Hi everyone,

I am intending to use GOSim to calculate similarities between different GO Terms obtained by Enrichment Analysis of expression data in a plant species. Therefore, I want to use specifically the 'getTermSim' function. However, since this function uses by default the human database, I want to change this and use the Arabidopsis thaliana database (org.At.tair.db) instead. As far as I understand, I have to compute first the ICs for this database from scratch, but I am having some trouble understanding how to achieve this, probably due to lack of experience. Can someone give me some guidance as how to use GOSim with another (non-human) species? Is there documentation I have missed?

Thank you!

To build the IC you need to tho this:

library(GOSemSim)
GOMF <- godata('org.At.tair.db', ont="MF")

And use this GOMF object to calculate the similarity between molecular function terms of Arabidopsis thaliana. You can find this information under Supported organisms' section of the vignette.