Hi,

I know this question has been asked before a long time ago and I don't see an answer of that question in the mailing list or in the vignette of GOsemsim package. So I was wondering what is the easiest possible way of calculating GO semantic similarity value for orthologus gene pairs between two species using the above R package or any other package you know of. I am not doing this for less annotated species I need to calculate that for orthologus genes between Human and Mouse (both of which are well annotated IMHO). So I would much appreciate it if anyone who has already done this before can point me to a resource which already has pre-calculated semantic similarity values for Mouse and Human orthologues or has inbuilt code to do that.

Thanks & regards

This is not supported by GOSemSim, if you are talking about using geneSim/mgeneSim, which will mapped gene ID to GO terms by GOSemSimDATA object which used OrgDb object internally, and if IC methods were used, we also need to pre-calculate information content of each GO term.

Cross species semantic similarity measurement can be possible if I implement a function to merge GOSemSimDATA objects (e.g. one from human and one from mouse, the function should be chainable, so multiple objects can be merged sequentially). In this way you can use the merged object as background annotation to calculate semantic similarity among genes using geneSim/mgeneSim.

This is now on the TODO list, I may add this functionality to next release.

Currently, it is still possible if you use Wang method which don't need pre-calculated IC. You can firstly map your input genes to GO terms and use mgoSim to calculate their similarities via Wang method which only use the GO structure.