AI and text mining for searching and screening the literature

Using EndNote for subject heading frequency counts

EndNote available to McGill useres from http://libraryguides.mcgill.ca/citation

EndNote allows you to calculate subject heading frequencies across a collection of records at an aggregated level. PubReminer does this too, but only for MEDLINE, so EndNote is a good option for other databases such as Embase.

Procedure

These instructions follow the well-detailed guidance provided in 

• Text Mining Opportunities: White Paper. Ottawa: CADTH. 2018 May. [Available from: https://www.cadth.ca/text-mining-opportunities-white-paper]

Export relevant records from PubMed, MEDLINE on Ovid, Embase on Ovid, or any other database that uses a controlled vocabulary (and includes that information in the data that is imported into EndNote), then examine the syntax of the subject headings in the keyword field (for MeSH terms from PubMed or MEDLINE on Ovid, note the asterisk for major subject headings and the /; note also that there are no semi-colons)

• Before exporting records to EndNote, you can set up some preprocessing for the subject headings that will be imported (into the keyword field, in this case) for better results, depending on how you want the headings to be tabulated:
  • Begin with an empty EndNote library
  • In EndNote 20, go to Library > define term lists > keywords
  • Select the correct delimiters — for example, if you want to treat the subheadings separately from the subject headings in PubMed or MEDLINE on Ovid, tick the box next to the “/” symbol to make sure that subheadings will be split apart from the subject headings and counted separately
  • Click on “update list”
  • Click “OK.”
• Import the records for analysis into the new EndNote library
• If you want to ignore the asterisk (i.e., treat major subject headings and minor subject headings in the same way), you can perform a Find and Replace to eliminate the asterisks from the keyword field:
  • Go to Edit > Find and Replace
  • Select the Keyword field (if that is the field into which the subject headings were in fact imported)
  • Find the * (uncheck Match Words) and Replace with blank
  • Click Change

To perform the frequency analysis:

• Go to Tools > Subject Bibliography
• Select Keywords from the list and click OK
• Choose Select All and click OK
• Click on Layout > Terms > Subject Terms Only
• Change the number of lines between entries by removing ^p^p next to Suffix (this will reduce the length of the saved or printed document)
• Change the display order to frequency by selecting By Term Count - Descending and click OK

• Print or Save