Endnote

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Overview

Endnote is software that stores your references, and formats citations and bibligraphies in papers and grants. The bookstore has copies for ~$70 (go to Computer Store, and log in to see current prices). The software does take 30 minutes to get started with, but is well worth learning. Here are reasons why Endnote is invaluable for academics. For storing references:

  • You can keep track of the references you have used in previous papers and grants.
  • You can keep track of your own publications and abstracts, including the associated PowerPoint, Word and PDF files.
  • You can search and download from PubMed and automatically get the PMCID (as needed for NIH grants).
  • Endnote can automatically retrieve pdf files with two clicks (works for ~50% of papers).

For formatting papers and grants:

  • You will never again have to worry about whether you have the correct formatting for papers - just select the style for that paper, and it's done.
  • If you revise a paper for a different journal, you can change the citations and bibliography in less than a minute.
  • Your NIH grants can include all the information needed (URL, PMCID).

However, there a two important setup steps you should take as you get started:

  1. Decide how you will organize your libraries.
    • I have one library for all of my papers and grants, and one library for each of the sections in my CV: original papers, chapters and reviews, commentaries and editorials, abstracts from conference presentations, invited talks, and conference papers.
  2. Set up a dummy library for searchers.

Here are some files that may be of help.

Endnote files
Endnote style file for NIH grants Grant (superscript and JAP) - with URL's.ens
Paul Macey's 2012 tutorial

Endnote Tutorial v2.ppt

Adding a new style

Many journals include Endnote Style files that you can import into Endnote for formatting your manuscript according ot instructions. The NIH requires citing the PMCID number, which will only happen if the style you choose specifies that option (as with the example above). If the journal style is not available already, simply download and save the style file into the Endnote "Styles Folder." The location of this folder is specified under the menus:

Edit => Preferences, to bring up the GUI below, then go to "Folder Locations" and you'll see the "Style Folder." [For SoN desktops, see note below.]

If you are working from your office computer in the School of Nursing, the "Style Folder" may not be easy to find. In that case, save the style (*.ens) file to your computer, double-click to open it in Endnote, then File => Save As, delete ethe "Copy" at the end of the name, and click "Save." The style will now be available on that computer.

Changing or Correcting the Bibliography

Because the bibliography is a "field" created each time Endnote formats the references, any change you make in the bibliography will be overwritten each time you format with Endnote. Make corrections in the Endnote library. For the style, select the correct "Output Style" and if necessary edit it. If you are stuck, copy the bibliography as created by Endnote and remove the fileds, either with the Word command or by pasting as text; both of these options should be done in a new Word document.

PMCID Numbers: Adding or Updating

The NIH requires PMCID numbers for each reference. As of Endnote version X6, these numbers will be automatically downloaded if you use the "PubMed" search within Endnote. Styles like the "Grand (superscript and JAP) - with URL's.ens" above will then display the PMCID in the bibliography.
 
If you have existing references without PMCID's, either because you downloaded them in an earlier version or because the PMCID had not been issued at the time of download, Endnote X6 has an option to automatically add the PMCID's. This option only works for references downloaded using the pubmed option in Endnote, and will not work for references you manually typed in. From the Endote library, select the references, right-click, "Find Reference Updates," and Endnote will look for updated fields, including the PMCID. Either select "Update All Fields" or "Update Empty Fields," click "Save Updates," and you're done. If "Find Reference Updates" does not work, your best option is to download a new copy of the reference using Endnote X6, and delete the old one from the library.
 
Note that PMID numbers are not the same as PMCID numbers. The NIH does not require PMID numbers; many people mistakenly believe you need the PMID number if there is no PMCID, but that is not correct. Note also that not all papers have PMCID numbers, and that many papers receive PMCID numbers months or years after they appear on Pubmed.

Correcting APA Listing Full Name Instead of Initials (APA 6th Style in X6)

At least as of version X6 of Endnote, the APA6th style incorrectly lists the full names of authors if their first names are in the database. To correct this, Edit the style. From the top menus, "Edit" => "Output Styles." Select ""Edit "APA 6th" " if it's listed otherwise selct the style from "Open Style Manager." Go to the "Author Name" section under "Bibliogprahy" and change the "Initials" format from "Full Name" to "A. B." (which is the correct APA format). Close the style window; when it asks for a name ("APA 6th Copy"), change that to just "APA 6th" to overwrite the style.
 
Open Style editing window:
 
Changing first name option:

Suggestions and Questions

Please add suggestions or questions using the comments below.