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ontoCAT: an R package for ontology traversal and search

Contributed by:Tomasz Adamusiak
Originally posted:26th July 2011: 12:38 pm
Last updated:26th July 2011: 12:50 pm
Short URL:http://gen2phen.org/node/44118
Public document Public - anyone can view
Dissemination number: 
418
ontology paper published in Bioinformatics
About this activity
Date: 
Jun 2011
Status: 
Published
Audience: 
Scientific
Institutions involved
Institutions involved: 
EMBL
If other, please specify: 
Swertz
Abstract, links and uploads
Abstract: 
Motivation: There exist few simple and easily accessible methods to integrate ontologies programmatically in the R environment. We present ontoCAT – an R package to access ontologies in widely used standard formats, stored locally in the filesystem or available online. The ontoCAT package supports a number of traversal and search functions on a single ontology, as well as searching for ontology terms across multiple ontologies and in major ontology repositories. Availability: The package and sources are freely available in Bioconductor starting from version 2.8: http://bioconductor.org/help/bioc-views/release/bioc/html/ontoCAT.html or via the OntoCAT website http://www.ontocat.org/wiki/r. Contact: natalja@ebi.ac.uk
External link: 
http://bioinformatics.oxfordjournals.org/content/early/2011/06/22/bioinformatics...
Citation: 
Kurbatova N, Adamusiak T, Kurnosov P, Swertz MA, and Kapushesky M. ontoCAT: an R package for ontology traversal and search Bioinformatics 2011 Jun: btr375v1-btr375.
DOI: 
10.1093/bioinformatics/btr375
Other
Contact name: 
Tomasz Adamusiak
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