Dead simple OWL design patterns

BackgroundBio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automate classification via consistent patterns of axiomatization. Many bio-ontologies originating in OBO or OWL follow this approach. These patterns need to be documented in a form that requires minimal expertise to understand and edit and that can be validated and applied using any of the various programmatic approaches to working with OWL ontologies.ResultsHere we describe a system, Dead Simple OWL Design Patterns (DOS-DPs), which fulfills these requirements, illustrating the system with examples from the Gene Ontology.ConclusionsThe rapid adoption of DOS-DPs by multiple ontology development projects illustrates both the ease-of use and the pressing need for the simple design pattern system we have developed.

[1]  Phillip Lord,et al.  The Semantic Web takes Wing: Programming Ontologies with Tawny-OWL , 2013, OWLED.

[2]  Mark A. Musen,et al.  The protégé project: a look back and a look forward , 2015, SIGAI.

[3]  David Osumi-Sutherland,et al.  The Drosophila anatomy ontology , 2013, J. Biomed. Semant..

[4]  Aldo Gangemi,et al.  Ontology Design Patterns for Semantic Web Content , 2005, SEMWEB.

[5]  Juancarlos Chan,et al.  Gene Ontology Consortium: going forward , 2014, Nucleic Acids Res..

[6]  Valentina Presutti,et al.  Template-Based Content ODP Instantiation , 2016, WOP@ISWC.

[7]  Judith A. Blake,et al.  Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon , 2014, Journal of Biomedical Semantics.

[8]  Robert Stevens,et al.  Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language , 2008, OWLED.

[9]  Tanya Z. Berardini,et al.  TermGenie – a web-application for pattern-based ontology class generation , 2014, J. Biomed. Semant..

[10]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Christoph Steinbeck,et al.  The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013 , 2012, Nucleic Acids Res..

[12]  Chris Mungall,et al.  Use of OWL within the Gene Ontology , 2014, bioRxiv.

[13]  Alexander D. Diehl,et al.  Logical Development of the Cell Ontology , 2011, BMC Bioinformatics.

[14]  Barry Smith,et al.  The environment ontology: contextualising biological and biomedical entities , 2013, Journal of Biomedical Semantics.

[15]  Nicholas Burton,et al.  The Virtual Fly Brain browser and query interface , 2012, Bioinform..

[16]  Jessica A. Turner,et al.  Modeling biomedical experimental processes with OBI , 2010, J. Biomed. Semant..