U24AI171008

Violin 2.0: Vaccine Information and Ontology Linked Knowledgebase - 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.

Regents Of The University Of Michigan

TO ASSIST PUBLIC AND PRIVATE NONPROFIT INSTITUTIONS AND INDIVIDUALS TO ESTABLISH, EXPAND AND IMPROVE BIOMEDICAL RESEARCH AND RESEARCH TRAINING IN INFECTIOUS DISEASES AND RELATED AREAS, TO CONDUCT DEVELOPMENTAL RESEARCH, TO PRODUCE AND TEST RESEARCH MATERIALS. TO ASSIST PUBLIC, PRIVATE AND COMMERCIAL INSTITUTIONS TO CONDUCT DEVELOPMENTAL RESEARCH, TO PRODUCE AND TEST RESEARCH MATERIALS, TO PROVIDE RESEARCH SERVICES AS REQUIRED BY THE AGENCY FOR PROGRAMS IN INFECTIOUS DISEASES, AND CONTROLLING DISEASE CAUSED BY INFECTIOUS OR PARASITIC AGENTS, ALLERGIC AND IMMUNOLOGIC DISEASES AND RELATED AREAS. PROJECTS RANGE FROM STUDIES OF MICROBIAL PHYSIOLOGY AND ANTIGENIC STRUCTURE TO COLLABORATIVE TRIALS OF EXPERIMENTAL DRUGS AND VACCINES, MECHANISMS OF RESISTANCE TO ANTIBIOTICS AS WELL AS RESEARCH DEALING WITH EPIDEMIOLOGICAL OBSERVATIONS IN HOSPITALIZED PATIENTS OR COMMUNITY POPULATIONS AND PROGRESS IN ALLERGIC AND IMMUNOLOGIC DISEASES. BECAUSE OF THIS DUAL FOCUS, THE PROGRAM ENCOMPASSES BOTH BASIC RESEARCH AND CLINICAL RESEARCH. SMALL BUSINESS INNOVATION RESEARCH (SBIR) PROGRAM EXPANDS AND IMPROVES PRIVATE SECTOR PARTICIPATION IN BIOMEDICAL RESEARCH. THE SBIR PROGRAM INTENDS TO INCREASE AND FACILITATE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, TO INCREASE SMALL BUSINESS PARTICIPATION IN FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. THE SMALL BUSINESS TECHNOLOGY TRANSFER (STTR) PROGRAM STIMULATES AND FOSTERS SCIENTIFIC AND TECHNOLOGICAL INNOVATION THROUGH COOPERATIVE RESEARCH AND DEVELOPMENT CARRIED OUT BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO FOSTER TECHNOLOGY TRANSFER BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. RESEARCH CAREER DEVELOPMENT AWARDS SUPPORT THE DEVELOPMENT OF SCIENTISTS DURING THE FORMATIVE STAGES OF THEIR CAREERS. INDIVIDUAL NATIONAL RESEARCH SERVICE AWARDS (NRSAS) ARE MADE DIRECTLY TO APPROVE APPLICANTS FOR RESEARCH TRAINING IN SPECIFIED BIOMEDICAL SHORTAGE AREAS. IN ADDITION, INSTITUTIONAL NATIONAL RESEARCH SERVICE AWARDS ARE MADE TO ENABLE INSTITUTIONS TO SELECT AND MAKE AWARDS TO INDIVIDUALS TO RECEIVE TRAINING UNDER THE AEGIS OF THEIR INSTITUTIONAL PROGRAM.

93.855 - Allergy and Infectious Diseases Research

National Institute of Allergy and Infectious Diseases (NIAID) [HHS - NIH]

Ann Arbor, Michigan 481091276 United States

Single Zip Code

Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed) (PAR-20-097)

Amendment Since initial award the total obligations have increased 293% from $753,786 to $2,963,743.