Award Number: U01AG088074
NIH RePORTER Project Details: https://reporter.nih.gov/search/tOEDLFqvn0-KEl4ettcBuQ/project-details/11184405
1.
PHASES OWL ontologies: https://github.com/Buffalo-Ontology-Group/phases
2.
PHASES Topic Modeling Tool: https://github.com/Buffalo-Ontology-Group/phases-nlp
3.
PHASES LinkML Assessment Standard: https://github.com/Buffalo-Ontology-Group/phases-assessment-instrument
Beera, D., Bowker, J., Reischer, H.N., Smith, S., Zheng, J., He, Y., Mavrovich, R., Kindya, S., Ravenel, J., Wilson, F., Beverley, J., Duncan, W.D. (2025). Utilizing BERTopic Modeling for Concept Discovery in the Domain of Gerotranscendence and Solitude. Journal of Biomedical Semantics.
Beera, D., Bowker, J., Reischer, H.N., Smith, S., Zheng, J., He, Y., Mavrovich, R., Kindya, S., Ravenel, J., Wilson, F., Beverley, J., Duncan, W.D. (2025). Abstract: Applying Topic Modeling Methods to the Promoting Health Aging through Semantic Enrichment of Solitude Research Ontology (PHASES). Bioinformatics Open Source Conference
Smith, S., Zheng, J., Yeh, F., Beera, D., Beverley, J., Duncan, W.D., He, Y. (2025). Abstract: OntoChimp: A ChatGPT-based Document Analysis Program for Identifying Key Concepts. International Conference on Intelligent Biology and Medicine 2025
Beverley, J., Bowker, J., Reischer, H.N., Mavrovich, R., Hurley, R., Smith, S., Zheng, J., He, Y., Beera, D., Duncan, W.D. (2025). Healthy Aging through Semantic Enrichment. Promoting Healthy Aging through Semantic Enrichment of Solitude Research (PHASES) Workshop
Principal Investigator
John Beverley, PhD, University at Buffalo, johnbeve@buffalo.edu
Assistant Professor at the University at Buffalo and Co-Director of the National Center for Ontological Research. He works at the intersection of ontology, formal logic, machine learning, and knowledge graph engineering, with applications in infectious diseases, ethics in health, and applied epistemology.
He holds a Ph.D. in Philosophy from Northwestern University and worked as a senior ontologist at the Johns Hopkins Applied Physics Laboratory. He has contributed to projects such as the Infectious Disease Ontology and works on the Basic Formal Ontology (BFO, ISO/IEC 21838-2).
MPI
William Duncan, PhD, University of Florida
Duncan brings more than 15 years of experience developing and using biomedical ontologies for health informatics, as well as computer programming.
These ontologies are used to harmonize diverse biomedical and biological data sources (such as dentistry, environmental metagenomics, and cancer data), detect inconsistencies, and gain new insights through the application of automated reasoning.
Co-Investigator
Yongqun He, PhD, University of Michigan, yongqunh@med.umich.edu
Dr. He is a Professor of Microbiology and Immunology and Director of He Labs at the University of Michigan, specializing in ontology development, biomedical informatics, and vaccine knowledge representation, with leadership roles in the OBO Foundry and the Ontology for Biomedical Investigations (OBI).
>Co-Investigator
Julie Bowker, PhD, University at Buffalo, jcbowker@buffalo.edu
Dr. Bowker is a Professor of Psychology at the University at Buffalo whose research focuses on solitude, peer relationships, and socioemotional development across the lifespan, with extensive publications on the psychological effects of being alone.
Co-Investigator
Hollen Reischer, PhD, University at Buffalo, hollen@buffalo.edu
Dr. Reischer is a visiting assistant professor in the Department of Psychology at the University at Buffalo specializing in gerotranscendence, positive aging, and the psychological dimensions of meaning-making and well-being in later life.
Post-Doc
Damayanthi Jesudas, PhD, University of Florida
Dr. Jesudas is a Research Assistant Scientist at the University of Florida with expertise in NLP and data-driven approaches to ontology development.
Consultant
Jie Zheng, PhD, University of Michigan, jiezhen@umich.edu
Dr. Zheng is a Research Scientist at the University of Michigan with expertise in bio-ontologies, health informatics, and semantic web technologies applied to translational and clinical research.
Consultant
Sam Smith, BS, University of Michigan
Mr. Smith is a research assistant at the University of Michigan working in biomedical ontology development and semantic data integration within the He Labs team.
Researcher
Regina Hurley, PhD University at Buffalo, rhurley3@buffalo.edu
Dr. Hurley is an Assistant Professor of Philosophy at the University at Buffalo whose work focuses on epistemology, applied ontology, and the ethical and conceptual foundations of data and information systems.