EndNote Intro for Biological / Agricultural / Environmental Sciences Researchers (LIB130)

by Ruth Gustafson – November 16, 2017

EndNote is free to all UCD faculty, staff and full-time students while at UC Davis.   Below is a link to a Wikipedia comparison table listing over 30 bibliographic/reference management software programs including some that are open-access:                                                                                             http://en.wikipedia.org/wiki/Comparison_of_reference_management_software                                          Many of the software vendors also have their own comparison tables or charts.

NOTE: Instructions on this course guide are geared to Windows/PC users.

Ruth Gustafson

Student Services
Student Services and Researcher Services Librarian



In this Guide:

EndNote @ UC Davis

Author: UC Davis Libraries

EndNote, licensed for all UCD full-time students, faculty, researchers and staff, is a bibliographic reference manager which enables citations to be stored, searched, and quickly inserted into research papers in the format of many scholarly journals or disciplinary styles such as CSE, NLM, ACS or APA. You can also use EndNote as your publication PDF organizational tool, to quickly locate, access and annotate PDFs you have downloaded.

NOTE: The above webpage provides links to DOWNLOAD EndNote desktop from the UCD SOFTWARE webpage. Scroll down to EndNote, available for both PC & Mac.

NEED HELP installing EndNote? Contact UCD IT Express for assistance at 530-754-HELP (4357), Monday – Friday, 7am-6pm.


  • EndNote Training — Official Channel  [YouTube]
    • Author: Clarivate Analytics (was Thomson Reuters before 1/2017)
    • 100s of videos including class recordings and short feature clips
  • EndNote X8: For Users [Clarivate LibGuide]
    • Author: Clarivate Analytics
  • EndNote: Getting Started [UC Davis LibGuide]
    • Author: Cory Craig
  • EndNote X8 on Windows — Short Course [YouTube]
    • Author: Clarivate Analytics (was Thomson Reuters before 1/2017)
    • EndNote X8 was released in November 2016.
    • Slightly over 24-minute video.
  • EndNote X8 Guided Tour: Windows

    • Author: Clarivate Analytics (was Thomson Reuters before 1/2017)
    • Over 47-page document
    • Date: September 2016
  • EndNote X8: Little EndNote How-To Book (PDF)
    • Author: Clarivate Analytics (was Thomson Reuters before 1/2017)
    • A 115-page ebook of instructions on how to accomplish specific tasks in EndNote, such as importing references from a specific online database.
    • Date: March 2017
  • EndNote X8: Library Sharing (up to 100 collaborators)
    • Author: Clarivate Analytics
    • This webpage explains sharing an entire library or groups within, including file attachments and PDF annotations, with up to 99 other EndNote X8 or X7 users. With version X7.2 (originally for 15 collaborators), this is the first time DESKTOP users could easily share groups and or share their library’s attachments and PDF annotations.
  • Getting Started Guide for Windows (online modules)
    • Author: Clarivate Analytics (was Thomson Reuters before 1/2017)
  • EndNote X8 – Quick Reference Guide (Windows)
    • Author: Clarivate Analytics
    • Date: 2016
  • Getting Started Guide for Mac (online modules)
    • Author: Clarivate Analytics (was Thomson Reuters before 1/2017)
  • EndNote X8 – Quick Reference Guide (Mac)
    • Author: Clarivate Analytics
    • Date: 2016
  • EndNote X8/X7/X6/X5 — New Features
    • Author: Clarivate Analytics (was Thomson Reuters before 1/2017)
    • Important new features for EndNote X8: feature icons will be similar whether on Windows or Mac; Find Reference Updates enables multi-reference updating; new option to update a reference manually; recently added references are tracked by different time-spans; can now share library with up to 100 other EndNote X8 or X7 users; new Find People search field to see who you’re sharing a library with; new activity feed added for library sharers to know what changes have been made to each shared library
    • Important new features for EndNote X7: Automatically import PDFs from a selected folder; organize folders of PDFs into separate groups during PDF import; automatically rename PDFs with customized settings during PDF import; create a CV with subheadings for different publication types.
    • New to X6: One-click synchronization; PDF viewing tab; rate your references; Read/Unread article tracking.
    • New features for EndNote X5: Add and Transfer File Attachments to the Web; View and Annotate PDF files; Update References Automatically; New Cite While You Write Options for working with attached PDFs. Also allows duplicates highlighting.


