PubMed import uses which filter?

When importing from PubMed directly (after a search of PubMed from within EndNote), the journal title field is populated with the Index Medicus abbreviation. However, when the same import is performed from a .txt file downloaded from the PubMed Web site, the full journal title is placed in the Journal field. Why? Is the direct import using a different import filter? If so, which one is it using so I can change it? 

This is EndNote X3 and Word 2007.


They both use files called “PubMed (NLM)” but they are two different auxiliary files with two different extensions.

The Online Search function from within EndNote uses a “Connection File”  [PubMed (NLM).enz].

Importing of a text file of search results from the PubMed website uses an “Import Filter” [PubMed (NLM).enf]

Both of these can be edited using EndNote but there are some limitations.

In general - for PubMed and most other databases - there may be slight differences between the actual search results [and the exact formatting of these results] between the native, web-based interface and the EndNote search function. There are two main reasons for this:

  • The EndNote search function is generalized for use with many different search targets and may not have the specificity that one individual database may require for very specialized searches.

  • Not all options/fields are made available to EndNote by all search hosts.

This is why we give you many different options for way to get you data into your EndNote library.

I hope this helps.

Jason Rollins, the EndNote team

Thanks, Jason! Mystery solved!


Hi, since in your message you wrote that the mistery was solved, I was wondering if you also managed to obtain full name of journal titles with pubmed connection files… I did not…

Thank you very much!

Since endnote with the journal terms list facility will adjust the titles to either full, or abbreviated as defined by the style in bibliographies, I don’t see any reason to worry about what version of the journal title is downloaded?