Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies
KAUST DepartmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Computer Science Program
Computational Bioscience Research Center (CBRC)
KAUST Grant NumberURF/1/3790-01-01
Permanent link to this recordhttp://hdl.handle.net/10754/663495
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AbstractAbstractBackgroundOntologies are widely used throughout the biomedical domain. These ontologies formally represent the classes and relations assumed to exist within a domain. As scientific domains are deeply interlinked, so too are their representations. While individual ontologies can be tested for consistency and coherency using automated reasoning methods, systematically combining ontologies of multiple domains together may reveal previously hidden contradictions.ResultsWe developed a method that tests for hidden unsatisfiabilities in an ontology that arise when combined with other ontologies. For this purpose, we combine sets of ontologies and use automated reasoning to determine whether unsatisfiable classes are present. We test the mutual consistency of the OBO Foundry and the OBO ontologies and find that the combined OBO Foundry gives rise to at least 636 unsatisfiable classes, while the OBO ontologies give rise to more than 300,000 unsatisfiable classes.We design and implement a novel algorithm that can determine justifications for contradictions across extremely large and complicated ontologies, and use these justifications to semi-automatically repair ontologies by identifying the minimal set of axioms that, when removed, result in a consistent and coherent set of ontologies. We applied our algorithm to each combination of OBO ontologies that resulted in unsatisfiable classes.ConclusionsWe identified a large set of hidden unsatisfiability across a broad range of biomedical ontologies, and we find that this large set of unsatisfiable classes is the result of a relatively small amount of axiomatic disagreements. Our results show that hidden unsatisfiability is a serious problem in ontology interoperability; however, our results also provide a way towards more consistent ontologies by addressing the issues we identified.
CitationSlater, L. T., Gkoutos, G. V., & Hoehndorf, R. (2020). Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. doi:10.1101/2020.05.16.099309
SponsorsGVG and LTS acknowledge support from support from the NIHR Birmingham ECMC, NIHR Birmingham SRMRC, Nanocommons H2020-EU (731032) and the NIHR Birmingham Biomedical Research Centre and the MRC HDR UK (HDRUK/CFC/01), an initiative funded by UK Research and Innovation, Department of Health and Social Care (England) and the devolved administrations, and leading medical research charities. The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research, the Medical Research Council or the Department of Health. RH and GVG were supported by funding from King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. URF/1/3790-01-01.
PublisherCold Spring Harbor Laboratory
Except where otherwise noted, this item's license is described as Archived with thanks to Cold Spring Harbor Laboratory