You may create an unlimited number of libraries in your installed (desktop) version of EndNote but it is recommended that you only set up ONE Library and use the Groups option to set up topical segregations of your library. Each library can contain an unlimited number of references. You may then have up to 5,000 custom, smart, and combination groups in your library. With one large library you can search across the entire library and you may cleanly sync with that corresponding library in EndNote Online, which allows only one library.

Expanded with EndNote X8: Library Share with up to 100 collaborators.  New with EndNote X7.2: Sharing EndNote library with up to 14 colleagues. See http://endnote.com/product-details/library-sharing

NOTE ESPECIALLY for Science journals term lists: It is highly recommended that you bring journal term lists in before creating your EndNote library. Many of the journal styles that you may use need data from the journal name term lists to appropriately output the journal name or standard abbreviation. After you create a new library, first import your journal term lists and then import/add references into this new library.

From EndNote click Tools>Open Term Lists> Journals Term Lists. Click on the Lists Tab from the new window. Click on Journals and choose Lower right button for “Import List…” Your location for these will most likely be in C:\Program Files\Endnote X?\Terms Lists folder. After navigating to this, double-click on the Terms Lists folder and then double-click on appropriate science term lists separately to load as many as you wish. For example, if you choose Bioscience, Medical and Zoological, you will have over 11,000 journal terms.

  • Setting EndNote Preferences [Youtube tutorial]
    • Author: Southern Cross University Library
    • Highly recommended for new EndNote users. Demonstrates EndNote X7 preferences for Display Fields, PDF Handling, Find Fulltext and OpenUrl.
    • Not included but you should also consider: display fonts (allowing viewing of references in various languages); Sync; and libraries to open during program start-up.
    • NOTE: Chapter 3 in EndNote X7 Online User Guide
  • Creating Groups [EndNote]
    • Create custom groups, smart groups, and group sets to organize subsets of your ever-expanding EndNote Library.
    • See Chapter 2 on Custom Groups in the ENL X7 User guide (link above in EndNote @ UCD section) and Chapter 5 for detailed information on creating Smart Groups and Combination Groups.


  • EndNote Groups [YouTube]
  • EndNote Sync [YouTube]
    • Author: Clarivate Analytics (was Thomson Reuters before 1/2017)
    • Slightly over 5-minute video on setting up EndNote Sync for EN Desktop >< EN Online synchronization.
    • Coverage: Version X7.1+
    • Date: 2014

Step-by-step instructions for UCD Library licensed subject databases and using direct export and filters are provided for PC and Mac users from the UCD EndNote webpage (see Section 1 above) from the Filters section on the left column.

