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, Health Expectations) 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.

Contents

1. 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 reference, 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 into your EndNote library. The University of Queensland Library has produced a medical journals term list which is based on a list of journals prepared by the makers of the EndNote software, augmented by further titles which have begun publication in recent years.

The medical journals term list records titles of journals indexed in the Medline/PubMed database. For each of those titles, it gives the full title, the Index Medicus/Medline/PubMed 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.

2. Importing the Medical Journals Term List

Warning for Macintosh users of EndNote 9: There is a bug with EndNote 9 for the Macintosh which affects the importing of term lists. Although the lists import correctly, EndNote ignores the data. To resolve this issue, you need to open the library using EndNote 9.0.1 for Windows. Then export the Journals term list and save it as a text file. Empty the Journals term list, and reimport the saved term list. Then when the library is opened on a Macintosh, the term lists will work. This bug does not affect terms which you insert yourself: it only affects imported term lists.

We strongly recommend that you delete all terms in your existing journals term list, and then import the Medical journals term list. You can import the new list into an existing list if you prefer, but this may create duplicate entries which will prevent EndNote from selecting the correct item from the term list. When importing a term list, EndNote will only remove duplicates if the data in all columns is identical.

To delete the existing terms in the journals term list:

1. Open your EndNote library
2. Click on Tools on the menu bar and choose Open Term Lists and then choose Journals
3. Click on the first journal title to highlight it.
4. Hold down the Shift key and scroll to the end of the list. Click on the last journal title to select all titles.
5. Click on the Delete Term button to delete all terms
6. Close the Term Lists dialogue box

To download the medical journals term list:

1. The list is available on the University of Queensland Library website.
2. Display the list and use your browser's Save As function to save this page as a text file (*.txt).

To import the medical journals term list:

1. Open your EndNote library
2. Click on Tools on the menu bar and choose Define Term Lists
3. Highlight Journals
4. Click on the Import List button
5. Select the text file to be imported and click on the Open button

If you open the Journals term list, it should now look something like this:

Note: If the list has not imported correctly, it may be necessary to delete the Journals term list and create a new Journals term list before importing. To do this, click on Tools on the top menu bar and select Define Term Lists. Highlight the Journals list and click on the Delete List button to delete it. Then click on the Create List button to create a new list called Journals. Make sure that you check the box to indicate that this is a journals list. Finally click on the Link Lists button to link your new list to the Journal (Secondary Title) field.

You can enlarge any of the columns to see the full details. The columns contain the following data:

Click on the X button to close the term list.

3. 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 "JAMA" (in some versions of EndNote it appears as "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.



7. This output style is correctly configured, and requires no editing. Click on the X button to close the edit window.
8. If the output style is not correctly configured, see the following section.

4. 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 Journal of Clinical Investigation, which instructs authors to "abbreviate the names of journals according to PubMed."

Check the output style named J Clinical Investigation, 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.

If you want EndNote to use the PubMed abbreviations in the “Abbreviation 2” column from your journals term list, then you will have to edit the style to reflect this.

To edit an output style:

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

NOTE:

Leave the original style unchanged so that you can return to it if you make a mistake during editing. You will now be editing and using a copy of the style.

3. In the “Journal Names” window check the Abbreviation 2 option, as shown below.




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

5. 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 will automatically 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:

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

When importing references to your library from the Ovid Medline database, we suggest that you use one of the filters which can be downloaded from the UQ Library web server. These filters have been configured so that they will import both the full journal title and the abbreviated journal title. The abbreviated journal title will be imported into the Journal field of each reference, and the full title will be imported into the Alternate Journal field, or vice versa, depending on which filter you have chosen.

If you are importing references from the PubMed database, some of 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. BIOSIS Previews or PsycInfo, the reference will probably have the full journal title, because 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.

6. Troubleshooting

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.

The most common reasons for the EndNote medical journals term list failing to match the journal titles in your references are:

• The journal is not included in the term list.
• The journal title in your reference begins with an article, e.g. The Journal of .... Remove all articles at the beginning of journal titles.
• The journal title in your reference includes a qualifying term, e.g. Journal of Immunology (Baltimore, Md). Remove the qualifying term.

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.
• Check the reference in your EndNote library. Some filters will import both the full and the abbreviated title, using the Journal field and the Alternate Journal field.
• Alternatively, see if you can find the abbreviated journal title on the PubMed Journals Database
• As a last resort,
  • Check the journal title in LocatorPlus, the online catalogue of the U.S. National Library of Medicine
  • 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, 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.
• Check the reference in your EndNote library. Some filters will import both the full and the abbreviated title, using the Journal field and the Alternate Journal field.
• Alternatively, see if you can find the full journal title on the PubMed Journals Database
• 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.

7. 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:

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

To delete a journal from the term list:

1. Open your EndNote library
2. Click on Tools>Open Term Lists>Journals Term List
3. Highlight the journal which you wish to delete
4. Click on the Delete Term button