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Promoting Healthy Aging through Semantic Enrichment of Solitude Research �(PHASES)

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John Beverley �Co-PI

Hollen Reischer

Subject-Matter

Expert

Julie Bowker

Subject-Matter

Expert

Bill Duncan�Co-PI

Damayanthi Jesudas

Post-Doc

Oliver He

UM Lead

Jie Zheng

Developer

Regina Hurley�Volunteer

Jeremy Ravenel�Agentic AI Contractor

Ray Mavrovich�Volunteer

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Outline

  • Milestones

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  • Engineering

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  • Dissemination

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Outline

  • Milestones

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  • Engineering

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  • Dissemination

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Milestones

Deliverables

Timeline

 

  • Descriptive stats for data sources
  • CQs and definitions to stakeholders
  • Meet with DCC
  • ~3 meetings with awardees

 

 

  • Descriptive statistics documentation
  • CQs/definitions vote

 

 

July 2024 – Dec 2024

 

  • 10 consensus-building exercises
  • Meet with DCC
  • ~3 meetings with awardees
  • Submit articles to conferences

 

 

  • CQs/definitions vote
  • alpha-stage OWL files
  • FOIS/KGC/GSA

 

 

 

Jan 2025 – June 2025

 

  • 10 consensus-building exercises
  • Meet with DCC
  • ~3 meetings with awardees
  • Portal interface deployed
  • Submit articles to conferences

 

 

  • CQs/definitions vote
  • Beta-stage OWL files
  • FHIR CDM
  • Portal interface
  • ICBO/US2TS/FOHTI
  • 1 article in proceedings

 

 

 

July 2025 – Dec 2025

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Milestones

Deliverables

Timeline

 

  • Descriptive stats for data sources
  • CQs and definitions to stakeholders
  • Meet with DCC
  • ~3 meetings with awardees

 

 

  • Descriptive statistics documentation
  • CQs/definitions vote

 

 

July 2024 – Dec 2024

 

  • 10 consensus-building exercises
  • Meet with DCC
  • ~3 meetings with awardees
  • Submit articles to conferences

 

 

  • CQs/definitions vote
  • alpha-stage OWL files
  • FOIS/KGC/GSA
  • BOSC/JOWO/ICIBM (accept)

 

 

 

Jan 2025 – June 2025

 

  • 10 consensus-building exercises
  • Meet with DCC
  • ~3 meetings with awardees
  • Portal interface deployed
  • Submit articles to conferences

 

 

  • CQs/definitions vote
  • Beta-stage OWL files
  • FHIR CDM
  • Portal interface
  • ICBO/US2TS/FOHTI
  • 1 article in proceedings

 

 

 

July 2025 – Dec 2025

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We Have...

  • Completed all stated deliverables for this period

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  • Completed a couple of deliverables for next year

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  • Made progress on many others

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  • Completed a handful of complementary sub-efforts not called out in the grant, but useful to the project and community as a whole

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Outline

  • Milestones

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  • Engineering

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  • Dissemination

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Outline

  • Milestones

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  • Engineering
    • Competency Question-Driven Design
    • PHASES Ontology Development
    • Topic Modeling
    • OntoCHIMP
    • LinkML

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Competency Question-Driven Design

  • Subject-matter experts generated list of high-value terms for domains of solitude and gerotranscendence

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  • As well as a lengthy list of �competency questions which �they would like answered �falling within the scoping, �validation, and relationship CQs

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Competency Questions

  • Competency questions are used to guide ontology development and generate automated checks to ensure answers are sufficient

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Competency Question

How does self-transcendence differ from gerotranscendence?

How does the experience and impact of solitude change across the lifespan?

What is solitude, and how is it distinct from social isolation, social withdrawal, and loneliness?

What validated instruments are used to measure gerotranscendence and solitude?

Is solitude necessary for developing gerotranscendence?

