Journal Article

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu and Shengqi Wang

in Bioinformatics

Volume 26, issue 7, pages 976-978
Published in print April 2010 | ISSN: 1367-4803
Published online February 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq064
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

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Summary: The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four information content (IC)- and a graph-based methods are implemented in the GOSemSim package, multiple species including human, rat, mouse, fly and yeast are also supported. The functions provided by the GOSemSim offer flexibility for applications, and can be easily integrated into high-throughput analysis pipelines.

Availability: GOSemSim is released under the GNU General Public License within Bioconductor project, and freely available at http://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html

Contact: boxc@bmi.ac.cn; sqwang@bmi.ac.cn

Supplementary information: Supplementary information is available at Bioinformatics online.

Journal Article.  1335 words. 

Subjects: Bioinformatics and Computational Biology

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