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Everything EndNote

Creating and setting up an EndNote library

Creating an EndNote library

1. Once installed, open EndNote by double-clicking on the EndNote icon OR by locating EndNote on the computer's hard drive.

2. Depending on the program's preferences, you may see differing options here: the most recently-used library may open or you may see a blank EndNote application window. To create a new library, go to File > New.

3. Name your library (the default name for a new library is "My EndNote Library") and pick a location on your computer's local hard drive where the library will be saved.

Do not save EndNote Libraries in synced cloud storage folders or on network drives such as OneDrive, iCloud Drive, Google Drive, Dropbox, etc., or OHSU network drives (H: or X:). EndNote libraries are not just simple files, they are databases, and they can become corrupted if they are stored anywhere other than on your computer's local hard drive.

4. Click Save. Note: EndNote libraries are comprised of two separate parts (the EndNote library, which has a .enl extension, and an associated data folder). Both parts will be saved in the specified location.



Setting up an EndNote library


Once you have created a library, there are a number of functions and options built into EndNote that allow you to optimize and customize your library.


Choosing and customizing Display Fields


You can choose up to ten fields to display as column headings in your library (note: all fields will still appear within each Reference)

1. Go to Edit - Preferences.

2. Choose Display Fields from the left-hand list.

3. Choose your desired field for each column from the drop-down menus. Note: If you want to remove a column so that fewer than ten fields appear, you can choose "[Do not display]" from the drop-down menu.

4. You can also choose to display Custom fields and rename those fields as desired.


Using the Find Full Text function


EndNote can look for the full text of articles freely available on the internet and articles available through the OHSU Library's journal holdings.

1. Go to Edit - Preferences

2. Choose Find Full Text

3. Make sure these options are checked: DOI, PubMed LinkOut and OpenURL.

4. In the OpenURL Path box, if it does not already appear there, paste the following link (without quotes): ""

5. In the Authenticate With box, use this link (without quotes): ""


6. If desired, check the Automatically invoke Find Full Text on newly-imported references. If this box is checked, EndNote will search both free sources and OHSU Library holdings for a .pdf version of the article in question and attach it to the Reference in question.


Using Term Lists


1. To ensure that your bibliographies will be formatted correctly, you should import a journal term list before you add any references to your library. The journal Term List includes journal name abbreviations, which may differ according to the bibliographic style used (NLM, APA, etc.)

2. Go to the Tools > Open Terms Lists > Journals Term List.

3. A blank table will appear. Click the Lists tab, highlight Journals, then click Import List.

4. Navigate to your EndNote folder: C Drive>Program Files>EndNote and choose the Terms Lists folder. Select the subject area for the type of references you will be working with (Medical, Chemical, BioSciences, etc.) and click Open.

5. The table will be filled with full journal titles and their official abbreviations. You can check this by clicking back to the Terms tab.


6. You can repeat these steps to include more than one journal list.

Adding references to your library

There are multiple methods for adding references to an EndNote library. References can be manually added to a library, imported from a database such as PubMed, or they can be added directly from the EndNote interface.

Manually adding a reference

References can be manually added one at a time to EndNote. This is the most labor-intensive and, in most cases, least efficient method of adding references. Manual entry of references should only be used when you are otherwise unable to locate the reference in a database.

    1. In EndNote, go to References > New Reference.

    2. A blank New Reference box will pop up. Select the correct Reference Type (the default is Journal Article). You can then manually add information about author, date, title, etc.

    3. The reference will automatically be saved and added to your library once you close the New Reference box (by clicking the X in the top right corner of the box).

Importing references from a database search


When searching PubMed, there are two ways to save citations into your EndNote library. If you are working with fewer than 200 results, you will likely want to use the Citation manager option. For result sets greater than 200, you will likely want to use the plain text file method. Before importing/exporting results, be sure you have the latest EndNote import filters for the databases you are searching installed on your computer.

Citation Manager option in PubMed (use this method if you have LESS than 200 PubMed citations to add to EndNote)

    1. Perform your search in PubMed.

    2. Select the references you want to save.

    3. From the Send to drop-down menu, choose Citation manager. Be sure the Number to send will capture all of your search results (e.g. if you have 75 results, Number to send should be at least 100).

    4. Click Create File

    5. Depending on your browser, the next steps will vary.

    • XIn both IE and Firefox, you will choose to open the file. In IE, the file may go to your Downloads folder. Either way, you should be presented with an option to choose a program to open the file.

    6. If EndNote is not already selected in Open With, select Other in the drop down box, navigate to EndNote and select it.

    7. If EndNote is open on your computer, the citations will import into EndNote. If EndNote is not open, you will be asked to choose a library to which the citations will be added.

Exporting References from PubMed as a Plain Text File (use this method if you have MORE than 200 PubMed citations to add to EndNote)

    1. Perform your search in PubMed.

    2. Select the references you want to save. If you want to export the entire set of results, do not select any references.

