GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
Open accessAbstract
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.
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“…and clustering methods, including semantic similarity, e.g. REVIGO [ 71] (default similarity cutoff is 0.7) and the Lin measure via GOSemSim [ 72, 73] (default similarity cutoff is 0.7), Jaccard-based redundancy control, e.g. ReCiPa [ 63] (max overlapping is 0.7, and low overlapping is 0.5),…”
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- Authors
- Yu, G., Li, F., Qin, Y., Bo, X., Wu, Y., & Wang, S.
- Affiliations
- Anhui Medical University (CN)
- Corresponding author
- Bo, Xiaochen
- Wang, Shengqi
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-02-23
- Volume
- 26
- Issue
- 7
- Pages
- 976-978
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2100761975
- Cited by
- 1,388
- References
- 18
- Citations by year
- 2026: 138 · 2025: 165 · 2024: 164 · 2023: 114 · 2022: 124 · 2021: 161 · 2020: 109 · 2019: 77 · 2018: 72 · 2017: 47 · 2016: 61 · 2015: 46 · 2014: 34 · 2013: 34 · 2012: 23
- FWCI
- 9.78
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (30530650)
- National Science Fund for Distinguished Young Scholars
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- semantic similarity, Gene Ontology, Gene Ontology terms, gene products, gene clusters, information content, cross-species comparison, R package, Bioconductor
- MeSH terms
- Algorithms, Animals, Genes, Humans, Natural Language Processing, Terminology as Topic, Proteins, Semantics, Software, Vocabulary, Controlled, Computational Biology
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