  • Direct Export for BioAg Related Databases [EndNote for Windows]
    • Most UCD licensed BioAg subject databases enable one to *directly* export source bibliographic information from the database into your EndNote Library. This is the most efficient method for building a large EndNote library very quickly. [NOTE: title link above is to Windows instructions for Direct Export of all UCD licensed databases enabling EndNote export]
    • BioAg related databases which enable Direct Export are: BIOSIS Previews; Web of Science/Science Citation Index; PubMed; CAB Abstracts; Food Science and Technology Abstracts; Agricola; Aquatic Sciences and Fisheries Abstracts; Environmental Sciences & Pollution Management; PsycINFO; Zoological Record; Fish, Fisheries & Aquatic Biodiversity Worldwide; and Wildlife & Ecology Studies Worldwide.
    • In addition, the Harvest UCD libraries online catalog and the Worldcat (OCLC Firstsearch) catalogs work with Direct Export.
    • CLASS EXERCISE: Add five references from any two databases listed above into an EndNote Library
    • CAUTION for Mac Users: Safari does not work with Direct Export — you must use FireFox.
  • Google Scholar [EndNote Import]
    • If you have not found a particular reference in online databases, before manually entering the reference, you might want to see if Google Scholar has the citation. If so, keep in mind that the bibliographic data may be quite minimal or incomplete. You can “Import” Google Scholar references into EndNote but Google only allows importing of one record at a time.
    • Search for your topic in Google Scholar, click under the item you want on the link “Cite” and then choose “Import into EndNote”. Below is a box that you can check off to “Remember my bibliography manager and show import links on search result pages.” NOTE: Google does not send coding for the reference type (book chapter, conference etc.) so the record automatically goes to the “journal article” reference format. Scan carefully each imported record in case a reference type change is needed.
  • Manual Data Entry [EndNote]
    • If your references/citations are not found in any literature database or if you wish to enter references/citations found in a print bibliography or other print source, you will need to enter the bibliographic data manually into your EndNote Library. You may also use manual entry to edit references including to attach PDFs or relative links to your EndNote references. Up to 45 PDFs or relative links may be added to each record.
    • See Chapter 5 in the online EndNote X5 Getting Started Guide for detailed information (link above in EndNote @ UCD section). Note that each record can contain up to 52 fields such as author, title, year etc with 8 custom fields available. There are 47 predefined reference types (or publication formats such as journal article, book section etc.) and 3 “unused” reference types available for customization.
    • Special Rules/Standardization: Other than author fields and corporate authors, extra punctuation or text styles should NOT be entered as the style files will provide this information. You should include scientific name italicizing and chemical/mathematical notation super/subscripting.
    • Author Entry: [Note: Place each name on a separate line] Lastname (surname), firstname Corporate name, EXAMPLE University of California Davis,
    • Journal Title Entry: Enter the full journal name (journal term lists in combination with style files can always generate journal title abbreviations, as required)
    • CLASS EXERCISE: Add one journal article (the default reference type) and one other format record of your choice (Book, book section, conference paper, conference proceedings, dataset, government document, patent, report, thesis etc.)


  • Manual Data Entry [YouTube]
    • Seven-minute overview for entering references manually into your EndNote Library including special features and syntax needed.
  • EndNote: Find Full Text
    • Author: UC Davis librarians
    • Find Full Text: NOTE — this does NOT find all PDFs but does well with recent publications. Limited to searching 250 items at one time. (If it doesn’t work, some other options are noted below and you may also manually add links/PDFs.)
    • Configure Endnote to use UC-eLinks as shown below (increases likelihood Endnote will find full text for you):
      1. Open EndNote.
      2. On the top menu: PCs: Select: Edit | Preferences | Find Full Text (tab) or Macs: Select: Endnote | Preferences | Find Full Text
      3. Check all 4 boxes.
      4. In the OpenURL Path text box, for NEW UCD-eLinks enter: https://search.library.ucdavis.edu/openurl/01UCD/01UCD_SP?                  For OLD UC-eLinks, enter:  http://ucelinks.cdlib.org:8888/sfx_local
      5. Click OK.
    • PDF Import [only EndNote X5 and newer]
      • You can Import PDFs (or folders of PDFs) of articles or other publications from your hard drive and EndNote will automatically create a record for each PDF.
      • IMPORTANT: records are attached to your PDFs only if your PDF has a DOI (Direct Object Identifier) as part of the record. You will need to add the bibliographic data yourself if there is no DOI.
      • Related:
  • Adding full text: import PDFs from a folder [YouTube]

