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

Features
3

the structure of the keywords should be changed, so that it takes the delimiters and splits by slash

Yes. Headings and subheadings have a many-to-many relationship, represented in PubMed format as one-heading to zero-or-more subheadings (one heading per line).

Here is a basic example of terms that I modified before importing.

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The original form of the record indexed with all the terms was:

MH  - Ankle Joint/innervation/physiology

Usually, I split lines like this into three. While it is redundant to include the heading as a term of its own, this puts all “Ankle Joint” entries in one group, without using subgroups or searches, regardless of subheadings. I find this convenient for working with the references.

Here is another example, this time including major topics, as indicated by an asterisk.

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In the original form each record had one of the following forms:

MH  - Imaging, Three-Dimensional
MH  - *Imaging, Three-Dimensional
MH  - *Imaging, Three-Dimensional/methods
MH  - Imaging, Three-Dimensional/*methods

In the transformation, I

  • retained commas from the original terms, and set JabRef’s delimiter to ;.
  • moved asterisks to the end of the heading and/or subheading to keep like-terms adjacent alphabetically
  • marked each keyword with [mh], because the abbreviated syntax for searching subject headings in PubMed is "Some Heading"[mh] and, brackets are not used in medline subject headings (as far as I know).

Notice that all of the entries in the second example deal with three-dimensional imaging, but if I am studying imaging methods, then I am particularly interested in the last group, where “methods” is a major topic and not merely incidental. Headings and/or subheadings can be a major topic.

More info:

  • The label OT - maps to keywords in JabRef. These terms need no special treatment.
  • The label RN - , for registry number named substances, also maps to keywords in JabRef. These terms often include characters that can be incorrectly interpreted as delimiters. I have not dealt with this recently, and I am not sure if JabRef has any difficulty with this.

Here is an example of a named substance registry number (no delimiter-like characters in this case).

RN  - 0 (Chromatin)