When writing a paper, using a good citation manager will make paper writing easier. There are several programs to use. These include Microsoft Word, Mendeley, Papers (mac), BibTeX, and EndNote. Personally, I think Mendeley is great for organizing papers, highlighting, and note taking. However, when it comes time to write a paper, I have always used EndNote. Now that I'm behind the desk and not in the lab, I have my students use EndNote for their papers. The challenge with EndNote is that there are certain pitfalls that I have learned to circumvent over my academic career. Although I enjoy helping my students get comfortable with EndNote, I think it's time to write a brief guide to some of the common pitfalls so that my students, your students, or the casual scientist EndNote user that happens to have stumbled onto my group web page.

Perhaps the most obvious place to start is with importing articles. Almost all journals have an option to download a citation that can be imported into EndNote. I find that it's always easier to import an article because there is less of a chance of typographical errors ending up in your library. There are two common ways that journals output their styles. This is via an EndNote output file or a RIS output file. Below you will see an example of and EndNote output file (RSC journals use this typically) and a RIS output file (ACS journals use this typically). As I collect examples for other journals, I will add them to the list.

RSC journals (EndNote output): On the journal web page, find the download citation link. Select EndNote as your output style and then click go. A file, RSC_.ris, will be downloaded. Opening the file will immediately open it into the current EndNote library.

ACS journals (RIS output): On the journal web page, find the Download Citation link on the right hand side. This will open a new window with some options in it.

Select the RIS option (selected by default). I prefer to include the abstract of the paper. Once you have selected the desired options, click Download Citation(s). A file with an RIS extension will be downloaded. Double click on the file to open it and it will import the file into your EndNote library.

Before we get into formatting your library and doing anything fancy, you may be wondering how you can go about inserting citations into your manuscript. For me, there are three ways that I like to insert citations.

Method 1 - Inserting from EndNote: In Word, position the cursor where you would like the citation to be inserted. Switch to EndNote. Select the citation that you want to insert and then click on the insert citation button (Alt+2).

Method 2 - Inserting from Word: In Word, position the cursor where you would like the citation to be inserted. In the EndNote tab of Word, click Insert Citation (see Figure below), and then select Insert Citation.

In the new window, you will be able to search your library for the reference you are looking for. Once you have found it and selected it, click on Insert.

Method 3 - Cite while you write: As you are writing your paper, you can add a citation by putting in any citation information inbetween "{}" brackets. For example, let's say that I am trying to cite a paper that I published back in 2016 in Chem. Commun., in issue 52, and on page number 4971. In the document, I would add {Katz, 2016}. Alternatively, I could put any of the information from that manuscript between the brackets (e.g., {Katz, 4971}, {4971, 52}, or {Katz, 4971, Chem. Commun., 2016, 52}). Personally, I prefer to use the doi number for my cite while you write citation as it's unique for the paper.

If you have instant formatting on (see Figure below to enable/disable it), then EndNote will either insert the citation or open up the insert citation dialog (see Method 2) in order to have you find the unique citation. If instant formatting is off, then you will have to click "Update Citations and Bibliography" upon which EndNote will insert the unambiguous citations and open the insert citation dialog box for you to find the unique citation.

There exists both a long form and an abbreviated, sometimes called short form, of many journal names. For example, the long form of the journal JACS is "the Journal of The American Chemical Society" while the abbreviated form of the journal title, despite us all calling it JACS, is "J. Am. Chem. Soc.". You may be wondering where you can find a list of most of the journal abbreviations. Each journal web page should indicate the journal abbreviation form. That's fine if you are looking for a few abbreviated names. However, when you are looking for several of them, this can be cumbersome. Try the searchable Abbreviation list found at the UBC library web page. I find it the easiest of all the lists to use.

When you are creating an EndNote library for your work (e.g., paper, thesis) you want to make sure that your journal name is in its long form (e.g., Chemical Communications) even if the journal you are submitting to prefers to have journal names in their abbreviated forms, sometimes called short forms, (e.g., Chem. Commun.). For me, the rational for this is as follows. If you want to use long form names in your thesis but your papers always use the abbreviated forms, then you will spend considerable time reformatting your library when you should be working on your thesis. As another example, if your paper gets rejected from journal A that uses one style and you have to format your EndNote library for Journal B that uses the other style, then you may spend hours changing something that can be changed with the click of a button.

Step 1: In EndNote, go to the define terms list in the tools menu. In the new window, select journal and then go to the terms tab. If you have any terms in this window, then delete them (see image below). Dupilicate terms are problematic, so starting with an empty list is important.

Step 2: As shown in the Figure below, in the Lists tab, make sure journals is selected and then click import list. EndNote comes with a default list of journals. Select Chemical, or click Here for my updated default list (I've added a few over the years that were not in EndNote X7). You should now have 1500+ journals in your terms list. You can manually add more journals to the list.

Step 3: We have to tell EndNote that we want to use a journal abbreviated form. In order to do this, we have to edit the output style. The output style is a style file for how you want ednote to output your references. For example, if you are writing a JACS paper, then you want to use the JACS output style because it has already been formated correctly. Once you have selected the output style you want, go to edit, output style, Edit "output style name" (see Figure below).

On the left hand side, you will see all the options you can change. Go to Journal names and make sure that Abbreviation 1 is selected.

Close your output style (it will promt to save it) and you now have your Journal names set up correctly.

If your output style contains article titles, then you may find that some words, molecules, formula, come out incorrect. For example, the title of the article may contain "CO2" but the reference always comes out as "Co2". This is easy to fix. Under the Edit menu, you will find the preferences option. In the EndNote preferences, the first list is "Change Case". As shown in the Figure below, you will see a section titled "Do not change the case of the following terms". add any word which you do not want EndNote to change the capitalization on.

Maybe you are looking at an old paper and you have lost the EndNote file. Maybe your EndNote file became corrupt. Maybe your computer crashed while writing your thesis (happened to me twice) and you only have a copy of the word document that your supervisor sent you. No matter what happened, there are rare ocassions when you have a word document but not the EndNote library. Don't worry. EndNote embeds the library in your word document so that you can always extract it and start a new library.

Step 1: scroll down to the reference section of your paper/thesis. As shown in the Figure below, right click on the references, go down to "Edit Citation(s)", and click on "More...".

Step 2: a new window will open up (see Figure below). This is the EndNote Edit & Manage Citations window. You can delete references and reorganize group references here. However, if you click on the tools button in the bottom left hand corner, then you can export a travelling library. This will prompt you to either create a new library or import the library into an existing EndNote library.

Could not find the answer?

The web page is always evolving. The aim is to take my students questions regarding EndNote and make a help section here for all. If you don't see the answer that you are looking for, then drop us an e-mail or check back frequently. Alternatively, if your students have a common question that you think should have an answer here, then drop us an e-mail or Twitter with the question and a solution and I'll do my best to post it in a timely fashion.

Contact Details

Department of Chemistry,
Memorial University,
St. John's, NL

Phone: 1-709-864-8745
Email: mkatz@mun.ca
Website: www.KatzResearchGroup.com