Journal titles can be a problem for the biosciences 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. Always check the “Instructions for Authors” of the journal to which you are submitting your paper to find the system of abbreviation required.

For example, Plant Physiology specifies that authors should “Write out in full all one-word journal titles. Use the BIOSIS List of Serials for abbreviations of multiple-word journal titles; write out in full the names of journals not listed there.” Archives of Microbiology requires “journal as abbreviated in Chemical Abstracts.” The Journal of Cellular Biochemistry specifies that “journal abbreviations should follow the Index Medicus style.” On the other hand, The American Journal of Botany instructs authors to “write out journal names in full”.

So there are at least four different requirements that the researcher may have to meet:

• Use BIOSIS/Biological Abstracts abbreviations: see Section 1 below
• Use Chemical Abstracts/CASSI abbreviations: see Section 2 below
• Use Index Medicus/Medline/PubMed abbreviations: see separate guide entitled Medical Journal Titles and EndNote
• Use the full journal title: see Section 3 below

Furthermore, as the researcher submits papers to different journals, the requirements will vary from journal to journal and Section 4 deals with this problem.

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 following sections explain how to do this.

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.

1.1 The Biosciences Journals Term List

The University of Queensland Library has produced a biosciences journals term list which contains the titles of biological journals, with BIOSIS abbreviations. The term list records titles of journals indexed in the Biological Abstracts database, along with the corresponding abbreviation from the BIOSIS Serial Sources directory.

Starting with version X1, the EndNote software includes a large term list called Zoological Records which includes BIOSIS abbreviations. You will find this term list in the Terms Lists folder of your EndNote software on your hard drive. We recommend this list for researchers in zoology and related disciplines.

1.2 Importing the Biosciences 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 Biosciences 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:

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

To download the biosciences journals term list:

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

To import the biosciences journals term list:

• Open your EndNote library
• Click on Tools on the menu bar and choose Define Term Lists
• Highlight Journals
• Click on the Import List button
• Select the text file to be imported and click on the Open button

If you open the journals term list, it should 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:

• Full Journal: Gives the full journal title.
• Abbreviation 1: Gives the BIOSIS/Biological Abstracts abbreviations, plus stops.
• Abbreviation 2: Gives the BIOSIS/Biological Abstracts abbreviations.
• Abbreviation 3: If the title includes the word and, gives the full journal title, with an ampersand instead of and

Click on the X button to close the term list.

1.3 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 Plant Physiology, which requires BIOSIS 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:

• Click on Edit>Output Styles>Open Style Manager
• Highlight the style named “Plant Physiology”
• Click on the Edit button
• When the edit window opens, you will see a number of options on the left-hand side.
• Click on Journal Names.
• When the new screen appears, the option Don't Replace will be checked.
• 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. You must edit this style to use the abbreviations in the Abbreviation 2 column of the terms list.
• Click on File>Save As to save the edited style under a new name, e.g. Plant Physiology_myedit.ens. You are now editing a copy of the style, and this is the version that you should use when formatting your paper.
• Check the Abbreviation 2 option, as shown below.
  
  

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

1.4 Maintaining Your Journals Term List

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:

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

When you are inputting references manually, it is probably best to use the full journal title. However it is quite acceptable to use an abbreviation of the title, providing that abbreviation appears in your journals term list.

1.5 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.

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 annual directory BIOSIS Serial Sources which is held in the Library. Unfortunately it ceased publication in 2005.
• When you have found the correct abbreviation, edit your Journals term list to include it (see below, section 1.6).
• 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 “Abbreviation 2”, some journals appear with an abbreviation which does not look like a BIOSIS abbreviation

• This means that you have imported some references with abbreviated journal names in the Journal field, and those abbreviations did not match any of the abbreviations in your Journals term list.
• Check the annual directory BIOSIS Serial Sources which is held in the Library. Unfortunately it ceased publication in 2005.
• When you have found the correct form of the full title, insert that in the Journal field of your reference.
• Check your Journals term list to see if this title (and its abbreviation) appear there. If not, edit your Journals term list to include it (see below, section 1.6).
• Beware: Your Journals term list may include an entry for the abbreviated title in the “Full Journal” column. If so, delete that entry. You can avoid this situation by disabling the automatic update of terms (see section 1.4 above).

1.6 Editing the Journals Term List

When you wish to cite a journal which does not appear in your term list, you will have to edit your Journals term list to insert the new title. 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 Tools>Open Term Lists>Journals Term List
• Click on the New Term button
• A dialogue box will open. Enter the full title in the “Full Journal” box and the BIOSIS abbreviation in the “Abbreviation 2” box.
• 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 Tools>Open Term Lists>Journals Term List
• Highlight the journal which you wish to delete
• Click on the Delete Term button

2.1 The Chemical Journals Term List

The University of Queensland Library has produced a chemical journals term list which contains the titles of chemical journals, with Chemical Abstracts Service Source Index (CASSI) abbreviations. The term list records titles of journals indexed in the CAplus database on SciFinderScholar, along with the corresponding abbreviation from the Chemical Abstracts Service Source Index.

