iSchool Professor Publishes Review on Biomedical Ontology Evaluation

Dr. Zhe He, Assistant Professor at the School of Information, has recently published a review paper titled “Assessing the Practice of Biomedical Ontology Evaluation: Gaps and Opportunities” in the prestigious Journal of Biomedical Informatics as the co-first-author, working alongside co-authors from The University of Texas Health Science Center and the University of Florida. The Journal of Biomedical Informatics has been the premier methodology journal in the field of biomedical informatics for more than 50 years.

In the big data era, ontologies play a key role in overcoming the difficulty in data integration and information extraction. In the medical domain, biomedical ontologies also lay a solid foundation for various health information systems such as electronic health records and clinical decision support systems. In this paper, Dr. He and his co-authors surveyed existing ontology evaluation methods that have been applied in both open domain and biomedical domain.  After categorizing the ontology evaluation methods in an integrated taxonomy, they assessed the ontology evaluation practice of a sample of 200 biomedical ontologies in the NCBO BioPortal (the world’s largest repository and development system of biomedical ontologies) and found that very few ontologies underwent rigorous evaluation in their initial development. They further discussed the opportunities for ontology developers to adopt the state-of-the-art ontology evaluation methods to improve the quality of biomedical ontologies.

The work done in ontological evaluation proves to be successful, meaningful, and highlights opportunities for ontology designers to adopt state-of-the-art ontology evaluation and quality assurance methods to address these concerns for their ontologies to support their meaningful use in various health information systems.

Dr. He has broad interests in biomedical and health informatics, biomedical ontologies, controlled vocabularies, clinical research informatics, knowledge discovery, knowledge representation, and ontology-enhanced data analytics. The overarching goal of his research is to improve the population health and advance biomedical research through the collection, analysis, and application of electronic health data from heterogeneous sources.

He has published over 40 peer-reviewed articles in leading biomedical informatics outlets, including 7 articles in the Journal of Biomedical Informatics, 2 articles in Artificial Intelligence in Medicine, 2 articles in Methods of Information in Medicine, and 6 articles in the American Medical Informatics Association Annual Symposium (AMIA) which is the top conference in the field of health and biomedical informatics. His 2013 AMIA paper on “Biomedical Ontologies” was chosen as the representative paper in the Informatics “Year In Review.” His JBI 2016 and AMIA 2015 papers were selected into Clinical Research Informatics 2016 “Year in Review.” He received two Distinguished Paper Awards of AMIA Annual Symposiums in 2015 and 2017, respectively. In 2017, he also received “Outstanding Faculty Research Award” from the College of Communication & Information. His research has been supported by National Institutes of Health, Amazon, NVIDIA, FSU Council on Research and Creativity, and FSU Institute for Successful Longevity. Dr. He recently had two other journal articles accepted, and is waiting for them to be published. To learn more about Dr. He, click here.