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Bioinformatics. 2014 May 1;30(9):1340-2. doi: 10.1093/bioinformatics/btu008. Epub 2014 Jan 9.

Ontodog: a web-based ontology community view generation tool.

Author information

1
Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 and Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

Abstract

Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end users, it is desirable to have community-based labels rather than the labels generated by ontology developers. Ontodog is a web-based system that can generate an ontology subset based on Excel input, and support generation of an ontology community view, which is defined as the whole or a subset of the source ontology with user-specified annotations including user-preferred labels. Ontodog allows users to easily generate community views with minimal ontology knowledge and no programming skills or installation required. Currently >100 ontologies including all OBO Foundry ontologies are available to generate the views based on user needs. We demonstrate the application of Ontodog for the generation of community views using the Ontology for Biomedical Investigations as the source ontology.

PMID:
24413522
PMCID:
PMC3998133
DOI:
10.1093/bioinformatics/btu008
[Indexed for MEDLINE]
Free PMC Article

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