Ontology-based Information Network to Support Vaccine Research

基于本体的信息网络支持疫苗研究

基本信息

批准号：
8311060
负责人：
Yongqun He
金额：
$ 26.5万
依托单位：
UNIVERSITY OF MICHIGAN AT ANN ARBOR
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-22 至 2014-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8311060
关键词：
Algorithms Attenuated Live Virus Vaccine Automated Annotation Bacterial Genes Brucella Brucella Vaccine Clinical Trials Collaborations Communicable Diseases Communities Consensus Controlled Vocabulary Data Databases Development Dictionary Ensure Escherichia coli Escherichia coli Vaccines Foundations Genome Genomics Goals Immune Immune response Immune system Immunity Informatics Information Networks Information Retrieval Journals Laboratories Literature MeSH Thesaurus Methodology Methods Modeling National Center for Integrative Biomedical Informatics Natural Language Processing Online Systems Ontology Organism Paper Preparation Process Proteins Publications Publishing Research Research Personnel Retrieval Scientist Semantics Smallpox Vaccine Staging Standardization Structure Subunit Vaccines System Testing Training Vaccine Research Vaccines abstracting base biomedical ontology computer based Semantic Analysis data integration editorial gene function genome-wide interest journal article knowledge base microorganism novel novel vaccines pathogen programs repository research study statistics text searching user-friendly vaccine candidate vaccine development vaccine evaluation web interface

项目摘要

Project Summary (Abstract): Since the introduction of Edward Jenner's smallpox vaccine in 1796, vaccines have proven invaluable for their ability to stimulate the immune system and to confer protection against pathogenic organisms. Progress in modern vaccine research has been accompanied by a dramatic increase in the number of vaccine-related papers in the published literature. It has become increasingly challenging to identify and annotate vaccine data from this large and diverse literature which no one scientist or team can fully master. Although vaccine databases exist that emphasize commercialized vaccines, no public central repository is available to store research data concerning commercial vaccines, vaccines in clinical trials, or vaccine candidates in early stages of development, in a fashion that render such data available for advanced analyses. To fill this need, we have developed VIOLIN (http://www.violinet.org), a web-based database system for annotation, storage, and analysis of published vaccine data. An ontology represents consensus-based controlled vocabularies of terms and relations, with associated definitions which are logically formulated in such a way as to promote automated reasoning. A bottleneck of vaccine research and further VIOLIN development is the lack of a vaccine ontology, which in turn makes a significant obstacle for vaccine data standardization, retrieval, integration, and advanced analysis and prediction. Our goal is to develop the community-based Vaccine Ontology (VO) and apply it to efficient vaccine literature mining and analysis of protective immune mechanisms. We will focus on two model pathogens: Escherichia coli and Brucella species. This project contains three specific aims: (1) develop a community-based Vaccine Ontology (VO), and apply it to establish a vaccine knowledgebase and to promote vaccine data integration and query through Semantic Web. The VO development will be achieved through collaboration with vaccine researchers, the Infectious Disease Ontology (IDO) Initiative, and the National Center for Biomedical Ontology (NCBO); (2) develop a VO-based natural language processing (NLP) system and apply it for more efficient retrieval of Brucella and E. coli vaccine information, automated annotation of journal articles with VO terms, and VO improvement. This task will be achieved by collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). (3) analyze and predict vaccine targets and protective immune networks attributable to the interactions between host and vaccine. This will be achieved mainly by VO-based literature mining and a novel genome- and literature-based statistical methodology. This project will be implemented by a strong collaborative team and supported from a large user community. The Vaccine Ontology and its applications to literature mining and for studying protective immunity against Brucella spp. and E. coli will lay a strong foundation for further advanced informatics research on vaccines against infectious diseases in the post-genomics and information era.

项目概要（摘要）：自从 1796 年爱德华·詹纳 (Edward Jenner) 的天花疫苗问世以来，事实证明疫苗对于人类来说具有无价的价值。它们刺激免疫系统并提供针对病原生物的保护的能力。进展情况现代疫苗研究伴随着与疫苗相关的数量急剧增加已发表文献中的论文。识别和注释疫苗数据变得越来越具有挑战性从这些庞大而多样的文献中，任何一个科学家或团队都无法完全掌握。虽然疫苗存在强调商业化疫苗的数据库，没有可用于存储的公共中央存储库有关商业疫苗、临床试验中的疫苗或早期候选疫苗的研究数据开发的方式，使这些数据可用于高级分析。为了满足这个需求，我们有开发了 VIOLIN (http://www.violinet.org)，这是一个基于 Web 的数据库系统，用于注释、存储和对已发布的疫苗数据进行分析。本体代表基于共识的受控术语词汇表和关系，以及相关的定义，这些定义以逻辑方式制定，以促进自动化推理。疫苗研究和进一步VIOLIN发展的瓶颈是缺乏疫苗本体，这反过来又对疫苗数据标准化、检索、集成和先进技术造成重大障碍。分析和预测。我们的目标是开发基于社区的疫苗本体（VO）并将其应用于高效疫苗文献挖掘与保护性免疫机制分析。我们将重点关注两个模型病原体：大肠杆菌和布鲁氏菌属。该项目包含三个具体目标：（1）开发基于社区的疫苗本体（VO），并应用其建立疫苗知识库并推广通过语义网进行疫苗数据集成和查询。 VO的发展将通过以下方式实现与疫苗研究人员、传染病本体论 (IDO) 倡议和国家生物医学本体中心（NCBO）；（2）开发基于VO的自然语言处理（NLP）系统并将其应用于更有效地检索布鲁氏菌和大肠杆菌疫苗信息，自动注释带有 VO 术语的期刊文章以及 VO 改进。这项任务将通过与国家综合生物医学信息学中心 (NCIBI)。 (3) 分析和预测疫苗靶点保护性免疫网络归因于宿主和疫苗之间的相互作用。这将实现主要通过基于 VO 的文献挖掘和一种新颖的基于基因组和文献的统计方法。这项目将由强大的协作团队实施并得到大型用户社区的支持。这疫苗本体及其在文献挖掘和研究布鲁氏菌保护性免疫中的应用种。和大肠杆菌将为进一步深入的疫苗信息学研究奠定坚实的基础后基因组学和信息时代的传染病。

项目成果

期刊论文数量（38）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology.

DOI：
10.1186/1471-2105-14-s4-s2
发表时间：
2013
期刊：
BMC bioinformatics
影响因子：
3
作者：
Xiang Z;He Y
通讯作者：
He Y

Databases and in silico tools for vaccine design.

DOI：
10.1007/978-1-62703-342-8_8
发表时间：
2013-01-01
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
0
作者：
He, Yongqun;Xiang, Zuoshuang
通讯作者：
Xiang, Zuoshuang

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

DOI：
10.1186/s13326-017-0169-2
发表时间：
2018-01-12
期刊：
Journal of biomedical semantics
影响因子：
1.9
作者：
He Y;Xiang Z;Zheng J;Lin Y;Overton JA;Ong E
通讯作者：
Ong E

Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics.

DOI：
10.3389/fcimb.2012.00002
发表时间：
2012
期刊：
Frontiers in cellular and infection microbiology
影响因子：
5.7
作者：
He Y
通讯作者：
He Y

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

DOI：
10.1093/nar/gkw918
发表时间：
2017-01-04
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Ong E;Xiang Z;Zhao B;Liu Y;Lin Y;Zheng J;Mungall C;Courtot M;Ruttenberg A;He Y
通讯作者：
He Y