getting started with endnote x

GETTING STARTED WITH ENDNOTE X

http://www.library.uthscsa.edu

What is EndNote?

EndNote is a software program that allows you to organize references into databases and to export selected citations into bibliographies. References can be transferred from MEDLINE, CINAHL, or other bibliographic databases, or can be typed in by hand. EndNote works with Microsoft Word to produce bibliographies and embedded references in hundreds of available styles. EndNote also makes it easy to change the style of your references.

EndNote is available for Windows or Macintosh computers. Although Information Services librarians can assist users with EndNote and are available to teach workshops on EndNote, it is not available for use on Library computers.

Creating an EndNote Library

Setting Up an EndNote Library Open EndNote. Select Create a new EndNote Library and click OK. Or, from the File menu, select New.... Name your new library and save it in a location that makes sense to you.

o EndNote library files have a .enl extension. In addition to the .enl file, EndNote also creates a folder with the same name as your library file, with a .data extension. This folder must be in the same location as the .enl library file.

o See page 8 for information on moving an EndNote Library to another computer. Installing EndNote’s List of Medical Journal Titles and Abbreviations Journal title abbreviations cause problems for EndNote users for several reasons:

References downloaded from UTHSCSA Ovid databases include the full journal title, but many biomedical reference formats require the use of the NLM journal abbreviation.

References downloaded from PubMed include only the NLM journal abbreviation, but some formats, most importantly APA, require the full journal title.

If references are downloaded from both Ovid databases and PubMed, EndNote’s journal titles field will include both full journal titles and abbreviations.

To avoid these issues, when setting up a new EndNote Library, before adding any references, you should import EndNote’s list of medical journal titles and abbreviations. To do this: 1. Open and name your new EndNote library as described above. 2. Under EndNote’s Tools menu, select Define Term Lists, then click on Journals. 3. Click the Import List button. Navigate to your EndNote program file and open the Term Lists folder. 4. Double click on medical.txt. (If you do not know where the program file is, or cannot access it, contact the

person who installed EndNote on your computer.) After the terms are installed, click Okay. Approximately 9000 biomedical journals titles and their NLM abbreviations will be installed in the Journals Terms List. To see the list, select Open Term Lists from the Tools menu, then select Journals Term List. Each title has two abbreviations, one with periods (labeled Abbreviation 1) and one without periods (Abbreviation 2). The Abbreviation 3 column will be empty.

When you import citations from PubMed and other databases with abbreviated titles, the titles will still appear abbreviated in your EndNote library. However, EndNote can now associate them with the full title when necessary.

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Transferring Citations from Ovid Databases (MEDLINE, EBM Reviews, etc.) Ovid offers a feature called “Direct Export” which allows you to transfer citations directly into an EndNote library. (Many databases include the same feature, with a different name. Look for options like “Export to Reference Software” or “Export to Procite/Reference Manager/EndNote.” Check the database’s help files for more information.)

Run your search in the Ovid database as usual. After selecting citations to save, use Ovid’s Results Manager (below) to specify fields and format. Under Fields, you must select Complete Reference in order for references to transfer properly. (Note that this does not include the full text of the article.) Under Citation Format, select Direct Export, then click Save under Action.

From the next screen, select Export Results to EndNote… and click Continue.

Your browser may display a message asking whether you want to save the file or open it. If so, you may have to experiments to see which works. In Firefox, open the file; other browsers usually want you to save it.

You will next be asked to locate the EndNote Library to which you wish to download your citations. (You

must already have set up the Library, as described above. If you start a new Library at this point, you will have to export your citations again.) After doing so, your citations will appear in a new window in your EndNote Library. To see the entire Library, select Show All from the References menu. Your Library will look like this:

Transferring Citations from EBSCO Databases (CINAHL, Academic Search Premier, etc.) EBSCO offers a feature called “Export” which allows you to transfer citations directly into an EndNote library.

Run your search in the EBSCO database as usual. Select citations to save by clicking the ADD icon (found to the right of each citation). When you have finished selecting citations, click on the Folder has items icon at the top of the page to view only the selected citations. Click Export to begin the transfer.


From the next screen, select Direct Export Results to EndNote… and click Save.

Your browser may display a message asking whether you want to save the file or open it. If so, you may have to experiments to see which works. In Firefox, open the file; other browsers usually want you to save it.

You will next be asked to locate the EndNote Library to which you wish to download your citations. (You

must already have set up the Library, as described above. If you start a new Library at this point, you will have to export your citations again.) After doing so, your citations will appear in a new window in your EndNote Library. To see the entire Library, select Show All from the References menu. Your Library will look like this:

Transferring Citations from PubMed (using Import Filters) PubMed does not have a Direct Export function. However, you can import citations from PubMed using Import Filters, which help EndNote “translate” your saved citations into a format it understands.

Saving citations in the correct format o After selecting citations from a database to import into an EndNote Library, select MEDLINE

from the drop-down DISPLAY menu. You must save them as a text file in MEDLINE format.

o From the SEND TO drop-down menu, select FILE, to save your references to a text file. o The default name for the saved file is pubmed-result.txt. You can change this, if you like. Be sure you

know where your file is being saved to on your computer!

Importing Under EndNote’s File menu, select Import. You’ll see a box like this:

Click here to locate the text file you saved

Import Option: See notes below

Keep as No Translation Duplicates:

See notes below

Import Data File: Click Choose File… to locate the text file you saved from PubMed. Import Option: Click on the down arrow next to Import Option to see the databases that are pre-selected or


that you have used before. Select the database from which you downloaded your citations. o If the database you need isn’t there, click Other Filters and select the desired database.

Duplicates: This lets EndNote know what to do if it finds identical citations. If you select Import into Duplicate Library, it will create another library with the same name as the original library, followed by DUPL. You can then examine the duplicates library and decide whether or not to add them to your Library by cutting and pasting. If you choose Import All, you can later use the method described in step 4 on page 3 of this handout to locate duplicates.

Click Import. You’ll probably see EndNote counting citations. If your file is downloaded as one big citation, you probably didn’t save them in the correct format, and you’ll need to redo your search and download again. If it still doesn’t import properly, you may need to update the filter. See the handout “EndNote Tips & Troubleshooting” for more information.

Transferring Citations from Other Sources (electronic journals, other databases, etc.) Many databases and some electronic journals include a “Direct Export” feature, with a different name. Look for options like “Export to Reference Software” “Export to Procite/Reference Manager/EndNote” or “Export in RIS Format.” Check the database’s help files for more information.

Saving Citations for Later Transfer This method also works if you want to save citations from a database onto a disk to import into EndNote later -- for example, if you are working on a computer that does not have a copy of your EndNote Library. You must save the citations in a format EndNote understands.

Selecting the Correct Format and Filter*

Database Action Format Use this EndNote filter CINAHL (EBSCO) Export Generic bibliographic management software CINAHL (EBSCO) MEDLINE (Ovid) Save Reprint/MEDLARS format MEDLINE (OVID) PsycINFO (Ovid) Save Reprint/MEDLARS format PsycINFO (OVID) PubMed* Save MEDLINE PubMed (NLM) Web of Science Save Field Tagged Web of Science (ISI) UTHSCSA Library Catalog (BLIS)*

Save Marked Records, then Export Saved List

End-Note (you must email the file to yourself; ‘saving to screen’ causes format changes) INNOPAC

* At this time, there is no direct export-type feature for databases marked with *; citations may only be imported using this method.

Adding References Manually Occasionally you will want to add a reference to your Library by typing it in, rather than by downloading. Here are some tips:

To add a reference manually, open your database, then select New Reference… from the References menu. Be sure to use the right Reference Type. The default is Journal Article, but other choices in the pull-down

menu include Book Section (used for book chapters) and Thesis. When you change Reference Types, EndNote automatically prompts you for fields needed for that type (editors’ names, chapter authors’ names, etc.).

In general, you don’t need to use any punctuation when entering (some exceptions are listed below). Authors’ names should be entered one per line, so press RETURN after each author’s name. They can be

entered in either of the following formats: Einstein, Howard G. or Howard G. Einstein


If using initials rather than first names for authors, be sure to include a space or period after each one: Einstein, H G or Einstein, H.G.

Complex names have their own rules. o For multiple-word last names enter the name last name first: de Gaulle, C. o Authors whose names have suffixes, such as Jr. or III, should be entered last name first, with a comma

after the first name or initials: Einstein, H.G., IV o Organizations, like the American College of Physicians, need to have a comma entered after the name, so

that EndNote will keep the word order correct Page numbers can be entered in complete form or as a range: 1492-1497 or 1492-7 Page numbers that skip pages are entered with commas. For example, an article that begins on page 124 and

goes through 127, then skips to 130, then skips to 191 and continues through 194 would be entered in either of these formats: 124-127, 130, 191-194 or 124-7, 130, 191-4

Linking PDFs or Other Files to EndNote References You can establish links to files on your computer by using EndNote’s Link feature. Linked graphics (or an icon) are inserted in the reference’s Image field and a paperclip icon appears next to the reference in list view.

