Quality control for terms and definitions in ontologies and taxonomies

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...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa, Barry Smith
• Keywords: BMCBI 2006, Important Computational Resources, Ontologies, Ontology