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Dear fellow ontology editors,<br>
The OBO Foundry would like to bring the results of a survey to your
attention in which
many of you have participated. <br>
We hereby thank you for your valuable contributions.<br>
<br>
The OBO Foundry has now set a number labeling guidelines (see below) to
ensure
rigid and traceable naming of classes in ontologies. <br>
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.<br>
<br>
The full paper with the naming conventions is accessable online under <br>
<a class="moz-txt-link-freetext"
href="http://www.biomedcentral.com/1471-2105/10/125">http://www.biomedcentral.com/1471-2105/10/125</a>
<br>
<br>
Best,<br>
Daniel Schober and Co-Authors<br>
<br>
<br>
---<br>
<br>
<b>Survey-based naming conventions for use in OBO Foundry ontology<br>
development<br>
<br>
</b>Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C,
Taylor CF, Rocca-Serra P, Sansone SA.<br>
<i>BMC Bioinformatics</i>. 2009 Apr 27;10:125.<span class="ti"></span><span
class="featured_linkouts"><br>
<br>
</span>Abstract:<br>
<b>Background: </b>A wide variety of ontologies relevant to the
biological and medical domains are<br>
available through the OBO Foundry portal, and their number is growing
rapidly. Integration of<br>
these ontologies, while requiring considerable effort, is extremely
desirable. However,<br>
heterogeneities in format and style pose serious obstacles to such
integration. In particular,<br>
inconsistencies in naming conventions can impair the readability and
navigability of ontology class<br>
hierarchies, and hinder their alignment and integration. While other
sources of diversity are<br>
tremendously complex and challenging, agreeing a set of common naming
conventions is an<br>
achievable goal, particularly if those conventions are based on lessons
drawn from pooled practical<br>
experience and surveys of community opinion.<br>
<b>Results:</b> We summarize a review of existing naming conventions
and highlight certain<br>
disadvantages with respect to general applicability in the biological
domain. We also present the<br>
results of a survey carried out to establish which naming conventions
are currently employed by<br>
OBO Foundry ontologies and to determine what their special requirements
regarding the naming<br>
of entities might be. Lastly, we propose an initial set of typographic,
syntactic and semantic<br>
conventions for labelling classes in OBO Foundry ontologies.<br>
<b>Conclusion:</b> Adherence to common naming conventions is more than
just a matter of aesthetics.<br>
Such conventions provide guidance to ontology creators, help developers
avoid flaws and<br>
inaccuracies when editing, and especially when interlinking,
ontologies. Common naming<br>
conventions will also assist consumers of ontologies to more readily
understand what meanings<br>
were intended by the authors of ontologies used in annotating bodies of
data.<br>
<p class="pmid">PMID: 19397794 [PubMed - in process]</p>
<p class="pmid pmcid">PMCID: PMC2684543</p>
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