To link a graphic or other file: o Open the reference to which you wish to link. o Under the References menu, select URL... or PDF.... o Navigate to the location on your computer where you have saved the file. After locating it, click Open.

You can also link to a URL by simply typing the URL into the reference’s URL field. For PDF files, you can drag the PDF’s icon to the PDF field.

Locating References within an EndNote Library

EndNote’s Search References... function (under the References pull-down menu) allows you to search for references within your database. You may specify which field (i.e., author, title, abstract) you wish to search and you may use and, or, and not to combine searches. Changing EndNote’s Behavior

The fields shown in the list view can be changed by going to the Edit menu and selecting Preferences…. Click on Display Fields, where you can choose which fields (such as Title, Journal Name, etc.) to display in list view, and what order they are displayed.

To view all fields of a single citation, double-click on the citation. Note that there are more fields than those shown here, including Keywords, where EndNote places subject headings, such MeSH terms, and Abstract.

As you add citations to your Library, it is likely that you will create duplicates. To remove duplicates, select

Find Duplicates from the References menu. EndNote will scan the Library, and will then show duplicate references it detects. Duplicates will be highlighted; you can delete them all at once by choosing Delete... from the References menu or by clicking the scissors icon. Alternately, you may want to examine the duplicates and delete them singly by clicking to select it, then deciding whether to delete it.

You can change the fields EndNote examines when scanning for duplicates by choosing Preferences... from

the Edit menu. Select Duplicates from the left frame. You can then select which fields EndNote will compare, and whether they need to match exactly or if EndNote should ignore spaces and punctuation. By default, EndNote compares the author, year, and article title fields. o Note that the same article downloaded from different databases may have slightly different authors, titles,

and even journal names (some databases do not include all authors for example, or may include a longer subtitle); EndNote will not usually recognize these as duplicates.



Producing a Bibliography

When EndNote is properly installed, it will also install a set of tools in the Tool menu on Microsoft Word or in WordPerfect. These tools are necessary to produce a bibliography. EndNote knows hundreds of bibliography styles, also called output styles; you just need to tell it which to use. It’s easy to change styles, if needed.

Be sure to check the journal’s Instructions to Authors (usually available on the journal’s website) or the appropriate style manual so that you will know if EndNote is formatting references correctly.

At the top of the EndNote screen, you’ll see a drop-down menu showing the style in current use. (The

default is Annotated.) Click on the arrow to see the default styles and any you have used. Click on Select Another Style... to see a list of the 1300+ styles EndNote knows. o Alternately, under the Edit menu, choose Output Styles, then Open Style Manager.

EndNote Styles

EndNote shows you the list of styles it knows. Select (by clicking to highlight the style name) the one recommended by your publisher or instructor and click Choose. Close the window by clicking the X in the upper right corner; your selection will be saved. o You can use the Find button to locate a specific style by name, or to limit to specific categories. o The Medicine category includes many biomedical journal formats, including Vancouver Style (Uniform

Requirements for Manuscripts Submitted to Biomedical Publications). o The Psychology category contains APA style, used by most nursing journals. o Click More Info for information about the style, such as which printed edition it is based on, as well as

notes about using the style within EndNote.

Sometimes, a style will not specify whether the journal title should be abbreviated or used in full. In these cases, it uses whichever has been downloaded. To check to make sure the style is using the correct form of the journal name, after you have selected your style, go to the Edit menu, choose Output Styles, then Edit “Name of Current Style.”

In the next window, click on Journal Names in the left column. To the right will be shown various journal title formats. Depending on what the style requires, select Use full journal name, Abbreviation 1, or Abbreviation 2 (which is the same as Abbreviation 1, but with the periods removed).

Close this window, clicking Yes to save this change and return to your EndNote library.

Leaving EndNote open, open your Word manuscript. When you want to enter a reference, select Find

Citation(s)... from the EndNote tools under the Tools in Word. Find Citation(s) allows you to do a quick search of the open Library, and retrieves all matches. Highlight the desired reference. Click Insert. o EndNote also installs an icon toolbar in Word, which can be used instead of the Tools.

