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Relationship auditing of the FMA ontology

Gu, Huanying and Wei, Duo and Mejino, Jose L V and Elhanan, Gai (2009) Relationship auditing of the FMA ontology. Journal of Biomedical Informatics 42(3):pp. 540-549.

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Abstract

The Foundational Model of Anatomy (FMA) ontology is a domain reference ontology based on a disciplined modeling approach. Due to its large size, semantic complexity and manual data entry process, errors and inconsistencies are unavoidable and might remain within the FMA structure without detection. In this paper, we present computable methods to highlight candidate concepts for various relation- ship assignment errors. The process starts with locating structures formed by transitive structural relationships (part_of, tributary_of, branch_of) and examine their assignments in the context of the IS-A hierarchy. The algorithms were designed to detect five major categories of possible incorrect relationship assignments: circular, mutually exclusive, redundant, inconsistent, and missed entries. A domain expert reviewed samples of these presumptive errors to confirm the findings. Seven thousand and fifty-two presumptive errors were detected, the largest proportion related to part_of relationship assignments. The results highlight the fact that errors are unavoidable in complex ontologies and that well designed algorithms can help domain experts to focus on concepts with high likelihood of errors and maximize their effort to ensure consistency and reliability. In the future similar methods might be integrated with data entry processes to offer real-time error detection.

Item Type:Journal (Paginated)
Projects:Foundational Model of Anatomy
Subjects:SIG Publications
ID Code:239
Deposited By:Franklin, Joshua Daniel
Deposited On:26 February 2010