Question: Semantic similarity across entire MeSH tree in meshes pkg
0
gravatar for lisa.federer
9 months ago by
lisa.federer0 wrote:

I am trying to use the meshSim function in the meshes package to calculate pairwise semantic similarity for vectors of MeSH terms, by their DUI. I am passing hsamd to the semData function, as suggested in the documentation:

meshSim(mesh_vec1, mesh_vec2, semData = hsamd, measure = "Wang")

But I am realizing that the default setup for the hsamd includes only the A branch of the MeSH tree (anatomical terms), and the MeSH terms in my dataset come from across multiple branches of the tree.

I have looked at the documentation for the meshdata function that is used to construct the hsamd data to see if it's possible to incorporate all of the branches of the MeSH tree, such as by modifying the code thusly (in this case to include branches A, B, and C:

meshdata("MeSH.Hsa.eg.db", category=c('A', 'B', 'C'), computeIC=FALSE, database="gendoo")

However, when I run this, it just seems to hang forever and I end up restarting my R session without it completing. The documentation for the meshdata function includes the info that "category" argument is described as "one of supported category," Does this really mean that this package can only calculate semantic similarity of terms in only one single branch of the tree?

For reference, here is the relevant session info:

R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
other attached packages:
 [1] MeSH.Hsa.eg.db_1.11.0 MeSHDbi_1.18.0        BiocGenerics_0.28.0   meshes_1.8.0

Any advice on this is much appreciated!

 

semantic similarity meshes • 281 views
ADD COMMENTlink modified 4 months ago by ahmettoprak420 • written 9 months ago by lisa.federer0

mixed category is not supported, similar to BP, CC and MF of GO. You should separate and analysis respectively.

ADD REPLYlink written 9 months ago by Guangchuang Yu1.1k
Answer: Semantic similarity across entire MeSH tree in meshes pkg
0
gravatar for ahmettoprak42
7 months ago by
ahmettoprak420 wrote:

Dear Lisa,

I have same problem.

Did you solve your problem. Please can you help me.

Thank you.

Ahmet Toprak

ADD COMMENTlink written 7 months ago by ahmettoprak420
Answer: Semantic similarity across entire MeSH tree in meshes pkg
0
gravatar for ahmettoprak42
4 months ago by
ahmettoprak420 wrote:

Dear Lisa,

I want to calculate disease semantik similarity. Bu I couldnt run the this code in category "C".

hsamd <- meshdata("MeSH.Hsa.eg.db", category='C', computeIC=T, database="gendoo")

Please help me.

ADD COMMENTlink written 4 months ago by ahmettoprak420
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