The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

Journal: Journal of biomedical semantics
Published Date: Jan 12, 2018

Abstract

Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).

Authors

  • Yongqun He
    University of Michigan Medical School, Ann Arbor, MI 48109 USA ; Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, 1301 MSRB III, 1150 W. Medical Dr., Ann Arbor, MI 48109 USA.
  • Zuoshuang Xiang
    University of Michigan Medical School, Ann Arbor, MI 48109 USA.
  • Jie Zheng
    State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, China.
  • Yu Lin
    Research School of Computer Science, Australian National University, Canberra, 2601, ACT, Australia.
  • James A Overton
    La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
  • Edison Ong
    University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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