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Review
. 2018 Apr:80:1-13.
doi: 10.1016/j.jbi.2018.02.010. Epub 2018 Feb 17.

Assessing the practice of biomedical ontology evaluation: Gaps and opportunities

Muhammad Amith  1 , Zhe He  2 , Jiang Bian  3 , Juan Antonio Lossio-Ventura  3 , Cui Tao  4
Affiliations
Review

Assessing the practice of biomedical ontology evaluation: Gaps and opportunities

Muhammad Amith et al. J Biomed Inform. 2018 Apr.

Abstract

With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natural language processing, as well as decision support for health information systems and biomedical research. Biomedical ontologies and controlled terminologies are intended to assure interoperability. Nevertheless, the quality of biomedical ontologies has hindered their applicability and subsequent adoption in real-world applications. Ontology evaluation is an integral part of ontology development and maintenance. In the biomedicine domain, ontology evaluation is often conducted by third parties as a quality assurance (or auditing) effort that focuses on identifying modeling errors and inconsistencies. In this work, we first organized four categorical schemes of ontology evaluation methods in the existing literature to create an integrated taxonomy. Further, to understand the ontology evaluation practice in the biomedicine domain, we reviewed a sample of 200 ontologies from the National Center for Biomedical Ontology (NCBO) BioPortal-the largest repository for biomedical ontologies-and observed that only 15 of these ontologies have documented evaluation in their corresponding inception papers. We then surveyed the recent quality assurance approaches for biomedical ontologies and their use. We also mapped these quality assurance approaches to the ontology evaluation criteria. It is our anticipation that ontology evaluation and quality assurance approaches will be more widely adopted in the development life cycle of biomedical ontologies.

Keywords: Biomedical ontologies; Knowledge representation; Ontology evaluation; Quality assurance.

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Conflict of interest statement

Declarations of interest: none

Figures

Figure 1
Figure 1
A Venn diagram showing the relationships between ontology evaluation and quality assurance in the literature.
Figure 2
Figure 2
Ontology development lifecycle with ontology evaluation and quality assurance.
Figure 3
Figure 3
Taxonomy of ontology evaluation
See this image and copyright information in PMC

References

    1. Agrawal A, He Z, Perl Y, Wei D, Halper M, Elhanan G, Chen Y. The readiness of SNOMED problem list concepts for meaningful use of electronic health records. Artif Intell Med. 2013;58(2):73–80. - PubMed
    1. Matney SA, Warren JJ, Evans JL, Kim TY, Coenen A, Auld VA. Development of the nursing problem list subset of SNOMED CT(R) J Biomed Inform. 2012;45(4):683–8. - PubMed
    1. Rector A, Qamar R, Marley T. Binding ontologies and coding systems to electronic health records and messages. Applied Ontology. 2009;4(1):51–69.
    1. Finnegan R. ICD-9-CM coding for physician billing. J Am Med Rec Assoc. 1989;60(2):22–3. - PubMed
    1. Bodenreider O. Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform. 2008:67–79. - PMC - PubMed

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