GO Semantic Similarity Analysis

Vignette

GOSemSim provides methods and utilities for semantic similarity analysis of Gene Ontology annotations, including:

  • semantic similarity measurement among GO terms, gene products, and gene clusters;
  • support for multiple similarity methods, including Wang, Resnik, Lin, Rel, Jiang, and TCSS;
  • preparation of GO annotation data from OrgDb objects or user-supplied annotation data frames;
  • score combination strategies for comparing sets of GO terms or genes.

Please go to https://yulab-smu.top/biomedical-knowledge-mining-book/ for the full vignette.

Citation

If you use GOSemSim in published research, please cite the most appropriate paper(s) from this list:

  1. Yu G. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, 2020, 2117:207-215. Humana, New York, NY.
  2. 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.

Need helps?

For questions, please post to Bioconductor support site and tag your post with GOSemSim.