From schober at imbi.uni-freiburg.de Fri May 29 08:27:08 2009 From: schober at imbi.uni-freiburg.de (Daniel Schober) Date: Fri, 29 May 2009 14:27:08 +0200 Subject: [Po-dev] naming conventions for OBO Foundry ontology engineering Message-ID: <4A1FD49C.1030603@imbi.uni-freiburg.de> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From schober at imbi.uni-freiburg.de Fri May 29 08:32:38 2009 From: schober at imbi.uni-freiburg.de (Daniel Schober) Date: Fri, 29 May 2009 14:32:38 +0200 Subject: [Po-dev] naming conventions for OBO Foundry ontology engineering Message-ID: <4A1FD5E6.6060106@imbi.uni-freiburg.de> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: