naming conventions for OBO Foundry ontology engineering

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naming conventions for OBO Foundry ontology engineering

Daniel Schober
Dear fellow ontology editors,
The OBO Foundry would like to bring the results of a survey to your attention in which many of you have participated.
We hereby thank you for your valuable contributions.

The OBO Foundry has now set a number labeling guidelines (see below) to ensure rigid and traceable naming of classes in ontologies.
Such naming conventions not only provide guidance to ontology creators, but they help developers to avoid errors when editing, and especially when interlinking, ontologies. This common naming scheme will ultimately assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data.

The full paper with the naming conventions is accessable online under
http://www.biomedcentral.com/1471-2105/10/125

Best,
    Daniel Schober and Co-Authors


---

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

Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA.
BMC Bioinformatics. 2009 Apr 27;10:125.

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.

PMID: 19397794 [PubMed - in process]

PMCID: PMC2684543


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