Adding more algorithms of semantic similarity

[llrs]

I found another semantic similarity, are you interested in having it in the package?

I could spend some time trying to implement it in R for your package, or simply to call their program from the package. Here I left the reference:

Jain, Shobhit, and Gary D. Bader. "An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology." BMC bioinformatics 11.1 (2010): 562. DOI: 10.1186/1471-2105-11-562

[GuangchuangYu]

You are welcome to contribute :)

[llrs]

I found that this method is already implemented in R in the ppiPre package in the function TCSSGeneSim, maybe it is worth to explain it to your users. However I didn't manage to make it work. I will contact the maintainer to know if I am doing something or if it is still working, otherwise I would borrow part of the code.
Also there is the IntelliGOGeneSim function with another algorithm of GO similarities.
I will not implement it from scratch 🛠️ 😄

[GuangchuangYu]

The ppiPre package copy many source code from GOSemSim and pretend that was implemented by themselves when they published a paper.

See https://guangchuangyu.github.io/2014/11/proper-use-of-gosemsim/.

I personally reject any source code derived from ppiPre.

[llrs]

In case I don't manage to re-implement the TCSS algorithm, here is another similarity taking into account the relationships between edges. Which I think will be easier to implement albeit it doesn't use information content. (I post this here as a reminder to myself)

Jia, Xu, et al. "Cancer-risk module identification and module-based disease risk evaluation: a case study on lung cancer." PloS one 9.3 (2014): e92395.

A list of methods can be found here.

[Raheemkhan007]

Can anyone help me in implementing TCSS for finding the semantic similarity .can anyone help me out of this or kindly send me a link from where i can get some help

[llrs]

@Raheemkhan007 I could help, but I haven't worked in this in a while.

I could look at it again, you can create a pull request and I would review it if you want. Or we can comment your troubles in a separated issue/branch or fork.

[Raheemkhan007]

@llrs i am working on it but i cant implement it in python. if you having any link according to it kindly share it with me

[llrs]

@Raheemkhan007 (almost) all information I have is posted here. If you implement it in python I can help in the translation to R. (Or it could be imported by R)

[llrs]

I won't be able to contribute with more implementations so I close the issue