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This article is part of the supplement: Proceedings of the Bio-Ontologies Special Interest Group 2012

Open Access Proceedings

A task-based approach for Gene Ontology evaluation

Erik L Clarke, Salvatore Loguercio, Benjamin M Good and Andrew I Su*

Author Affiliations

The Scripps Research Institute, La Jolla, CA, USA

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Journal of Biomedical Semantics 2013, 4(Suppl 1):S4  doi:10.1186/2041-1480-4-S1-S4

Published: 15 April 2013

Abstract

Background

The Gene Ontology and its associated annotations are critical tools for interpreting lists of genes. Here, we introduce a method for evaluating the Gene Ontology annotations and structure based on the impact they have on gene set enrichment analysis, along with an example implementation. This task-based approach yields quantitative assessments grounded in experimental data and anchored tightly to the primary use of the annotations.

Results

Applied to specific areas of biological interest, our framework allowed us to understand the progress of annotation and structural ontology changes from 2004 to 2012. Our framework was also able to determine that the quality of annotations and structure in the area under test have been improving in their ability to recall underlying biological traits. Furthermore, we were able to distinguish between the impact of changes to the annotation sets and ontology structure.

Conclusion

Our framework and implementation lay the groundwork for a powerful tool in evaluating the usefulness of the Gene Ontology. We demonstrate both the flexibility and the power of this approach in evaluating the current and past state of the Gene Ontology as well as its applicability in developing new methods for creating gene annotations.