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Medical Journal Titles and EndNote

  1. Introduction
  2. Importing the Medical Journals Term List
  3. Checking an EndNote Output Style
  4. Editing an EndNote Output Style
  5. Maintaining Your Library
  6. Troubleshooting
  7. Editing the Journals Term List

 

Introduction

Journal titles can be a problem for the medical researcher. This is because the editors of some publications require that references should give full journal titles, and other editors require that references should give abbreviated journal titles.

 For example, JAMA specifies that authors should “abbreviate names of journals according to Index Medicus”. Many other medical journals, including The Medical Journal of Australia, follow the same policy. On the other hand, some journals (for example, The British Journal of Psychiatry) require journal titles to be given in full.

The Index Medicus abbreviations are the abbreviations used in the Medline/PubMed database. These abbreviations are assigned by the U.S. National Library of Medicine (NLM), and are sometimes known as the “NLM abbreviations” or “Medline abbreviations”. There are also other systems of journal abbreviations in use: always check the “instructions for authors” of the journal to which you are submitting your paper to find the style of abbreviation required.

NOTE

The medical journals term list supplied with EndNote lists 8,908 journals which began publication before 1996. UQL have produced an updated term list which incorporates all those titles, plus a further 490 titles which began publication between 1996 and 2002. This list is available at: http://www.library.uq.edu.au/faqs/endnote/filters/medical_2002.txt
If you are a new EndNote user or haven't dealt with the Medical Journal Titles you must read the following information before downloading the file.

 

Term Lists

EndNote copes with the problem of journal abbreviations by means of its term lists. A term list can be set up for any field in an EndNote record, but the term list linked to the Journal field is particularly sophisticated, because it
allows you to store not only the titles of all the journals which appear in your EndNote library, but also up to three different abbreviations for each of those titles. It is possible to import ready-made term lists from other sources.

The medical journals term list records titles of journals indexed in the Medline/PubMed database. For each of those titles, it also gives the Index Medicus abbreviation and the same abbreviation with stops after each element.
Note that there are some journal titles that do not appear in the medical journals term list (see Section 6 below).

 

NOTE:

A journals term list is specific to a particular EndNote library. If you have more than one EndNote library, you will need to create a journals term list for each library.

 

Checking an EndNote Output Style

Now that you have imported the journals term list, you will have to make sure that the EndNote output styles which you use are configured to select the correct column in that list.

For example, if you were submitting a paper to JAMA, which requires Index Medicus abbreviations of journal titles, the output style would have to be configured to take journal titles from the third column (“Abbreviation 2”) of
your journals term list.

To check the configuration of the output style:

  1. Click on Edit>Output Styles>Open Style Manager
  2. Highlight the style named “J Amer Medical Association”
  3. Click on the Edit button
  4. When the edit window opens, you will see a number of options on the left-hand side
  5. Click on Journal Names
  6. When the new screen appears, the option Abbreviation 2 should be checked as shown below:

 

This output style is correctly configured and requires no editing. Click on the button to close the edit window.

 

Editing an EndNote Output Style

 

Not all styles will be correctly configured. Some will have to be edited.

For example, look at the output style for the British Journal of Psychiatry, which requires that journal titles be given in full, without abbreviation.
 
Check the output style for the British Journal of Psychiatry, following the instructions given above (section 3). With this output style, the option checked under Journal Names is Don't Replace. This means that when formatting your
paper, EndNote will ignore the journals term list and simply use whatever appears in the Journal field in each of your references.


NOTE:

This is not a problem, if you are sure that you have always used full journal titles in your references, but if you have imported references from Medline/PubMed with abbreviated journal titles, then these abbreviated titles will appear in your formatted paper

 

If you want EndNote to use the “Full Journal” column from your journals term list, then you will have to edit the style to reflect this.

To edit an output style:

  • Open the output style edit window, as explained above (section 3)
  • Click on File>Save As to save the edited style under a new name, e.g. Brit J  Psychiatry_myedit.ens

NOTE:

Leave the original style unchanged so that it will be available if you should need it for other purposes. You will now be editing a copy of the style.

  • In the “Journal Names” window check the Full Journal Name option as shown below:

Click on the button to close the edit window. When prompted, click on the Yes button to save the changes.

