GOSemSim: GO semantic similarity measurement
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
GOSemSim is an R package for semantic similarity
computation among GO terms, sets of GO terms, gene products and gene
GOSemSim implemented five methods proposed by Resnik,
Schlicker, Jiang, Lin and Wang respectively.
Guangchuang Yu, School of Public Health, The University of Hong Kong.
Please cite the following article when using
Yu G†, Li F†, Qin Y, Bo X*, Wu Y and Wang S*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010, 26(7):976-978.
Find out more on Featured Articles.
GOSemSim is easy, follow the guide in the Bioconductor
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") ## biocLite("BiocUpgrade") ## you may need this biocLite("GOSemSim")
- Information content based methods proposed by Resnik, Schlicker, Jiang and Lin
- Graph structure based method proposed by Wang
Combine methods for aggregating multiple GO terms
- goSim and mgoSim for measureing semantic similarity among GO terms
- geneSim and mgeneSim for measureing semantic similarity among genes
- clusterSim and mclusterSim for measureing semantic similarity among gene clusters
- 20 species that have OrgDb available in Bioconductor
- Many other species with e GO annotation query online via AnnotationHub)
Find out details and examples on Documentation.
- clusterProfiler for Ontologies/pathways enrichment analyses
- DOSE for Disease Ontology Semantic and Enrichment analyses
- meshes for MeSH Enrichment and Semantic analysis
Find out more on projects.
Projects that depend on GOSemSim
- BiSEp: Toolkit to Identify Candidate Synthetic Lethality
- LANDD: Liquid Association for Network Dynamics Detection
- ppiPre: Predict Protein-Protein Interactions Based on Functional and Topological Similarities
- BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
- clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters
- DOSE: Disease Ontology Semantic and Enrichment analysis
- meshes: MeSH Enrichment and Semantic analyses
- Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
- tRanslatome: Comparison between multiple levels of gene expression
- Please make sure you have followed the important guide before posting any issue/question
- For bugs or feature requests, please post to [github issue](https://github.com/GuangchuangYu/GOSemSim/issues)
- For user questions, please post to [Bioconductor support site](https://support.bioconductor.org/) and [Biostars](https://www.biostars.org/). We are following every post tagged with **GOSemSim**
- Join the group chat on and