VIOLIN 2.0: Vaccine Information and Ontology LInked kNowledgebase

VIOLIN 2.0：疫苗信息和本体链接知识库

基本信息

批准号：
10687095
负责人：
Yongqun He
金额：
$ 74.35万
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：
2022
资助国家：
美国
起止时间：
2022-08-19 至 2027-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10687095
关键词：
Acceleration Acquired Immunodeficiency Syndrome Address Adjuvant Adverse event Antigens Applications Grants Area Basic Science Bioinformatics COVID-19 COVID-19 pandemic Cessation of life Clinical Clinical Trials Collaborations Communicable Diseases Communities Community Developments Community Outreach Consensus Data Databases Detection Development Dimensions Disease Educational workshop Ensure Epidemiology Evaluation Event FAIR principles Face Funding Generations Grant HIV Harvest Immune Immune response Immunologic Factors Informatics Information Retrieval Knowledge Knowledge Discovery Knowledge Extraction Licensing Life Cycle Stages Link Literature Machine Learning Malaria Manuals Methods Modern Medicine Molecular Monitor National Institute of Allergy and Infectious Disease Natural Language Processing Ontology Pattern Public Health Reproducibility Research Resources Safety Semantics Source Standardization System Systems Analysis Technology Tuberculosis United States National Institutes of Health Vaccination Vaccine Adjuvant Vaccine Antigen Vaccine Design Vaccines Visualization Work community engagement data access data integration disability experience fighting gene expression database hackathon improved informatics tool innovation insight interoperability invention knowledge graph knowledge integration knowledgebase machine learning method meetings method development outreach pathogen predictive signature programs research and development response statistical and machine learning text searching tool vaccine adverse event vaccine development vaccine formulation vaccine safety vector web interface web site

项目摘要

Project Summary: Vaccination is one of the most successful innovations in the fight against infectious disease. However, we still lack effective and safe vaccines against many major infectious diseases (e.g., HIV, tuberculosis, and malaria). We also lack a comprehensive and interoperable vaccine knowledgebase to accelerate vaccine development and better understand vaccine safety. Based on the preliminary version of our current VIOLIN vaccine knowledgebase, we propose to develop VIOLIN 2.0, a new generation Vaccine Information and Ontology LInked kNowledgebase. Strong preliminary data were generated: Originally funded by an NIH-NIAID R01, our VIOLIN has grown to include information on >4,000 vaccines for >200 pathogens. In addition, we have led the development of the community-based Vaccine Ontology (VO) and Ontology of Adverse Events (OAE) for vaccine and adverse event representation. We have also developed the widely used Vaxign and Vaxign-ML vaccine design programs and applied them to predict vaccines for many diseases including COVID-19. Many ontology- and bioinformatics-based methods and tools, including natural language processing (NLP) tools, have also been developed to analyze vaccine information and identify new scientific insights. However, the existing VIOLIN also faces new challenges in areas such as knowledge integration, interoperability, and analysis. In this proposal, we aim to systematically develop VIOLIN 2.0, which will be a community-based comprehensive vaccine knowledgebase (KB) with data FAIRness. Basic science, clinical, and public health (safety, epidemiology, vaccine coverage) knowledge will be included with robust linkage and analysis. Four specific aims are proposed: Aim 1: Implement a pipeline for automatic knowledge harvest, standardization, and integration using advanced ontology and natural language processing technologies. Aim 2: Expand the vaccine KB and management. Three specific knowledge aspects will be included: (i) vaccine formulation and development, (ii) protective responses, and (iii) vaccine safety. Aim 3: Provide VIOLIN 2.0 knowledge browser, query, and showcases. For showcase demonstration, three use cases will be built up, including pattern detection of vaccine components (including protective antigens and vaccine adjuvants), vaccine-induced host immune signatures, and vaccine adverse events. The patterns identified will be utilized with statistical and machine learning methods to support rational vaccine design and immune signature prediction. Aim 4: Community engagement and outreach. Many events such as hackathons and workshops will be held to support the development and applications of community-based ontologies, standards, and tools. VIOLIN 2.0 will significantly enhance the VIOLIN with breadth and depth of vaccine information, include knowledge not available in the current VIOLIN (e.g., vaccine adverse events), and develop new methods for efficient and scalable knowledge extraction and analysis. Our study will advance the understanding of vaccine mechanisms, and support rational vaccine design against COVID-19 and other infectious diseases.

项目概要：疫苗接种是对抗传染病最成功的创新之一。然而，我们仍然缺乏有效和安全的疫苗来预防许多主要传染病（例如艾滋病毒、结核病和疟疾）。我们还缺乏全面且可互操作的疫苗知识库来加速疫苗接种开发并更好地了解疫苗安全性。基于我们当前的 VIOLIN 的初步版本疫苗知识库，我们建议开发VIOLIN 2.0，新一代疫苗信息和本体链接知识库。生成了强有力的初步数据：我们的 VIOLIN 最初由 NIH-NIAID R01 资助，现已发展壮大包括针对超过 200 种病原体的超过 4,000 种疫苗的信息。此外，我们还主导了以下产品的开发：基于社区的疫苗本体论 (VO) 和不良事件本体论 (OAE)，用于疫苗和不良反应事件表示。我们还开发了广泛使用的 Vaxign 和 Vaxign-ML 疫苗设计计划并应用它们来预测包括 COVID-19 在内的许多疾病的疫苗。许多本体论和基于生物信息学的方法和工具，包括自然语言处理（NLP）工具，也已被开发用于分析疫苗信息并确定新的科学见解。然而，现有的小提琴在知识整合、互操作性和分析等方面也面临新的挑战。在本提案中，我们的目标是系统地开发 VIOLIN 2.0，这将是一个基于社区的具有数据公平性的综合疫苗知识库 (KB)。基础科学、临床和公共卫生（安全性、流行病学、疫苗覆盖率）知识将包含在强有力的联系和分析中。四提出了具体目标：目标 1：实施自动知识收获、标准化、使用先进的本体和自然语言处理技术进行集成。目标 2：扩大疫苗知识库和管理。将包括三个具体知识方面：（i）疫苗配方和开发，(ii) 保护性反应，以及 (iii) 疫苗安全性。目标3：提供VIOLIN 2.0知识浏览器，查询、展示。为了进行展示演示，将建立三个用例，包括模式疫苗成分（包括保护性抗原和疫苗佐剂）、疫苗诱导宿主的检测免疫特征和疫苗不良事件。确定的模式将用于统计和机器学习方法支持合理的疫苗设计和免疫特征预测。目标 4：社区参与和外展。将举办许多活动，例如黑客马拉松和研讨会支持基于社区的本体、标准和工具的开发和应用。 VIOLIN 2.0将显着增强VIOLIN疫苗信息的广度和深度，包括当前 VIOLIN 中不具备的知识（例如疫苗不良事件），并开发新方法高效且可扩展的知识提取和分析。我们的研究将增进对疫苗的了解机制，并支持针对 COVID-19 和其他传染病的合理疫苗设计。