A Generic, Functionally Comprehensive Approach to Maintaining an Ontology as a Relational Database

Authors: Jennifer Leopold, Alton Coalter, Leong Lee

Abstract:

An ontology is a data model that represents a set of concepts in a given field and the relationships among those concepts. As the emphasis on achieving a semantic web continues to escalate, ontologies for all types of domains increasingly will be developed. These ontologies may become large and complex, and as their size and complexity grows, so will the need for multi-user interfaces for ontology curation. Herein a functionally comprehensive, generic approach to maintaining an ontology as a relational database is presented. Unlike many other ontology editors that utilize a database, this approach is entirely domain-generic and fully supports Webbased, collaborative editing including the designation of different levels of authorization for users.

Keywords: Ontology Editor, Relational Database, CollaborativeCuration.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1081569

References:

[1] Davies, J., Fensel, D., and Van Harmelen, F. (eds.) (2004), Towards the Semantic Web: Ontology-driven Knowledge Management. West Sussex, England, John Wiley & Sons.
[2] Goodwin, R., Lee, J., Stanoi, G., and Leveraging, M. (2005), "Relational Database Systems for Large-Scale Ontology Management," CIDR Conference, www.alphaworks.ibm.com/ topics/semantics.
[3] Vysniauskas, E. and Nemuraite, L. (2006), "Transforming Ontology Representation from OWL to Relational Database," Information Technology and Control, vol. 35, no. 3A.
[4] Nyulas, C., O-Connor, M., and Tu, S. (2007), "DataMaster - a Plug-in for Importing Schemas and Data from Relational Databases into Protégé," 10th International Protégé Conference, July 15-18.
[5] "GO Database Guide," The Gene Ontology Consortium ÔÇö Amigo, www.geneontology.org/ GO.database.shtml.
[6] Denney, M. (2002), "Ontology Building: A Survey of Editing Tools," www.xml.com/pub/a/ 2002/11/06/ontologies.html
[7] Dean, M. and Schreiber, G. (eds) (2004), "OWL Web Ontology Language Reference," W3C Recommendation, www.w3.org/TR/2004/REC-owl-ref-20040210.
[8] Maglia, A., Leopold, J., Pugener, A., and Gauch, S. (2007), "An Anatomical Ontology for Amphibians," Proceedings of the Pacific Symposium on Biocomputing (PSB 2007), Wailea, Maui, pp. 367-378.
[9] Hitzler, P., Krotzsch, M., Ehrig, M., and Sure, Y. (2005), "What is Ontology Merging?" American Association for Artificial Intelligence.
[10] Cuenca-Grau, B., Parsia, B., Sirin, E., and Kalyanpur, A. (2006), "Modularity and Web Ontologies," Proc. of KR.
[11] Day-Richter, J. (2006), "The OBO Flat File Format Specification, version 1.2," The Gene Ontology, www.geneontology.org/GO.format. obo-1_2.shtml.