The first project, “Methods for Auditing and Enhancing Completeness of Ontologies,” awarded by NSF, proposes to detect and correct errors within biomedical ontologies. An ontology is a formalized mechanism that models the concepts in a given domain as well as the relationships between the concepts. For example, Gene Ontology captures knowledge such as concepts in the gene function or gene product’s domain and also models relationships between genes.
According to the abstract, Cui’s project will focus on: (1) Development of a robust reasoning framework for detecting and repairing missing subclass or hierarchical relations. This will result in suggestions that directly enhances the subclass completeness of ontologies; (2) Development of novel methods for identifying missing concepts and creating appropriate name labels for the identified missing concepts. This will result in enhancement in the concept completeness of ontologies; (3) Generation of supporting evidence for suggested solutions by leveraging rich extrinsic knowledge.
The second project, “An Ontology-Driven Faceted Query Engine for the Kentucky Cancer Registry,” is a multiple-Principal Investigator (PI) project awarded by NIH and builds upon Cui’s ontology work to provide better data access for cancer researchers by turning ontologies into nested facet systems. GQ Zhang, director of the University of Kentucky Institute for Biomedical Informatics with a courtesy appointment in the Department of Computer Science, is the contact PI on this project and Cui is the other PI. In addition to Cui and Zhang, the project team includes Co-investigators Drs. Eric Durbin and Shiqiang Tao from the UK Institute for Biomedical Informatics.
According to the project narrative, “The main goal of this project is to develop OncoSphere, a novel ontology-driven faceted query system to enhance web-based exploration of Kentucky Cancer Registry data. Success of this study will address a fundamental barrier in making query interfaces easier to use, ultimately as easy as shopping on Amazon, to support a broad range of cancer data exploration modalities. Ultimately, this study can lead to the creation of a new generation of tools for querying data in the NCI’s Surveillance Epidemiology and End Results program as well as other related cancer resources.”
Previously, Cui’s NIH-funded research expanded and broadened research resources across centers that accelerate the understanding of biological mechanisms responsible for Sudden Unexpected Death from Epilepsy (SUDEP). She also created a novel search interface (x-search.net) that allows researchers across the world to access The National Sleep Research Resource (sleepdata.org), consisting of a large collection of integrated and curated sleep data from multiple previously NIH-sponsored, completed studies.
Cui received her Ph.D. in computer science from Case Western Reserve University in 2014. She served as assistant professor in the Division of Biomedical Informatics at UK between August 2015 and July 2016 and joined the Department of Computer Science in 2016.