need a method to convert MeSH tree number to MeSH UID about rtx HOT 12 CLOSED

maybe this can be done with the NCBI eUtils API?

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Link to the fine manual here:

https://www.ncbi.nlm.nih.gov/books/NBK25501/

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It looks like it can be done using NCBI eUtils. From the mesh tree structure page Congenital Abnormalities is listed with with the id C16.131.

If we then search this using esearch.fcgi we get the following result. And if we search the resulting mesh id using esummary.fcgi we can see that this is this is indeed congenital abnormalities.

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nice, thanks Finn. can you expose this as a new method in QueryNCBIeUtils.py ?

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Actually looking at the method get_mesh_uids_for_mesh_term it looks like this method already doing what I described above so I think if we just plug the tree number into that it will work. I'll test on a few mesh tree numbers and report back.

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So it almost works. That method adds [MeSH Terms] to the search so it doesn't work for tree numbers but I made a new method that does the same thing without the addition of [MeSH Terms] called get_mesh_uids_for_mesh_tree so that should work going forward.

Another thing to consider: This method should work for other searches of the mesh database not just mesh tree numbers so would it be better to call it something like get_mesh_uids_for_mesh_query instead?

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@finnagin What's the status of this issue? Has the new code been implemented and thoroughly tested?

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New code has been implemented but has only had limited testing. I can test it some more I'll just need to generate a list of mesh tree numbers to try.

@dkoslicki Are there any tree numbers that I should try to make sure that they work or should I just find some tree numbers arbitrarily from the mesh website?

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If I recall correctly, one of the get_mesh functions in QueryNCBIeUtils was returning MeSH tree numbers (for anatomy and/or phenotypes). You might try there for testing (but just some from the website should work too). After you run a few more tests, you can go ahead and close this issue.

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I did more testing and every example I tried worked so I'm going to go ahead and close this issue.

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