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Outline

  • Milestones

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  • Engineering
    • Competency Question-Driven Design
    • PHASES Ontology Development
    • Topic Modeling
    • OntoCHIMP
    • LinkML

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PHASES Ontology Development

  • Hub-and-Spoke + Systematic Disambiguation

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  • Reused from:

� UBERON� MFO � BCIO � HPO� EMO � OBI

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Beta-Stage OWL File

https://github.com/Buffalo-Ontology-Group/phases/pull/33

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Element

Definition

transcendence

A mental disposition borne by agents such that, if realized, is realized in shifting in goals, values, and attachments towards connections to past and future generations and in seeking coherence in one’s life narrative.

self-transcendence

A transcendence disposition that, if realized, is realized in shifting one’s focus beyond the self toward broader existential, moral, or spiritual concerns, including care for others, connection with nature, or alignment with perceived universal values.

gerotranscendence

A self-transcendence disposition borne by older adults that is shaped by the aging process and is associated with reflections on mortality and reevaluation of one's life narrative

ego integrity theory

The psychological theory developed by Erikson positing the acceptance of life as it has been lived, including acceptance of death, as the major driving psychological goal of older adults.

solitude

A mental disposition that, if realized, is realized in being physically alone or in the absence of social interactions, whether desired or not.

loneliness

A subjective affective feeling of dissatisfaction with a lack social interactions and relationships.

being physical alone

A process in which an individual is physically distant from other persons or social groups, such that there is limited or no opportunity for in-person social interaction.

social isolation state

A process in which an individual objectively lacks social connection such that there is little or no opportunity for social interaction.

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Outline

  • Milestones

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  • Engineering
    • Competency Question-Driven Design
    • PHASES Ontology Development
    • Topic Modeling
    • OntoCHIMP
    • LinkML

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Topic Modeling

  • Problem: Reading thousands of articles to build a research map is slow, inconsistent, and hard to scale.

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  • Solution: Topic modeling to scan research and find key themes, such as:
    • Solitude and mental health
    • Aging and spiritual growth
    • Loneliness and social support

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  • Benefits:
    • Identifies pattern in text
    • Suggests terms to build an ontology

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  • From the Handbook of solitude, content extracted and assigned to a specific topic using BERTopic modeling

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  • Alongside the topic ID, topic label and a probability score is given for each document, showing how confidently it belongs to the assigned topic

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  • Topic ID of -1 implies lack of fit into any of topic themes

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Paragraphs from Handbook of Solitude

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  • From the Handbook of solitude, content extracted and assigned to a specific topic using BERTopic modeling

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  • Alongside the topic ID, topic label and a probability score is given for each document, showing how confidently it belongs to the assigned topic

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  • Topic ID of -1 implies lack of fit into any of topic themes

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Cluster ID (224 in total)

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  • From the Handbook of solitude, content extracted and assigned to a specific topic using BERTopic modeling

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  • Alongside the topic ID, topic label and a probability score is given for each document, showing how confidently it belongs to the assigned topic

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  • Topic ID of -1 implies lack of fit into any of topic themes

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Key word from cluster

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  • From the Handbook of solitude, content extracted and assigned to a specific topic using BERTopic modeling

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  • Alongside the topic ID, topic label and a probability score is given for each document, showing how confidently it belongs to the assigned topic

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  • Topic ID of -1 implies lack of fit into any of topic themes

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Confidence doc fits topic

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Results from Topic Modeling

  • Solitude and gerotranscendence obviously central topics across SME provided documents

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  • Ontology Development Value
    • Topic keywords = Candidate ontology classes
    • BERTopic clusters = Class-subclass structure, defined classes
    • Topic scores flag ambiguous or outlier content

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  • Next Steps
    • Validate clusters with experts
    • Apply same pipeline to other domains (e.g., vaccines, behavioral health)

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Outline

  • Milestones

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  • Engineering
    • Competency Question-Driven Design
    • PHASES Ontology Development
    • Topic Modeling
    • OntoCHIMP
    • LinkML

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OntoCHIMP

  • The Ontology-driven CHatGPT-based Information Mining and Processing tool automatically identifies key terms in documents for ontology development

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  • OntoChimp uses LLMs to facilitate automation by:
    • Identifying multi-word key terms from SME provided corpora
    • Grouping them into buckets for analysis
    • Checking if they exist in known ontologies (via BioPortal)
    • Flagging promising terms for SME review

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  • Built as part of the OntoAnimal toolset at University of Michigan

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High-Level Workflow

  • Key Components
    • ChatGPT is leveraged for term identification
    • spaCy Python library used for grammar & term structure identification
    • Sentence Transformers are used for semantic grouping
    • BioPortal Annotator is used check term coverage in existing ontologies

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  • Benefits
    • Faster, more scalable ontology development
    • Works across domains: solitude, vaccines, and more
    • Highlights gaps where new ontology terms are needed
    • Flags high-value concepts for expert input (scored 0–5)

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BioPortal annotator comparison

Tested on Three Vaccine Documents

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Looking Ahead

  • Testing conducted on vaccine data for proof of concept while awaited corpus identification from SMEs

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  • Will next test on solitude and gerotranscendence relevant text and compare manual results with OntoCHIMP, tinker, improve, etc.

