CTS Ontology Workshop 2023

Ontologies, AI and Electronic Health Records

More about the Clinical and Translational Science Ontology Group (CTSOG) and previous meetings.

Feb 23 - 24, 2023 - Charleston, SC

Background

The Clinical and Translational Science Ontology Group (CTSOG) invites you to join us February 23-24, 2023, in Charleston, SC to discuss the role of ontologies in improving electronic health records (EHR) systems by advancing semantic interoperability, translational research, and artificial intelligence (AI). As health data increases in volume and complexity, and artificial intelligence applications gain momentum, the need for careful planning and interoperability becomes more critical. The purpose of this workshop is to explore new paradigms in EHRs, by examining successes and failures of ontologies and AI in different areas of biomedicine and their role in equitable healthcare.

Themes

• Improving the EHR with ontologies and with AI
• The functions of the EHR and other healthcare documents
• Social Determinants of Health
• Mental health
• ChatGPT

Organizers

Workshop Co-organizers

Bill Hogan, Jihad Obeid, Barry Smith

CTSOG Co-chairs

Bill Hogan (University of Florida College of Medicine, Gainesville, FL), hoganwr@ufl.edu

Barry Smith (University at Buffalo, Buffalo, NY), phismith@buffalo.edu

Sponsors

• Medical University of South Carolina, the Biomedical Informatics Center and:

                     

Venue

Biomedical Informatics Center

Medical University of South Carolina

Address: 22 Westedge St, Charleston, SC 29403

Directions: From Courtyard Marriott on Lockwood

• 10 minute walk, 0.4 miles, safe crosswalks along the route
• Hotel shuttle – runs periodically, need to ask hotel desk for timing details.

Paid parking:

• Parking deck at 10 WestEdge (building before 22 WestEdge, with Publix on bottom floor)
• App-based parking next to 22 WestEdge building (signage with instructions posted onsite)

Hotel

Courtyard by Marriott Charleston Waterfront

Address: 35 Lockwood Dr, Charleston, SC 29401

Phone: (843) 722-7229

Feb. 22-23 reservation link

Feb. 24-25 reservation link (use this link if you are extending your stay in Charleston through the weekend)

If you have any issues registering, please call the hotel directly at 843-722-7229 and mention you are visiting for the CTSA Ontology meeting.

Registration

Registration is free.

However, registration is required for planning purposes. Please register for the workshop using this form.

Draft Agenda: Thursday Feb 23

08:30a: Breakfast and Networking

09:00a: Introduction to the meeting

09:15-11:00a Working sessions/Presentations

• Barry Smith and Jobst Landgrebe: Discussion on AI and Medicine, with a special focus on ChatGPT

Abstract: How are we to explain the peculiar tendency of ChatGPT to throw up what are called ‘hallucinations’? To answer this question we will draw on our book Why Machines Will Never Rule the World, whose core thesis is that an artificial intelligence that could equal or exceed human intelligence—sometimes called "artificial general intelligence" (AGI)—is for mathematical reasons impossible. The argument for this thesis rests on the fact that (1.) human intelligence is a capability of a complex dynamic system—the human brain and central nervous system, and (2.) systems of this sort (like all organic systems) cannot be modelled mathematically in a way that would allow the models to operate inside a computer. We survey on this basis the potential of AI in the future of clinical and translational research.

--break--

11:00-12:30p Working sessions/Presentations

• Discussion and brief presentations. Topics to include:

The Clinical and Translational Science ontology landscape in 2023

Opportunities for AI in medicine

Will AI make ontologies redundant?

TBD

12:30-01:30p Networking and Working Lunch

01:30-3:00p Working sessions/Presentations

• Yonghui Wu: A large language model for electronic health records.

Abstract: Natural language processing (NLP) powered by pretrained language models is the key technology for medical AI systems utilizing clinical narratives. We develop from scratch a large clinical language model—GatorTron—using >90 billion words of text (including >82 billion words of de-identified clinical text). GatorTron models scale up the clinical language model from 110 million to 8.9 billion parameters and improve five clinical NLP tasks, which can be applied to medical AI systems to improve healthcare delivery.