 

Maintaining Your Library

 

When you import references into your EndNote library using a filter (or connection file), or when you input references manually yourself, EndNote willautomatically update your Journals term list. The Journal field in each
reference will be checked against every entry in the term list (including the abbreviations). If EndNote does not find a matching entry in the term list, it will insert the new journal title into the first column of the term list.

If you are importing references with abbreviated titles in the Journal field, the automatic updating of the Journals term list could cause problems. If the abbreviation is not already in the Journals term list, it will be added to the
first column (“Full Journal”). To avoid this, you can disable the automatic updating of the term lists.

To disable automatic updating of terms:

  • Select Edit>Preferences
  • When the dialogue box opens, highlight Term Lists in the left-hand window
  • Uncheck the options “Update lists when importing or pasting references” and  “Update lists during data entry”

NOTE:

  • If you are importing references from the PubMed database , the references will give only the abbreviated journal title. However, as long as this abbreviation matches one of the abbreviations in the medical journals term list, EndNote will be able to identify the full journal title for it when formatting papers using an output style that is configured to use full journal titles.
  • If you are importing references from other databases , e.g. PsycInfo, the reference will probably have the full journal title, as most databases no longer use abbreviated journal titles. However, as long as this title matches one of the titles in the medical journals term list, EndNote will be able to identify the Index Medicus abbreviation for it when formatting papers using an output style that is configured to use those abbreviations.
  • When you are inputting references manually , you will have to use the full journal title, as you are unlikely to know the Index Medicus abbreviation. Again, as long as this title matches one of the titles in the medical journals term list, EndNote will be able to identify the Index Medicus abbreviation for it when formatting papers using an output style that is configured to use those abbreviations.

 

Troubleshooting

 

NOTE:

The abbreviations used by Medline/PubMed are not the only abbreviations used by journal editors. Check the “instructions for authors” of the journal to which you are submitting your paper.

Even if you follow all the instructions given above, there will still be occasional problems with journal titles when you are formatting papers with EndNote.

a. Using an output style configured to use “Abbreviation 2”, some journals still appear in full:

  • This means that there is no entry for that journal abbreviation in your journals term list
  • See if you can find the abbreviated journal title on the PubMed Database Journal Browser at:            http://www.ncbi.nlm.nih.gov/entrez/jrbrowser.cgi
  • As a last resort:
    • Check the journal title in LocatorPlus, the online catalogue of  the U.S. National Library of Medicine at: http://locatorplus.gov/
    • If the journal title is listed, there should be a “Title Abbreviation field in the catalogue record, giving the official NLM abbreviation.
  • When you have found the correct abbreviation, edit your Journals term list to include it (see below, section 7).
  • If you cannot locate an official abbreviation for this journal title, then the editor of the publication to which you are submitting the paper will probably prefer that you cite the journal title in full.

b. Using an output style configured to use “Full Journal Name”, some  journals  still appear in abbreviated form:

  • This means that you have imported some references with abbreviated journal names, and those abbreviations did not match any of the abbreviations in your Journals term list.
  • See if you can find the full journal title on the PubMed Database Journal Browser at:  http://www.ncbi.nlm.nih.gov/entrez/jrbrowser.cgi
  • When you have found the full journal title, edit your Journals term list to include it (see below, section 7)
  • Beware: Your Journals term list may include an entry for the abbreviated title in the “Full Journal” column. If so, delete that entry.

 

Editing the Journals Term List

When new journals begin publication, or existing journals change their titles, you will have to edit your Journals term list to insert the new titles.
Sometimes you may also need to delete entries, for example when an abbreviated title has found its way into the Full Journals list.

To edit the Journals term list:

  • Open your EndNote library
  • Click on Terms>Open List>Journals
  • Click on Terms>New Term
  • A dialogue box will open. Enter the full title in the “Full Journal” window and the Index Medicus abbreviation in the “Abbreviation 2” window
  • Click on the OK button and the journal will be added to the term list

To delete a journal from the term list:

  • Open your EndNote library
  • Click on Terms>Open List>Journals
  • Highlight the journal which you wish to delete
  • Click on Terms>Delete Term

 

This information has been provided by the University of Queensland Library.
Their assistance is gratefully acknowledged.