Category Theory & Biomedical Ontologies

Category Theory, Biomedical Ontologies and Models
Ira Kalet, PhD
April 29, 2014

Many projects are under way to create or derive computational models of biological processes, using one or more biomedical ontologies or other biomedical knowledge resources as a basis for the model structure.
One such project, which we have started, is to model the local/regional spread of tumor cells (metastasis) so that an accurate target for radiation therapy can be defined.
This approach uses the structure of the lymphatic system as defined in the UW Foundational Model of Anatomy (FMA) to produce a tumor dissemination model for any specific anatomic site where the primary tumor may be located.
Such models are tedious to build manually and are prone to errors in transcription of the structures.

We plan to further develop this approach to modeling tumor dissemination as a case study for developing automated methods to generate dynamic models from biomedical ontologies.

The project will use Category Theory, a mathematical formalism that is just now finding application to ontological modeling, as a way to facilitate the mapping from an ontology to a model.

We will apply the formalism to the FMA/tumor dissemination problem as a proof of concept.
The specific medical problem we are addressing has the potential to significantly increase the accuracy of radiation therapy target volume definition. This is a critical step in more fully utilizing the power of modern computer controlled radiation therapy treatment machinery and techniques. The general methods may help researchers to generate new models, insure that such models are consistent, and also possibly aid in identifying any inconsistencies in the biomedical ontologies themselves.

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