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Survey-based naming conventions for use in OBO Foundry ontology development
Daniel Schober1, Barry Smith, Suzanna E Lewis
1EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. schober@imbi.uni-freiburg.de
BMC Bioinformatics
|April 29, 2009
Summary
Establishing common naming conventions for OBO Foundry ontologies improves integration and understanding. This research reviews existing practices and proposes new guidelines for biological and medical ontologies.
Area of Science:
- Bioinformatics
- Ontology Engineering
- Computational Biology
Background:
- The OBO Foundry portal hosts a rapidly growing number of biological and medical ontologies.
- Heterogeneity in ontology format and style impedes integration efforts.
- Inconsistent naming conventions negatively impact ontology readability, navigability, and alignment.
Purpose of the Study:
- To address obstacles in integrating biological and medical ontologies.
- To propose a set of common naming conventions for OBO Foundry ontologies.
- To enhance the usability and interoperability of ontologies.
Main Methods:
- Reviewing existing naming conventions for biological ontologies.
- Conducting a survey of current naming practices within OBO Foundry ontologies.
- Analyzing community opinions and practical experiences.
Main Results:
- Identified disadvantages of current naming conventions for broad biological applicability.
- Determined existing naming conventions and specific requirements of OBO Foundry ontologies.
- Proposed initial typographic, syntactic, and semantic conventions for OBO Foundry class labeling.
Conclusions:
- Common naming conventions are crucial for ontology development and integration, not merely aesthetic.
- Standardized conventions guide ontology creators and aid developers in avoiding errors during editing and interlinking.
- Adherence to conventions enhances ontology consumers' understanding of intended meanings in annotated data.
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