Accelerate BASSO Network Center

Accelerate BASSO Network Center

PHASES

Promoting Health Aging through Semantic Enrichment of Solitude Research

Award Number: U01AG088074

NIH RePORTER Project Details: https://reporter.nih.gov/search/tOEDLFqvn0-KEl4ettcBuQ/project-details/11184405

Principal Investigators

John Beverley and Bill Duncan

Introduction

Promoting Healthy Aging through Semantic Enrichment of Solitude Research (PHASES) unites two historically separate literatures — solitude and gerotranscendence — to better understand how time spent alone in later life contributes to either flourishing or decline. While solitude is often linked to loneliness and negative health outcomes, gerotranscendence emphasizes the potential for growth, meaning, and psychological well-being in older age.
PHASES will bridge these perspectives by developing interoperable ontologies — the Solitude Ontology and Gerotranscendence Ontology — grounded in the Behavior Change Intervention Ontology and Open Biological and Biomedical Ontologies standards. These ontologies will underpin a public web portal integrating data from the National Library of Medicine and Open Science Foundation, featuring a recommender system and question-answer interface to support cross-disciplinary discovery.
Led by experts from the University at Buffalo, University of Florida, and University of Michigan, PHASES will train stakeholders to use this infrastructure, foster integrative research on solitude and aging, and promote data-driven insights into how being alone can support healthy aging.

Publications

Journal Publications

Jesudas BD, Wilson F, Mavrovich RA, Kindya S, Yeh FY, Smith S, Ravenel J, Zheng J, He Y, Reischer HN, Bowker JC, Beverley J & Duncan WD (2026). Utilizing BERTopic modeling for concept discovery in the domain of gerotranscendence and solitude. J Biomed Semantics. 2026;17(1):17. https://doi.org/10.1186/s13326-026-00348-7 Epub 2026 Sep 1. PMID: 42681660. PMCID: PMC13536857.

Conference Proceedings

Jublou M, Ravenel J, Duncan WD & Beverley J (2026). Healthy Aging in the Era of LLMs. ONTOLLM 2026, 3rd Workshop on the Convergence of Large Language Models and Ontologies, at the Joint Ontology Workshops (JOWO) 2026. September 21-22, 2026. Camera-ready preprint: https://foisconference.org/assets/pdfs/jowo/ontollm-3.pdf Forthcoming; CEUR volume not yet assigned.

Beverley J, Bowker JC, Reischer HN, Mavrovich RA, Hurley R, Kindya S, Smith S, Zheng J, He Y, Beera D & Duncan WD (2025). Towards Healthy Aging through Semantic Enrichment. PHASES: Workshop on Promoting Healthy Aging through the Semantic Enrichment of Social Sciences, at the Joint Ontology Workshops (JOWO) 2025. CEUR Workshop Proc, vol 4176, paper phases-2. https://ceur-ws.org/Vol-4176/phases-2.pdf

Poster Presentations

Jesudas BD, Yeh FY, Smith S, Ravenel J, Zheng J, He Y, Reischer HN, Bowker JC, Beverley J & Duncan WD (2026). Semantic Mapping of Psychological Assessment Questions to BERTopic-Derived Solitude-Related Concepts Using SciBERT Embeddings. 17th International Conference on Biological and Biomedical Ontology (ICBO 2026). July 15-17, 2026. Washington, DC, USA.

He Y et al. (2026). Ontological Modeling and Analysis of Human Suicide Behavior from Genotype to Phenotype with Psychological and Environmental Factors. 17th International Conference on Biological and Biomedical Ontology (ICBO 2026). July 15-17, 2026. Washington, DC, USA.

Smith S, Zheng J, Yeh FY, Jesudas BD, Beverley J, Duncan WD & He Y (2025). OntoChimp: A ChatGPT-powered Tool for Identifying Key Concepts in Ontological Development and Its Evaluation in the Vaccine Domain. 13th International Conference on Intelligent Biology and Medicine (ICIBM 2025), Poster Session II. August 3-5, 2025. Columbus, OH, USA.

Jesudas BD, Wilson F, Mavrovich RA, Kindya S, Yeh FY, Smith S, Ravenel J, Zheng J, He Y, Reischer HN, Bowker JC, Beverley J & Duncan WD (2025). Applying Topic Modeling Methods to the Promoting Health Aging through Semantic Enrichment of Solitude Research Ontology (PHASES). Bioinformatics Open Source Conference (BOSC) 2025, poster B-107. July 21-22, 2025. Liverpool, UK. https://www.open-bio.org/events/bosc-2025/bosc-2025-schedule/

Team

John Beverley

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 PhD 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).

Bill Duncan

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.

Yongqun He

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).

Julie Bowker

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.

Hollen Reischer

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.

Damayanthi Jesudas

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.

Jie Zheng

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.

Sam Smith

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.

Regina Hurley

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.

Maxime Jublou

Developer

Jeremy Ravenel

Developer