by Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang
Abstract:
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.
Reference:
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products (Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang), In Bioinformatics (Oxford, England), volume 26, 2010.
Bibtex Entry:
@article{Yu2010,
abstract = {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.},
author = {Yu, Guangchuang and Li, Fei and Qin, Yide and Bo, Xiaochen and Wu, Yibo and Wang, Shengqi},
doi = {10.1093/bioinformatics/btq064},
issn = {1367-4811},
journal = {Bioinformatics (Oxford, England)},
keywords = {SML-LIB-BIBLIO,lang:ENG},
mendeley-tags = {SML-LIB-BIBLIO,lang:ENG},
month = apr,
number = {7},
pages = {976--8},
pmid = {20179076},
title = {{GOSemSim: an R package for measuring semantic similarity among GO terms and gene products}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20179076},
volume = {26},
year = {2010}
}