Finding disease similarity based on implicit semantic similarity
Journal of Biomedical Informatics
Functional evaluation and analysis of predicted miRNA-mRNA regulatory network
Proceedings of the 2012 ACM Research in Applied Computation Symposium
Ontology-Based genes similarity calculation with TF-IDF
ICICA'12 Proceedings of the Third international conference on Information Computing and Applications
Proceedings of the 19th ACM SIGKDD international conference on Knowledge discovery and data mining
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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.