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Bioinformatics Advance Access published online on May 7, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn194
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Identification of OBO Nonalignments and Its Implications for OBO Enrichment

Michael Bada * and Lawrence Hunter

University of Colorado at Denver and Health Sciences Center, Department of Pharmacology, MS 8303, RC-1 South, 12801 East 17th Avenue, L18-6400A, P.O. Box 6511, Aurora, CO 80045, USA

*To whom correspondence should be addressed. Dr. Michael Bada, E-mail: mike.bada{at}uchsc.edu


  Abstract

Motivation: Existing projects that focus on the semiautomatic addition of links between existing terms in the Open Biomedical Ontologies can take advantage of reasoners that can make new inferences between terms that are based on the added formal definitions and that reflect nonalignments between the linked terms. However, these projects require that these definitions be necessary and sufficient, a strong requirement that often does not hold. If such definitions cannot be added, the reasoners cannot point to the nonalignments through the suggestion of new inferences.

Results: We describe a methodology by which we have identified over 1,9800 instances of nonredundant nonalignments between terms from the GO biological-process (BP), cellular-component (CC), and molecular-function (MF) ontologies, ChEBI, and the Cell Type Ontology (CL). Many of the 39.838.1% of these nonalignments whose object terms are more atomic than the subject terms are not currently examined in other ontology-enrichment projects due to the fact that the necessary and sufficient conditions required for the inferences are not currently examined. Analysis of the ratios of nonalignments to assertions from which the nonalignments were identified suggests that BP-MF, BP-BP, BP-CL, and CC-CC, BP-BP, and BP-CL terms are relatively well-aligned, while BP-ChEBI-MF, BP-ChEBI, and CC-MF and ChEBI-MF terms are relatively not aligned well. We propose four ways to resolve an identified nonalignment and recommend an analogous implementation of our methodology in ontology-enrichment tools to identify types of nonalignments that are currently not detected.

Availability: The nonalignments discussed in this article may be viewed at http://compbio.uchsc.edu/Hunter_lab/Bada/ nonalignments_20087_03_0614.html. Code for the generation of these nonalignments is available upon request.

Contact: mike.bada{at}uchsc.edu

Associate Editor: Prof. Alfonso Valencia

Received on May 15, 2007; revised on March 29, 2008; accepted on April 16, 2008

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