--break--

3:15-5:00p Working sessions/Presentations

• Richard Ohrbach and Barry Smith: Defining 'Injury'

Abstract: This session is intended as a contribution to the ontology component of a broader investigation of injury and pain. SNOMED-CT defines an injury as a 'disorder resulting from physical damage to the body'. The WHO defines an injury as a 'bodily lesion at the organic level, resulting from acute exposure to energy (mechanical, thermal, electrical, chemical or radiant), in amounts that exceed the threshold of physiological tolerance.' We will explore these and other definitions with a view to establishing a more coherent understanding of the ontology of injury and of related phenomena such as lesion, trauma, pain, and so forth. Further topics for possible discussion are listed here. For the ontology of pain, see in particular here

Draft Agenda: Friday Feb 24

09:00-09:30a Breakfast and Networking

09:30-10:45a Working sessions/Presentations

• William Hogan: Semantic Representation of Occupations as Social Determinants of Health.

The ontological representation of occupation presents several challenges. For example, is it your occupation if you have not yet done it? Are you a nuclear engineer before you start your first job doing it? Also, if an occupation is a role (in the BFO sense), then how does it differ from a job role? If I have an occupation of professor, and have had four job roles as professors at different organizations, then that is one occupation numerically but four job roles. How to handle non-employment situations such as "retired" and "homemaker"? What if you concurrently hold two jobs in different "occupations"? I will discuss these issues in the context of recent discussions at the OMRSE monthly meeting and present some options for ontological representation of occupation and related entities.

--break--

11:00-12:30p Working sessions/Presentations

• Justin Reese: Unsupervised machine learning to define subtypes of long COVID using the Human Phenotype Ontology. Co-authors

Abstract: Stratification of patients with post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) would allow precision clinical management strategies. However, long COVID is incompletely understood and characterized by a wide range of manifestations that are difficult to analyze computationally. Additionally, the generalisability of machine learning classification of COVID-19 clinical outcomes has rarely been tested.

We present a method for defining subtypes of long COVID by computationally modeling PASC phenotype data and applying unsupervised machine learning. We extracted Long COVID phenotype data expressed as HPO (Human Phenotype Ontology) terms from electronic healthcare records (EHRs), and then used semantic similarity of phenotype data to calculate a matrix of pairwise patient similarity. This matrix was then used to clustered patients using unsupervised machine learning (k means clustering).

We identified six clusters of PASC patients, each with distinct profiles of phenotypic abnormalities, including clusters with distinct pulmonary, neuropsychiatric, and cardiovascular abnormalities, and a cluster associated with broad, severe manifestations and increased mortality. There was significant association of cluster membership with a range of pre-existing conditions and measures of severity during acute COVID-19. We assigned new patients from other healthcare centers to clusters by maximum semantic similarity to the original patients, and showed that the clusters were generalisable across different hospital systems. The increased mortality rate originally identified in one cluster was consistently observed in patients assigned to that cluster in other hospital systems.

Semantic phenotypic clustering provides a foundation for assigning patients to stratified subgroups for natural history or therapy studies on PASC.

12:30-01:30p Networking and Working Lunch

1:00-03:15p Working sessions/Presentations from industry partners

TBD

03:15-3:30p Closing Remarks

Participants

• Alekseyenko, Alex, Medical University of South Carolina
• Baker, Hamilton, Medical University of South Carolina
• Doole, John, TriNetX
• Heider, Paul, Medical University of South Carolina
• Landgrebe, Jobst, Cognotekt, Cologne
• Hogan, William, co-organizer, University of Florida
• Hutchinson, Tom, University of Pennsylvania, Institute for BioInformatics
• Masci, Anna Maria, National Institute of Environmental Health Sciences (NIEHS)
• Obeid, Jihad, co-organizer, Medical University of South Carolina
• Ohrbach, Richard, University at Buffalo
• Reese, Justin, Lawrence Berkeley National Laboratory
• Scheuermann, Richard, J. Craig Venter Institute
• Simpson, Kit, Medical University of South Carolina
• Skowronek, Matt, TriNetX
• Smith, Barry, co-organizer, University at Buffalo
• Topaloglu, Umit, Center for Biomedical Informatics and Information Technology (CBIIT) National Cancer Institute
• Yonghui Wu, University of Florida