NCBO User Profile: Gary An, University of Chicago

Building Models to Help Translational Researchers Test Hypotheses

Gary An picture“Through Interactions with the NCBO I have realized that the development of agent-based modeling is intimately tied to the advances in the ontologies and tools provided by the NCBO via BioPortal.”






  Gary An, MD

  Associate Professor of Surgery

  Section of General Surgery

  Department of Surgery

  The University of Chicago



Research Interests:

Gary An is a trauma/critical care surgeon at The University of Chicago engaged in translational computational research.  His work on system-level simulations of trauma and sepsis led him to a more general concern about the ability of biomedical researchers to represent their knowledge and hypotheses in a form that can be “executed,” so that the dynamic consequences of their hypotheses can be seen and evaluated.


Need for NCBO Services:

Achieving these goals requires harnessing advances in automated text analysis/information extraction and building upon the knowledge structures within biomedical ontologies to develop methods to help evolve the formal representation of knowledge. The NCBO’s BioPortal REST services provide vital technology to access repositories of community knowledge. The following figure highlights the role of NCBO technology in Gary’s research.


Specific Uses of NCBO Services:

Agent-based models (ABM) can be thought of “executable ontologies” for hypothesis representation, providing a natural link to the NCBO library. Dr. An is working to develop a web-based constructor (Agent-based Modeling Format--ABMF) that utilizes BioPortal REST services to survey and integrate community knowledge held in BioPortal, and provide a semi-automated pathway to existing ABM code generators, simulation engines and toolkits. Facilitating the translation of a mental model/hypothesis to a tangible simulation based on that hypothesis can provide an in silico environment for “instantiating thought experiments,” thereby enhancing the ability of researchers to explore and examine possible explanations for the phenomena they are studying.  He believes that this new class of “executable ontologies” will lead to advances in the way biomedical knowledge is represented and communicated.