Parse medical subject headings (MeSH) when importing PubMed text files

Features
4

Here is an example of MeSH terms that were imported to JabRef without prior transformation.

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The heading and subheadings remain altogether in a string, exactly as they appear in the source file. This is an acceptable but inconvenient result because:

  • Subheadings after the first one are difficult to see.
    (try browsing for “Carbamates/adverse effects” or “Carbamazepine/adverse effects”)
  • Finding a specific heading and subheading combination requires regex or boolean expressions.

The keywords in the screenshot above are split by commas, but the entry viewer shows all the MeSH terms strung together as one giant keyword.

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Adding to the complication, MeSH terms include commas that should not be interpreted as a delimiter, so the defaults in Jabref split MeSH terms in unexpected places. This may be possible to prevent by changing the delimiter in Jabref. For sure, the problem can be remedied by changing the delimiter after-the-fact in the bibtex file.

Edit:

  • If the delimiter set in File > Preferences > Entries does not match the delimiter used in the keywords field of the bibtex entries, then the keywords will not be parsed properly in the entry editor (as expected).
  • Jabref always inserts a comma between MeSH terms during import, regardless of the delimiter provided in settings (as shown in the code from @Siedlerchr).
    This is a problem with PubMed files, because MeSH terms include commas that should not be interpreted as delimiters.
  • Commas within MeSH terms are indistinct from those added by Jabref between terms, so the input file has to be modified to allow correct parsing of keywords after the import.

Note: Jabref inserts the user-specified delimiter between MeSH terms when retrieving entries directly from PubMed (via Jabref’s Web Search). Unfortunately, records retrieved this way are missing the major topics (indicated by * in exports from PubMed) and have commas instead of slashes separating headings from subheadings and separating subheadings from each other. Here is an example.

keywords = {
    Breast Neoplasms, drug therapy, genetics, metabolism, pathology
}

Capitalisation is the only way to distinguish the heading from its subheadings, and there is no indication of which is the major topic.

Here is the same example imported from a PubMed file (including my pre-import modifications).

keywords = {
    Breast Neoplasms/drug therapy* [mh];
    Breast Neoplasms/genetics [mh];
    Breast Neoplasms/metabolism [mh];
    Breast Neoplasms/pathology [mh]
}

Now I can see easily from the keywords that drug therapy for breast neoplasms is the main subject of the article, and the article also deals with genetics, metabolism, and pathology of the same disease.