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YuLab-SMU / GOSemSim

:golf: GO-terms Semantic Similarity Measures
https://yulab-smu.top/biomedical-knowledge-mining-book/
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Adding more algorithms of semantic similarity #12

Open llrs opened 7 years ago

llrs commented 7 years ago

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 commented 7 years ago

You are welcome to contribute :)

llrs commented 7 years ago

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 :hammer_and_wrench: :smile:

GuangchuangYu commented 7 years ago

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 commented 7 years ago

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 commented 6 years ago

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 commented 6 years ago

@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 commented 6 years ago

@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 commented 6 years ago

@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 commented 4 years ago

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