gastric Cancer Patients”(U063430,BMU2019JI010)国家重点研发计划精准医学研究专项“疾病表型组-实验组学数据分析、注释与整合”(2017YFC0908404)中国医学科学院医学与健康科技创新工程项目“生物医学本体支持的通用数据元素表示和应用系统建设”(2018-I2M-AI-009)。
基金This work was supported by Chinese Academy of Medical Science(CAMS)Innovation Fund for Medical Sciences(CIFMS)(No.2018-I2M-AI-009 to XY)Independent Subject Project Funded by Basic Scientific Research Fund of Chinese Academy of Chinese Medical Science(No.zz110318 to YZ)the University of Michigan Global Reach Award(to YH).
文摘Since the boom of biomedical big data studies,various big data processing technologies have been developed rapidly.As an important form of knowledge representation,ontology has become an important means for the utilization and integration of biomedical big data.The emergence of new technologies for ontology development has resulted in the generation of many biomedical ontologies by many ontology development communities.The Open Biological and Biomedical Ontology Foundry,an academic organization for bio-ontology developers,has provided a set of principles to guide community-based open ontology construction.The Open Biological and Biomedical Ontology Foundry have also built many widely used ontologies,such as Gene Ontology,Human Phenotype Ontology,and Chemical Entities of Biological Interest.Other various ontology repositories have also been created and used to support ontology reuse.Many efficient tools for ontology applications,such as data annotation and terms mapping,have also been developed.High quality ontologies are also being used to develop new methods and tools for biomedical data analysis.The applications of Gene Ontology and Human Phenotype Ontology for data analysis and integration in recent years are reviewed here.To promote the development and applications of biomedical ontologies in China,a research community,OntoChina,was founded recently.OntoChina aims to support the development of reference ontologies,especially bilingual and Chinese translated ontologies.OntoChina also encourages ontology developers to follow the Open Biological and Biomedical Ontology Foundry principles.