    3. From the Send to drop-down menu, choose the File destination. From the Format  drop-down menu, choose MEDLINE.

    4. Click Create File.

    5. Save the downloaded file to your desktop, downloads folder, or other easily discoverable location.

    6. In EndNote choose File > Import > File.

    7. In the Import File field, click Choose, locate the file you just downloaded, select it, and click Open.

    8. In the Import Option field choose PubMed (NLM). Note: the first time you do this, you will need to choose Other Filters and then select PubMed (NLM) from the list of import filter options.

    9. Click Import and the records will be imported into your EndNote library.

Importing references from other databases

Ovid databases

Ovid databases (e.g. Ovid MEDLINE, PsycINFO, etc.) available to OHSU library users include an option for direct export into EndNote.

    1. Perform your search and select the references you want to save.

    2. On your desktop, open the destination EndNote library for the references.

    3. In Ovid, select Export.

    4. In the Export Citation List box, select Export To > EndNote. If you want to include all of the citation information, be sure to choose Select Fields to Display > Complete Reference.

    5. Click the Export Citations button. The references will automatically be added to the open EndNote library

OHSU Library Catalog

References to books and other materials in the OHSU Library catalog can be added to EndNote using the Export feature.

    1. Search the library catalog for your item.

    2. Once you have identified the appropriate book or other record, find the drop-down menu Save/Export Options on the right side of the page. Select Export RIS. (Note: Using the EndNote export option in the drop-down box will direct you to EndNote's web version. Do not use this method if you want to add the reference to an EndNote library on your hard drive.)

    3. A Push to RIS box will open; click Ok.

    4. Save the RIS file to an easily discoverable location.

    5. In EndNote, choose File > Import.

    6. Locate the file you just downloaded (it will have an .ris extension) and select it.

    7. In the Import Options field choose Reference Manager (RIS). Note: the first time you do this, you will need to choose Other Filters and then select Reference Manager (RIS) from the list of import filter options. Click Import.

Other databases

The steps for importing references from other databases accessible through the OHSU Library follow the same basic principles as those for importing references from PubMed. Once you have identified a set of references you want to add to your EndNote library, you need to export those references by creating and downloading a file to be imported into EndNote. It is important that the correct Import Filter is selected in EndNote in order for EndNote to be able to read the file that is being imported. The Import Filter you choose will be determined by the database.

Adding references directly from EndNote

You can also search databases such as PubMed directly in EndNote and add references from there. This method should generally not be your first choice for adding references, and is most effective when you are searching for a specific reference that you know, for example, is indexed in PubMed. This guide from EndNote provides detailed instructions on how to search for and add references directly from EndNote.

Adding a reference from a .pdf

You can create a new reference directly from a pdf in many cases. EndNote uses the Digital Object Identifier (DOI) that is embedded in the .pdf to create a new reference. If the .pdf does not have a DOI, the PDF will be imported, but you will need to edit the reference once it is created. For that reason, be sure to check references created from .pdf for accuracy once they have been added to EndNote.

    1. Go to File > Import and choose File or Folder (depending on whether you are importing one or multiple .pdfs).

    2. Click Choose and navigate to the .pdf.

    3. In the Import Options drop down box, select PDF.

    4. Click Import. A new reference will be created with the .pdf attached.

Creating and formatting a bibliography

1. In Word, position the cursor after the text you are citing.

2. Still in Word, go to EndNote X8 > Go to EndNote

3. Open the relevant EndNote library and highlight the reference you want to cite.

4. From here, there are a number of ways to add the citation to your paper:

5. In Word, go to Tools > EndNote > Insert Selected Citation

6. In EndNote, go to Tools > Cite While You Write > Insert Selected Citations

7. With both Word and EndNote open, you can copy and paste or drag and drop the reference into the spot in your document where you want to cite it. (Note: this method will also work with other word processing programs.)

8. Whichever method you use, the reference will now appear in your Word document.

Formatting your bibliography

Formatting Your Bibliography

Once you have inserted citations into your paper, you can format (or re-format) your bibliography at any time, just be sure your EndNote library is open. The formatted references will automatically be added to the end of your Word document.

1. In Word, go to EndNote X8 > Style and select the bibliographic style you want to use.

2. If you do not see the style that you want to use in your list of options, click Select Another Style to see all available bibliography formats and select the one you want to use.

3. This is not a complete list. Additional output styles are available to download from EndNote's website (here) or may be provided directly from individual journals.

4. You can change the font, size and other features of your bibliography. Go to EndNote X8 and click the small arrow in the lower right corner of the Bibliography box. This will open the Configure Bibliography box. Click the Layout tab to make changes to the appearance of your bibliography.

Creating a stand-alone reference list or bibliography

There may be times when you will want to create a stand-alone reference list or bibliography that is not otherwise part of a Word document

1. Select the references in your EndNote library you wish to include in the bibliography

2. In EndNote, go to File > Export

3. Name the file, Save file as type > RichText Format and select your chosen Output Style

4. Click Save (be sure to note where the file is saved).

5. Now you can open the file in Microsoft Word as a stand-alone bibliography