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J Biomed Semantics. 2018 Jan 12;9(1):3. doi: 10.1186/s13326-017-0169-2.

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

Author information

1
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA. yongqunh@med.umich.edu.
2
Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
3
Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
4
Center for Computational Science, University of Miami, Coral Gables, FL, USA.
5
Knocean Inc., Toronto, ON, Canada.
6
Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.

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).

KEYWORDS:

And ontology design pattern; Interoperability; Ontoanimal tools; Ontobee; Ontofox; Ontology; Ontorat; Semantic alignment; Software; eXtensible ontology development

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