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Exploring biomedical ontology mappings with graph theory methods

Abstract

BACKGROUND: In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. METHODS: We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. RESULTS: With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

Type Journal
ISBN 2167-8359 (Print)
Authors Kocbek, S.; Kim, J. D.
Responsible Garvan Author Dr Simon Kocbek
Publisher Name PeerJ
Published Date 2017-03-02
Published Volume 5
Published Pages e2990
Status Published in-print
DOI 10.7717/peerj.2990
URL link to publisher's version https://www.ncbi.nlm.nih.gov/pubmed/28265499
OpenAccess link to author's accepted manuscript version https://publications.gimr.garvan.org.au/open-access/14431