Cui Tao, PhD awarded grant to construct vaccine knowledge base

UTHealth Houston School of Biomedical Informatics (SBMI) Professor Cui Tao, PhD, FACMI was recently awarded a National Institute of Allergy and Infectious Diseases (NIAID) grant worth $3,692,855. With the funds, Tao and her peers will craft a vaccine knowledge base which includes a wide range of information spanning the full vaccine lifecycle. The ultimate goal is to create ontology-based standardization and integration of vaccine information and support deep mechanism analysis and rational vaccine design.

By capturing and integrating heterogeneous vaccine knowledge in an efficient manner, the researchers will develop VIOLIN 2.0 – a new generation, comprehensive vaccine knowledge base. VIOLIN 2.0 will include knowledge of basic science, clinical matters, and public health (safety, epidemiology, vaccine coverage). This information will be included for robust linkage and analysis. The researchers from SBMI will contribute by developing advanced informatics tools to extract, accumulate, organize, annotate, and link growing bodies of vaccine information from heterogeneous 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 also holds the Dr. Doris L. Ross Professorship. “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. 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 then develop machine learning and big data algorithms for the use cases.

Several SBMI faculty members will assist Dr. Tao including Assistant Professor Licong Cui, PhD and Associate Dean for Innovation and Professor Hua Xu, PhD. Tao will also partner with two fellow Principal Investigators (PI) from outside of UTHealth Houston. The first is Oliver He, PhD from the University of Michigan and the second is Junguk Hur, PhD from the University of North Dakota.

Her fellow researchers will be responsible for carrying out the specific aims, overseeing the leadership plan, and adherence to all applicable laws and regulations. Tao notes that “a multiple-PI approach was chosen for this project because of the unique and complementary skills and expertise we all have.”

Dr. He is a vaccine informatician with a strong background in microbiology, immunology, ontology, and bioinformatics. As such, he will lead the VIOLIN knowledge base management and showcase task forces and serve as a domain expert in many areas of the vaccine knowledge base component. Dr. Hur’s expertise is in the literature mining and he developed a bioinformatics approach which serves a text-mining tool.  An integral part of this research application is the multiple ontology-based literature mining approaches centered on the interaction network analysis. Having Dr. Hur’s expertise in that arena is critical. He will lead the outreach and dissemination task force as well.

Dr. 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. She will lead the Biomedical Informatics task force for the project. Together with Dr. He, Tao has been the founding chair of the International Workshop on Vaccine and Drug Ontology Studies (VDOS) series for the past 10 years. She is eager to continue her longstanding professional relationship with Drs. He and Hur.

“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,” says Tao. “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.”

The UTHealth Houston grant budget is $1,144,720 and with those funds, Tao and the team at SBMI will hire graduate research assistants. Interested students need experience with ontology, knowledge graphs, machine learning, and natural language processing (NLP). Any students who have interests in vaccine informatics and clinical informatics in general are welcome to contact Dr. Tao for additional details.