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  • Worth exploring comparison of different LLM models and orchestration of agents

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  • Potential ingest to alignment tool from Jeremy’s work

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Comparison

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OntoChimp

Topic Modeling (LDA / BERTopic)

Focus

Term extraction for ontology population

Discovering themes for ontology scaffolding

Method

ChatGPT + embeddings + BioPortal validation

Statistical modeling + semantic clustering

Output

Candidate multi-word terms, grouped semantically

Topic keywords, document probabilities, hierarchies

Strength

Fast, term-level targeting

Reveals conceptual structure and latent themes

Best for

Identifying terms across diverse text sets

Structuring domains from large, coherent corpora

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Outline

  • Milestones

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  • Engineering
    • Competency Question-Driven Design
    • PHASES Ontology Development
    • Topic Modeling
    • OntoCHIMP
    • LinkML

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Data Standards

  • Several Assessment Instruments for gathering data about solitude and gerotranscendence

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    • Adult Self-Transcendence Inventory (ASTI) Assessment
    • Self-Transcendence Experience (STE) Trait - Often Assessment
    • Noetic Experiences and Integration Scale (NEIS) 
    • Self-Transcendent Experience Scale (STE-S) Assessment
    • etc.

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  • Studies conducted using these instruments should be F.A.I.R.

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Data Standards

  • Linked Data Modeling Language (LinkML)*
    • Author schemas in yaml
    • Data elements have identifiers
    • Map data elements to �ontology terms
  • Compile into multiple formats
    • JSON
    • RDF
    • TSV
    • etc.
  • Publish schema documentation

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https://buffalo-ontology-group.github.io/phases-assessment-instrument/asti_schema/

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* https://linkml.io/linkml/

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Outline

  • Milestones

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  • Engineering

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  • Dissemination

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Outline

  • Milestones

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  • Engineering

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  • Dissemination
    • Graduate Seminar
    • Systematic Review
    • Proceedings Publications and Conference
    • NSF Proto-OKN Award

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PHASES Graduate Seminar

  • UB faculty Regina Hurley worked with the team to construct a seminar covering the ontology engineering aspects of the project

Note: This was one of our deliverables for Year 2

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Outline

  • Milestones

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  • Engineering

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  • Dissemination
    • Graduate Seminar
    • Systematic Review
    • Proceedings Publications and Conference
    • NSF Proto-OKN Award

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Subject-Matter Experts

  • Hollen Reischer and Julie Bowker have initiated a systematic review of solitude and gerotranscendence literatures, to be submitted to a Psychology journal

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Outline

  • Milestones

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  • Engineering

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  • Dissemination
    • Graduate Seminar
    • Systematic Review
    • Proceedings Publications and Conference
    • NSF Proto-OKN Award

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Joint Ontology Workshop 2025

  • Our team will be traveling to Catania, Sicily to host the first PHASES workshop as part of the Joint Ontology Workshop, which is a major portion of the Foundational Ontologies in Information Science conference

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Publications

  • Our team has two papers and one abstract accepted to conferences, to be subsequently published in proceedings

Note: Deliverables included publishing two proceedings across years 1 and 2

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Outline

  • Milestones

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  • Engineering

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  • Dissemination
    • Graduate Seminar
    • Systematic Review
    • Proceedings Publications and Conference
    • NSF Proto-OKN Award

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Proto-OKN

  • Our team was selected to join the NSF’s Proto-OKN Theme 2 sub-award

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  • Which focuses on integrating ontologies into a central hub for the purposes of cross-domain querying using semantic web tools

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  • John Beverley (PI) & Regina Hurley (Co-I) & a graduate student were awarded 200K to make the PHASES RDF files accessible to the Proto-OKN effort