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. 2009 Jun;42(3):540-9.
doi: 10.1016/j.jbi.2009.02.006. Epub 2009 Feb 25.

Content-specific auditing of a large scale anatomy ontology

Ira J Kalet  1 , Jose L V Mejino, Vania Wang, Mark Whipple, James F Brinkley
Affiliations

Content-specific auditing of a large scale anatomy ontology

Ira J Kalet et al. J Biomed Inform. 2009 Jun.

Abstract

Biomedical ontologies are envisioned to be usable in a range of research and clinical applications. The requirements for such uses include formal consistency, adequacy of coverage, and possibly other domain specific constraints. In this report we describe a case study that illustrates how application specific requirements may be used to identify modeling problems as well as data entry errors in ontology building and evolution. We have begun a project to use the UW Foundational Model of Anatomy (FMA) in a clinical application in radiation therapy planning. This application focuses mainly (but not exclusively) on the representation of the lymphatic system in the FMA, in order to predict the spread of tumor cells to regional metastatic sites. This application requires that the downstream relations associated with lymphatic system components must only be to other lymphatic chains or vessels, must be at the appropriate level of granularity, and that every path through the lymphatic system must terminate at one of the two well known trunks of the lymphatic system. It is possible through a programmable query interface to the FMA to write small programs that systematically audit the FMA for compliance with these constraints. We report on the design of some of these programs, and the results we obtained by applying them to the lymphatic system. The algorithms and approach are generalizable to other network organ systems in the FMA such as arteries and veins. In addition to illustrating exact constraint checking methods, this work illustrates how the details of an application may reflect back a requirement to revise the design of the ontology itself.

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Figures

Fig. A.1
Fig. A.1
A Protégé class browser display showing the regional parts of a lymphatic tree, a subdivision of the lymphatic system.
Fig. A.2
Fig. A.2
A diagram showing some of the lymphatic chains and nodes in the head and neck region, illustrating the “efferent to” and “afferent to” relations. In this diagram, node A is efferent to node D, and is afferent to nodes B and C. The arrows just show the direction of flow of lymphatic fluid.
Fig. A.3
Fig. A.3
Lymphatic paths from the Soft palate
See this image and copyright information in PMC

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References

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