Understanding and Communicating Spatially–Oriented Ontologies

Understanding and Communicating Spatially–Oriented Ontologies
Melissa Clarkson
Dissertation defense: December 10, 2014

Ontologies have become increasingly important for both representation of biomedical knowledge and for using that knowledge to facilitate data integration.

However, ontologies are generally not presented in ways that are easy for users to comprehend, which limits their use.

In this work I address this problem within the cont ext of two spatially-oriented ontologies:
the Foundational Model of Anatomy (FMA) and
the Ontology of Craniofacial Development and Malformation (OCDM).
I describe an approach to communicating these ontologies that involves (1) identifying content patterns within an ontology, (2) creating a simplified tutorial to explain basic concepts within the ontology, (3) involving potential users in the design of an ontology browser interface, and (4) creating graphics to support the process of building and communicating the ontology.
This approach should be applicable to any spatially-oriented ontology, and should result in visualizations that will enhance understanding of ontologies.

What tools currently exist to view the FMA?

ontology visualization

FlexViz through BioPortal

Ontology Viewer



Note that the relationship “Epithelial cell” “part of” “Unilaminar epithelium” is not true for all instances of the concept “Epithelial cell”.

Foundational Model of Anatomy (FMA)


“Systemic capillary network of subdivision of cardinal body Part”
is this a meaningful name?

Extraglomerular mesangial cell

Gray’s 40th, 2009


Challenges in Converting Frame-Based Ontology into OWL: the Foundational Model of Anatomy Case-Study
Olivier Dameron, PhD, Daniel L. Rubin, MD, MS, and Mark A. Musen, MD, PhD
AMIA Annu Symp Proc. 2005; 2005: 181–185.

NLM Walkthrough
Meliha Yetisgen-Yildiz, PhD
Institute of Translational Health Sciences

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.

see also: