Generating Disease to MeSH term profiles

What we would like is a disease-specific MeSH term profile, i.e.
For a given disease,  which mesh terms are commonly associated.  The first step is finding how many references for a given MeSH term co-occur with the disease MeSH term.
Since MeSH has a structure,  this is more specifically (for a given disease term and a given [...]

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Next Step Plan

Plan is to generate “profiles” – look at all MeSH terms associated with a disease,  and all MeSH terms associated with a gene,  and somehow compute “similarity”.  Sounds simple, neh?
Currently grappling with what to exclude:  should I exclude any article that cites a disease term (seems too stringent) – this would really cut out a [...]

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Gene2Pubmed

Found another source of gene-pubmed links in Entrez Gene:  There’s a gene2pubmed table!  Turns out the pubmed citations you get in Entrez Gene are curated,  and stored in their own table.  Includes NCBI curated things as well as citations taken from public repositories.  Anyways,  this means more links for me to use – at the [...]

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Another year, grabbing new versions

Updated the “getter” script for Entrez Gene to get gene2refseq.   Tried cloning it for the MeSH download – appears to be OK for now.  Set that up to download the descriptors, supplemental concepts and the mesh tree file.
Connecting the MeSH supplemental concepts back to genes should be possible via the RefSeq links.  RefSeq links have [...]

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Consistency check

Had a new idea – dump the SQL table to disk then compare the PMIDs from the SQL dump to the ones in my data file.   Differences look like valid PMIDs…and they have the correct title in PubMed (checked 1).
BUT…they are in the disease-pubmed EUtils grab!  So what might have happened is I accidentally loaded [...]

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