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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

Additional files

Additional file 1:

Ratings and estimates by relation. Ratings and estimates for ontologies (top) and cross products (bottom), by relation.

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Additional file 2:

Ratings and estimates by source. Ratings and estimates for ontologies (top) and cross products (bottom), by source.

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Additional file 3:

Axioms with OBO relation ontology and OBO relation ontology candidate relations in the OBO and OBO crossproducts samples. Only 25 axioms with the relations realized_by and lacks_part would be converted to OWL axioms without unintended existential quantification in the investigated samples according to a proposal for an enhanced mapping of the flatfile OBO format to OWL [25]. † http://www.obofoundry.org/ro/ro.owl webcite; 21 relation types (without obsolete relation types) ‡ http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo webcite; 151 relation types *: OBO sample with 63 relation types and 1186 axioms investigated; XP sample with 102 relation types and 1650 axioms **: Number of OBO relation ontology resp. OBO relation ontology candidate relation types found in the specific sample ***: Absolute number of investigated axioms with the indicated relation types in the sample (percentage of total sample).

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