Biological Model Development as an Opportunity to Provide Content Auditing for the Foundational Model of Anatomy Ontology

Abstract

Constructing a biological model using an established ontology provides a unique opportunity to perform content auditing on the ontology. We built a Markov chain model to study tumor metastasis in the regional lymphatics of patients with head and neck squamous cell carcinoma (HNSCC). The model attempts to determine regions with high likelihood for metastasis, which guides surgeons and radiation oncologists in selecting the boundaries of treatment. To achieve consistent anatomical relationships, the nodes in our model are populated using lymphatic objects extracted from the Foundational Model of Anatomy (FMA) ontology. During this process, we discovered several classes of inconsistencies in the lymphatic representations within the FMA. We were able to use this model building opportunity to audit the entities and connections in this region of interest (ROI). We found five subclasses of errors that are computationally detectable and resolvable, one subclass of errors that is computationally detectable but unresolvable, requiring the assistance of a content expert, and also errors of content, which cannot be detected through computational means. Mathematical descriptions of detectable errors along with expert review were used to discover inconsistencies and suggest concepts for addition and removal. Out of 106 organ and organ parts in the ROI, 8 unique entities were affected, leading to the suggestion of 30 concepts for addition and 4 for removal. Out of 27 lymphatic chain instances, 23 were found to have errors, with a total of 32 concepts suggested for addition and 15 concepts for removal. These content corrections are necessary for the accurate functioning of the FMA and provide benefits for future research and educational uses.

Connected graphs of the right side lymphatic network: the original extracted from FMA (top), and the final audited version (bottom).

Figure 1.

Values under the lymphatic_drainage property of the FMA object Soft_palate are queried and used to generate a full map of lymphatic flow downstream from the origin site. All unlabeled arrows between lymphatic objects represent the efferent_to relationship.

Figure 2.

Illustrations of error subclasses. Edges marked with part indicate a regional part relationship, l.d. indicates lymphatic drainage, and all unmarked edges refer to efferent_to relationships between lymphatic objects. Dotted lines refer to missing connections which should exist; lines that are crossed out refer to erroneous connections that should be removed.