Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for estimating GO semantic similarities. Support many species, including Anopheles, Arabidopsis, Bovine, Canine, Chicken, Chimp, Coelicolor, E coli strain K12 and Sakai, Fly, Human, Malaria, Mouse, Pig, Rhesus, Rat, Worm, Xenopus, Yeast, and Zebrafish.

Guangchuang YU, School of Public Health, The University of Hong Kong http://ygc.name

Please cite the following article when using GOSemSim:

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. 

URL: http://bioinformatics.oxfordjournals.org/content/26/7/976.full

All source code is copyright, under the Artistic-2.0 License. For more information on Artistic-2.0 License see http://opensource.org/licenses/Artistic-2.0

To install:

• the latest released version: biocLite("GOSemSim")
• the latest development version: install_github("GuangchuangYu/GOSemSim")

Find out more at http://www.bioconductor.org/packages/release/bioc/html/GOSemSim.html and check out the vignette.

I am very glad that many people find GOSemSim useful and GOSemSim has been cited by 114 (by google scholar, Aug, 2014).

There are two R packages BiSEp and tRanslatome depend on GOSemSim and three R packages clusterProfiler, DOSE and Rcpi import GOSemSim.

SemDist package copy some of the source code from GOSemSim with acknowledging within source code and document.

ppiPre package copy many source code from GOSemSim without any acknowledgement in souce code or document and did not cited GOSemSim in their publication. This violates the restriction of open source license.

For R developers, if you found functions provided in GOSemSim useful, please depends or imports GOSemSim. If you would like to copy and paste source code, you should acknowledge the source code was copied/derived from GOSemSim authored by Guangchuang Yu [email protected] within source code, add GOSemSim in Suggests field and also includes the following reference in the man files for functions that copied/derived from GOSemSim and cited in vignettes.

\references{
  Yu et al. (2010) GOSemSim: an R package for measuring
  semantic similarity among GO terms and gene products
  \emph{Bioinformatics} (Oxford, England), 26:7 976--978,
  April 2010. ISSN 1367-4803
  \url{http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976}
  PMID: 20179076
  }

You are welcome to use GOSemSim in the way you like, but please cite it and give it the proper credit. I hope you can understand.

• proper use of GOSemSim
• using GOSemSim to rank proteins obtained by co-IP

• If you have any, let me know. Thx!