Alternately, you can select Go to EndNote from the Tools menu. Locate the desired reference by scrolling through the list or by using EndNote’s Search function. Insert the citation into your Word document by choosing Insert Selected Citation(s) from Cite While You Write in EndNote’s Tools menu, or from the Word Tools menu.

EndNote will embed the citation in the desired format, and append the bibliographic reference at the end of the paper. o This may not be instantaneous; if you have many references, you will probably first see a generic citation

that looks like this: {Albretsen, 1998 #11} before the formatted citation appears.

Repeat this process for each citation.

You can add or remove citations; depending on the format, EndNote renumber or re-alphabetize as necessary. Remove citations by deleting the embedded reference, which will cause the bibliographic reference to be

deleted also.

Remember to proofread your bibliography! There may be small formatting errors or even typos that you should correct manually.

Changing the Format of a Bibliography Select Format Bibliography from the EndNote Tools inWord’s Tools menu. Click on the arrow next to

With Output Style: to locate the desired output style. If the correct style is not shown in the With Output Style: click Browse and select the style from the

resulting list. When the correct style is shown, click Format. Miraculously, your citations will be reformatted and a

bibliography will be produced at the end of the paper.

Creating an Independent Bibliography

Sometimes you may want to produce a bibliography that is not attached to a paper. Here’s one way to do it, using the Export command:

Open your EndNote Library. When creating an independent bibliography, EndNote will include all references in the window.

If you do not wish to include all the Library’s references in the bibliography, use Search to locate the set of references to use in your bibliography. You can also manually select references by holding down the control key while clicking the references. Then choose Show Selected from the References menu so that only the selected references are showing.

Sorting: Although you will choose a style for the format of the references, the Export command does not sort the references in an independent bibliography. Instead, select Sort References from the References menu.

Click here to select fields to sort, and the sort order. In this example, references will be sorted first by author, then by year, then by journal title, then by article title.

This field is being sorted in descending order (Z-A or 9-0). Click the icon to change the order.

This field is being sorted in ascending order (A-Z or 0-9).

Select a style for your citations. (For more information, see page 5 of this handout.) Choose Export from the File menu. The standard Save box appears. By default, the citations will be saved as a .txt (text) file, with the same name

as your Library. The file type may be changed to .htm (html format) or .rtf (rich text format). You may name the file anything you wish, and save it wherever you like.

Open the exported file in a word processor such as Microsoft Word to edit it and to save it as a regular document (.doc). Be sure to proofread your bibliography for any formatting errors or even typos that you should correct manually.



If you simply need to print out the selected reference, select Print rather than Export from the File menu. Note that, although you select a style for the citations, you cannot change the pre-set margins and header with this option.

Inserting Linked Graphics

In addition to inserting references into your paper, you can also insert the graphics and accompanying captions that you have linked to your EndNote library (see page 5 for information on linking).

To insert a graphic: In the Word document, click to position the cursor where you would like the graphic or its citation (depending

on the bibliographic style being used) to appear. From the EndNote tools in Word’s Tools menu, select Find Figure(s). Use the text box to search your

EndNote library for the reference to which the graphic is attached. When you find the correct reference, click it, then click Insert.

Moving an EndNote Library to Another Computer If you need to move your EndNote Library to another computer, or want to share it with another EndNote user, you will need to move two separate files, which will be located in the same folder. These two files are your EndNote Library, which will have the extension .enl, and a folder with the same name as your EndNote Library, but with a .Data extension. In EndNote X, these two files can be compressed into a single file, which makes moving the file or attaching it to an email message simple. To do this, go to EndNote’s File menu, select Send to..., the select Compressed library. The library and data file will be compressed into a single file with a .enlx extension. To open this file, simply double-click it (note: you must have EndNote on your computer to open the file). Need More Help? Check the handout EndNote Tips and Troubleshooting, which covers updating filters and styles, editing styles to use journal title abbreviations, customizing your display, merging libraries, and more.

EndNote’s Help files contain a lot of very good information, and is generally well-written. Advanced users are advised to review the table of contents and read sections of interest.

And as always, you can contact Janna Lawrence, MLIS, at [email protected] or Brian Bell, MLIS, at [email protected]. Both can also be reached by calling the Briscoe Library at 567-2400 and are happy to help you with EndNote questions.

getting started with endnote x

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