A four-year, $1.2 million grant that will help create a vaccine knowledge base has been given to researchers at UTHealth Houston, which is a subcontractor on a larger, $3.7 million grant awarded by the National Institute of Allergy and Infectious Diseases (NIAID).
In addition to the other awardees, a team led by Cui Tao, PhD, the Doris L. Ross Professor in the School of Biomedical Informatics (SBMI) at UTHealth Houston, aims to create aims to standardize and integrate vaccine information as well as support rational vaccine design.
By efficiently capturing and integrating heterogeneous vaccine knowledge, the researchers will develop VIOLIN 2.0 – a new generation, comprehensive vaccine knowledge base that will include information about basic science, clinical matters, and public health, such as safety, epidemiology, and vaccine coverage. UTHealth Houston researchers will contribute to the project by developing advanced informatics tools to extract, accumulate, organize, annotate, and link growing bodies of vaccine information from outside sources. The vaccine data will come from clinical trials, literature, gene expression databases, reliable websites, and surveillance systems.
“We hope this project will enhance the work of the vaccine research community,” said Tao, who is leading the Biomedical Informatics task force for the project. “To get the project started, we will first develop the VIOLIN 2.0 meta-data ontology, create an annotated corpus on automatic knowledge extraction, improve the web interface, and spend the first year establishing potential use cases.”
The step-by-step project goals include implementing ontology-guided literature mining for automatic knowledge graph enrichment. Ontology is a set of concepts and categories in a subject area or domain that shows their properties and the relations between them.
To do this, the team will focus on vaccine safety and efficacy on phenotypes, medical entities, and relationships. Next, they will develop strategies to evaluate the quality of the knowledge graph. The last task is to develop machine learning and big data algorithms for the use cases.
Tao is an internationally recognized expert in medical informatics with a focus on big data modeling and analysis. She has extensive experience working with complex clinical and public health data while also serving as a leader in vaccine informatics.
Several SBMI faculty members will assist Tao, including Hua Xu, PhD, the Glassell Family Distinguished Professor and Associate Dean for Innovation, and Licong Cui, PhD, associate professor at the school. Tao will also partner with two fellow principal investigators from outside of UTHealth Houston: Oliver He, PhD, from the University of Michigan, with whom Tao serves as founding chair of the International Workshop on Vaccine and Drug Ontology Studies, and Junguk Hur, PhD, from the University of North Dakota.
“I’ve collaborated with these scientists for many years as we’ve worked on vaccine and ontology-based research since 2010 while publishing peer-reviewed papers and editorials together,” Tao said. “As we share all data and continue to advance the vaccine research field, I look forward to going live with the VIOLIN 2.0 application in the near future.”
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