    • View first 2:00 for class. From Swinburne library, Swinburne University of Technology, Melbourne, Australia. Three-minute YouTube video on bringing in a folder of PDFs to EndNote X5 (still applicable to X6)
  • Troubleshooting PDF imports
    Scroll down to search the KnowledgeBase for Article # 108622. This EndNote article gives suggestions if there are problems importing PDFs from your C: drive
  • PDF Auto Import Folder [YouTube}
    • Author: Thomson Reuters
    • This video demonstrates setting up the PDF Auto Import (or “watch”) folder in EndNote. This feature is new with EndNote version X7. It permits one to “… designate a watch folder on your computer and, whenever anything new is added to it, EndNote will match it to the corresponding reference and attach it.” {Published 12/16/13}

Using your class library, look at pull-down Style menu (below References and Groups options) which is pre-set to “Annotated”.

CLASS EXERCISE: Select all of your references with Ctrl-A and change “Annotated” to “Select Another Style” and look for your favorite journal and choose that style. Your formatted references will be displayed in the Preview window near the bottom or the right side.

  • Output Styles [EndNote]
    • The Thomson Reuters EndNote Output (or publication or bibliographic) Styles collection contains more than 6,000 bibliographic styles with excellent coverage of most biological and agricultural journals.
    • NOTE: The initial download of EndNote software will only install the most commonly used output styles unless you choose to load more styles immediately after installation.

EndNote’s Cite While You Write (CWYW) feature inserts EndNote commands into Word’s Tools menu (or on an EndNote tab in Word 2007 and 2010 for Windows). This provides you with direct access to your EndNote references while writing in Microsoft Word. CWYW commands enable EndNote to implement bibliographic formatting to the document that is currently open in Word. You may also generate a stand-alone bibliography using CWYW in Word and choosing the small boxed arrow icon to the bottom right of the Bibliography group in the center top pane.

See Chapter 8 in the online EndNote X7 Getting Started Guide for detailed information (link above in EndNote @ UCD section).

CLASS EXERCISES: Keep EndNote Library open and open MS Word. Paste a paragraph of any text (an abstract from a citation in your library works well) into MS Word and change style from default to a preferred style for your discipline.

CAUTION: Make sure this setting is correct — “Instant Formatting is On”

Before requesting help, first search the EndNote FAQ collection, the EndNote (software) KnowledgeBase collection, or look for an appropriate YouTube EndNote training video, online training, or webinar (see links below).

If you have strictly EndNote installation questions, contact UCD IT Express for assistance at 530-754-HELP (4357), Monday – Friday, 7am-6pm.

If you still have EndNote questions, your course instructor (listed at the top of this Library Course Guide) is your first person to contact. If your instructor is not available, a team of UCD librarians work with EndNote users and may be contacted by email. See the last link below.

As part of the UC Davis license with EndNote, technical support is available from the vendor. Years of experience of UCD librarians indicates that the most prompt and useful vendor assistance is provided by phone. If you still need assistance after trying all steps below, please call the EndNote tech help Monday-Friday, 6am-5pm Pacific Time, 800-336-4474 and at the prompt press 4, and then select the “ResearchSoft Products” option.

  • EndNote FAQs
    • Author: Thomson Reuters
    • Extensive FAQ resources focusing on: Working With Word Processors / CWYW; Compatibility, Installing, Uninstalling, and Upgrading; EndNote User Interface; Managing Libraries; Importing Data Into EndNote; Output Styles and more. If not found in the FAQ, search the “Support Knowledge Base for EndNote articles” found at bottom of this webpage http://endnote.com/support/search-knowledgebase
  • YouTube channel — EndNote training
    • Wide variety of tutorial videos ranging from 2 minutes to about an hour. Most popular videos are on: How To Use EndNote in 7 Minutes; EndNote Fast Start – Windows class; Importing Text Files from PubMed; Bibliographies Made Easy; and more. A few of the webinar classes have also been recorded and stored on this YouTube channel — these webinar recordings are usually the hour-long ones.
    • Coverage: 2007-present
    • Related:
      • Using EndNote Find Full Text (Captioned)
      • