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Open Access Correspondence

Survey-based naming conventions for use in OBO Foundry ontology development

Daniel Schober12, Barry Smith3, Suzanna E Lewis4, Waclaw Kusnierczyk5, Jane Lomax1, Chris Mungall4, Chris F Taylor16, Philippe Rocca-Serra1 and Susanna-Assunta Sansone1*

Author Affiliations

1 EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

2 Institute of Medical Biometry and Medical Informatics (IMBI), University Medical Center, 79104 Freiburg, Germany

3 Center of Excellence in Bioinformatics and Life Sciences, and Department of Philosophy, University at Buffalo, NY, USA

4 Berkeley Bioinformatics and Ontologies Project, Lawrence Berkeley National Labs, Berkeley, CA 94720 USA

5 Department of Information and Computer Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway

6 NERC Environmental Bioinformatics Centre (NEBC), Mansfield Road, Oxford, OX1 3SR, UK

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BMC Bioinformatics 2009, 10:125  doi:10.1186/1471-2105-10-125

Published: 27 April 2009

Abstract

Background

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion.

Results

We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies.

Conclusion

Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data.