2.2 Importing the Chemical 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 Chemical 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:

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

To download the chemical journals term list:

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

To import the chemical journals term list:

• Open your EndNote library
• Click on Tools on the menu bar and choose Define Term Lists
• Highlight Journals
• Click on the Import List button
• Select the text file to be imported and click on the Open button

If you open the journals term list, it should 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:

• Full Journal: Gives the full journal title.
• Abbreviation 1: Gives the Chemical Abstracts/CASSI abbreviations.
• Abbreviation 2: Gives the Chemical Abstracts/CASSI abbreviations, with stops removed.
• Abbreviation 3: If the title includes the word and, it is given here with an ampersand instead of and.

Click on the X button to close the term list.

2.3 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 Archives of Microbiology, which requires Chemical Abstracts abbreviations of journal titles, the output style would have to be configured to take journal titles from the second column (“Abbreviation 1”) of your journals term list.

See section 1.3 above for information on checking and editing an output style.

2.4 Maintaining Your Journals Term List

See section 1.4 above for information on maintaining your journals term list.

2.5 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.

a. Using an output style configured to use "Abbreviation 1", some journals still appear in full

• This means that there is no entry for that journal abbreviation in your journals term list.
• To find the correct abbreviation, check the list of Core Journals Covered in CAplus on the web or check the printed Chemical Abstracts Service Source Index, which is held in the Library.
• When you have found the correct abbreviation, edit your Journals term list to include it (see above, section 1.6).
• 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 “Abbreviation 1”, some journals appear with an abbreviation which does not look like a CASSI abbreviation

• This means that you have imported some references with abbreviated journal names in the Journal field, and those abbreviations did not match any of the abbreviations in your Journals term list.
• Check the list of Core Journals Covered in CAplus on the web or check the printed Chemical Abstracts Service Source Index, which is held in the Library.
• When you have found the correct form of the full title, insert that in the Journal field of your reference.
• Check your Journals term list to see if this title (and its abbreviation) appear there. If not, edit your Journals term list to include it (see above, section 1.6).
• Beware: Your Journals term list may include an entry for the abbreviated title in the “Full Journal” column. If so, delete that entry. You can avoid this situation by disabling the automatic update of terms (see section 1.4 above).

If the journal to which you are submitting your paper requires you to cite journal titles in full, then you have two options:

• Either, configure your output style so that it takes journal titles from the first column (“Full Journal”) in your journals term list (see section 3.1 below).
• Or, configure your output style so that it ignores any journals term list and takes journal titles from the Journal field in your references (see section 3.2 below).

3.1 Taking Journal Titles from the “Full Journal” Column in the Term List

If you have maintained a journals term list for your library, you can edit the output style so that it takes journal titles from the first column (“Full Journal”) in your journals term list. Check the output style as explained in section 1.3 above. Ensure that the option Full Journal Name is selected.

When EndNote formats your paper, if it does not find an entry for a journal in the terms list, it will just take the journal title from the Journal field of the reference. In most cases, this will be satisfactory. However, if the journal title as given in the Journal field is abbreviated, then the abbreviated title will appear in your formatted paper. In such cases, you must edit the reference in your library to give the full journal title in the Journal field.

If you do not know the full title, you may be able to find it from one of the following sources on the web:

• British Library Current Serials File
• PubMed Journals Database
• MELVYL Catalog (Under Search, select the option Journal Title)
• Journal Abbreviations Sources

3.2 Taking Journal Titles from the Journal Field

If you want the EndNote output style to ignore the Journals term list and take journal titles from the Journal field in your references, then you should check the output style as explained in section 1.3 above. Ensure that the option Don't Replace is selected.

When you format your paper, you may find that some journal titles are abbreviated. This means that the Journal field for that reference in your EndNote library contains an abbreviation of the journal title. You must edit the reference in your library to give the full journal title in the Journal field.

If you do not know the full title, you may be able to find it in one of the journals term lists mentioned in this guide or one of the websites listed in section 3.1 above.

You may find that you usually use one system of journal abbreviations (e.g. BIOSIS), but you occasionally submit papers to journals that use a different system of abbreviations (e.g. Index Medicus/PubMed). An EndNote library will only support one journals term list, so how can you cope with more than one system of journal abbreviations?

We recommend that you save a copy of your normal journals term list by exporting it. Then you can delete all terms in the list and import a different term list to format your paper. When you have finished writing that paper, you can delete the new terms and import the original term list from the file to which you exported it.

Here is the procedure in detail:

Step A. Export a copy of the original Journals term list:

• Click on Tools>Define Term Lists
• Highlight the Journals list
• Click on the Export List button
• Give the file a name and choose a folder in which to save it
• Click on the Save button

Step B. Delete all terms in the Journals term list:

• Click on Tools>Open Term Lists>Journals Term List
• Click on the first journal title to highlight it.
• Hold down the Shift key and scroll to the end of the list. Click on the last journal title to select all titles.
• Click on the Delete Term button to delete all terms
• Close the Term Lists dialogue box

Step C. Import the new Journals term list:

• Click on Tools>Define Term Lists
• Highlight Journals
• Click on the Import List button
• Select the text file to be imported and click on the Open button

Step D. Format your paper using the new Journals term list.

Step E. Delete the new Journals term list:

Follow the procedure in Step B above.

Step F. Import the original Journals term list:

• Click on Tools>Define Term Lists
• Highlight Journals
• Click on the Import List button
• Select the file which you exported in Step A above
• Click on the Open button