Presence-Biomedical Ontology Fellow - applications open

Presence, led by Dr. Abraham Verghese and Sonoo Thadaney, champions the human experience in medicine. One of our key initiatives is to reduce medical errors those not addressed by QI foci, but due to the lack of necessary and appropriate human interaction) by harnessing technology for the human experience in medicine. More about Presence 

Dr. Mark Musen studies the development of semantic technology for use in biomedicine and leads the National Center for Biomedical Ontology. Workers in biomedicine create ontologies to model the entities and the relationships among entities in a given discipline.  By creating an ontology, developers can clarify the essential features of some area of endeavor and provide a coherent means of talking about it and studying it.

The Presence-Biomedical Ontology Fellow will work under the guidance of Drs. Musen and Verghese to research and define a framework for the ontology of the psycho-social aspects of healthcare and disease prevention. In essence, the accuracy with which we measure, trend, and record body chemistry (serum sodium, for example) is not matched by anything that begins to resemble that accuracy when it comes to understanding and gathering data on questions such as: Who is this person? What is their social capital?  What are their values and beliefs (infomation readily captured on social media but not in the EHR.)  What was the nature of the exchange in their first interview with the physician? What roles did each take on?  Were those roles useful? Was the physician role therapeutic or reactive?  What is the nature of the patient’s body type?- What signs of disease does it actually show? (As opposed to: what was ticked on the drop-down boxes.) How accurate and skilled was the physical exam? (The “data on the data” to quote Dr. Musen.)

We would like to eventually apply this ontology for precision health, medical diagnosis, intervention, disease prevention, and disease management.  

Building on Presence Ontology 2017-18 Fellow Amrapali Maitra's Work

Amrapali Maitra, MD, PhD

Mark Musen, MD, PhD

Our works seeks to build an ontology of presence, the domain of human connection in medicine.  Ontologies are classification systems that can be used to represent knowledge within biomedical and clinical domains.  To our knowledge, ontologies have not yet been used to model the subjective experiences of presence in medicine.

In the field of medicine, frameworks for understanding human connection have typically dealt with categories of patients, providers, actions, and environments.  These categories are important, but they do not encompass all potential data within encounters.   An ontology for presence could be used by clinicians to better practice presence; by educators to teach strategies for developing presence to trainees; and by patients and familiesto understand how to harness connections toward personalized care, equity, and inclusion in medicine.

Through expert synthesis, literature review, and ethnographic observation, we developed a preliminary Presence Ontology (which will soon be uploaded on Bioportal).  Keywords for our literature review included Patient-Physician Relationship; Patient-Physician Communication; Empathy, Patient-Centered Care, Non-Verbal Communication, Technology; Burnout; Satisfaction; Trust; Joy of Practice; and Mindfulness among others.  The class diagram, shown below, delineates categories and relationships in the ontology.

We are in the process of further validation and revision of our ontology.  We hope it serves as a starting point from which to conceptualize and further investigate the role of presence in medicine.

Presence Ontology



Skills & Background Required

We are seeking a trainee with experience in clinical medicine who is creative, thoughtful, and eager to learn.  Although experience in formal ontology, formal logic, or object-oriented design would be extremely valuable, it is more important to be able to think logically, to recognize what is salient in a problem and what is not, and to translate concepts with imprecise definitions into distinctions where the meaning is clear and consistent.

Time Commitment

At least a 25% time commitment, over one year, is needed to make progress in this work. 


Applicant dependent and to be discussed with final candidate.

Application Process

Please submit a written cover letter and CV to Sonoo Thadaney, Executive Director, Presence, ( You may also direct any questions to her.