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Methods Inf Med 2012; 51(06): 463-478
DOI: 10.3414/ME11-01-0047
Original Articles
Schattauer GmbH

Spatial-symbolic Query Engine in Anatomy[*]

A. Puget
1   Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA, USA
,
J. L. V. Mejino Jr.
1   Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA, USA
,
L. T. Detwiler
1   Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA, USA
,
J. D. Franklin
1   Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA, USA
,
J. F. Brinkley
1   Structural Informatics Group, Department of Biological Structure, University of Washington, Seattle, WA, USA
› Author Affiliations
Further Information

Publication History

received:31 May 2011

accepted:18 May 2011

Publication Date:
20 January 2018 (online)

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Summary

Objectives: Currently, the primary means for answering anatomical questions such as ‘what vital organs would potentially be impacted by a bullet wound to the abdomen?’ is to look them up in textbooks or to browse online sources. In this work we describe a semantic web service and spatial query processor that permits a user to graphically pose such questions as joined queries over separately defined spatial and symbolic knowledge sources.

Methods: Spatial relations (e.g. anterior) were defined by two anatomy experts, and based on a 3-D volume of labeled images of the thorax, all the labeled anatomical structures were queried to retrieve the target structures for every query structure and every spatial relation. A web user interface and a web service were designed to relate existing symbolic information from the Foundational Model of Anatomy ontology (FMA) with spatial information provided by the spatial query processor, and to permit users to select anatomical structures and define queries.

Results: We evaluated the accuracy of results returned by the queries, and since there is no independent gold standard, we used two anatomy experts’ opinions as the gold standard for comparison. We asked the same experts to define the gold standard and to define the spatial relations. The F-measure for the overall evaluation is 0.90 for rater 1 and 0.56 for rater 2. The percentage of observed agreement is 99% and Cohen’s kappa coefficient reaches 0.51. The main source of disagreement relates to issues with the labels used in the dataset, and not with the tool itself.

Conclusions: In its current state the system can be used as an end-user application but it is likely to be of most use as a framework for building end-user applications such as displaying the results as a 3-D anatomical scene. The system promises potential practical utility for obtaining and navigating spatial and symbolic data.

Keywords

Spatial relations - anatomy - query processing - ontologies - semantic web

* Supplementary material published on our website www.methods-online.com