Relationship auditing of the FMA ontology

Document Type

Article

Publication Date

6-1-2009

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 relationship 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. © 2009 Elsevier Inc. All rights reserved.

Identifier

65649151925 (Scopus)

Publication Title

Journal of Biomedical Informatics

External Full Text Location

https://doi.org/10.1016/j.jbi.2009.01.001

ISSN

15320464

PubMed ID

19475727

First Page

550

Last Page

557

Issue

3

Volume

42

Grant

R01HL087706

Fund Ref

National Institutes of Health

This document is currently not available here.

Share

COinS