To MIREOT or not to MIREOT? A case study of the impact of using MIREOT in the Experimental Factor Ontology (EFO)

Luke T. Slater, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf

Research output: Chapter in Book/Report/Conference proceedingConference contribution


MIREOT is a mechanism for the selective re-use of individual ontology classes in other ontologies. Designed to minimise effort and to support orthogonality, it is now in widespread use. The consequences for ontology integrity and automated reasoning of using the MIREOT mechanism have so far not been fully assessed. In this paper, we perform an analysis of the Experimental Factor Ontology (EFO), an ontology which uses the MIREOT process to gather classes from a large range of other ontologies. Our study examines the effect of combining EFO with the ontologies it references by actually importing them into the EFO. We then evaluate the consistency and status of the combined ontologies. Through our investigation, we reveal that EFO in combination with all its referenced ontologies is logically inconsistent. Furthermore, when EFO is individually combined with many of the ontologies it references, we find a large number of unsatisfiable classes. These results demonstrate a potential problem within a major ontological ecosystem, and reveals possible disadvantages to the use of the MIREOT system for developing ontologies.
Original languageEnglish (US)
Title of host publication2016 Joint International Conference on Biological Ontology and BioCreative - Food, Nutrition, Health and Environment for the 9 Billion, ICBO-BioCreative 2016
StatePublished - Jan 1 2016

Bibliographical note

KAUST Repository Item: Exported on 2020-12-23
Acknowledgements: LTS and GVG were supported by the National Science Foundation (grant IOS:1340112). RH was supported by funding from the King Abdullah University of Science and Technology.


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