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Open Access Highly Accessed Research article

Unintended consequences of existential quantifications in biomedical ontologies

Martin Boeker1*, Ilinca Tudose1, Janna Hastings2, Daniel Schober1 and Stefan Schulz13

Author Affiliations

1 Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Germany

2 Chemoinformatics and Metabolism, European Bioinformatics Institute, Hinxton, UK

3 Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria

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BMC Bioinformatics 2011, 12:456  doi:10.1186/1471-2105-12-456

Published: 24 November 2011

Abstract

Background

The Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL), which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors.

Results

We analyzed ontologies and ontology cross products available via the OBO Foundry site http://www.obofoundry.org webcite for existential restrictions (someValuesFrom), from which we examined a random sample of 2,836 clauses.

According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' κ = 0.78). We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (κ = 0.07). We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations.

Conclusions

The current OWL releases of OBO Foundry (and Foundry candidate) ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints.