Methodology article
Quality control for terms and definitions in ontologies and taxonomies
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* Corresponding author: Jacob Köhler jacob.koehler@bbsrc.ac.uk
1 Biomathematics and Bioinformatics Division, Rothamsted Research, Harpenden, UK
2 Department of Philosophy, University at Buffalo, NY, USA
3 Institute for Formal Ontology and Medical Information Science, Saarland University, Saarbrücken, Germany
4 Technical Faculty, Bielefeld University, Bielefeld, Germany
BMC Bioinformatics 2006, 7:212 doi:10.1186/1471-2105-7-212
Published: 19 April 2006Abstract
Background
Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way.
Results
We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO.
Conclusion
Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.