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Matching disease and phenotype ontologies in the ontology alignment evaluation initiative

Harrow, I., Jimenez-Ruiz, E. ORCID: 0000-0002-9083-4599, Splendiani, A. , Romacker, M., Woollard, P., Markel, S., Alam-Faruque, Y., Koch, M., Malone, J. & Waaler, A. (2017). Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. Journal of Biomedical Statistics, 8, 55. doi: 10.1186/s13326-017-0162-9


Background: The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease.

Results: Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track. AML, FCA-Map, LogMap(Bio) and PhenoMF systems produced the top results for ontology matching in comparison to consensus alignments. The results against manually curated mappings proved to be more difficult most likely because these mapping sets comprised mostly subsumption relationships rather than equivalence. Manual assessment of unique equivalence mappings showed that AML, LogMap(Bio) and PhenoMF systems have the highest precision results.

Conclusions: Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype.

Publication Type: Article
Additional Information: © The Author(s). 2017Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0International License (, which permits unrestricted use, distribution, andreproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to theCreative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver( applies to the data made available in this article, unless otherwise stated.
Publisher Keywords: Biomedical ontology; Ontology alignment; OAE; Evaluation; Phenotype; Disease
Subjects: Q Science > QH Natural history > QH301 Biology
R Medicine
Departments: School of Science & Technology > Computer Science
Text - Published Version
Available under License Creative Commons Attribution.

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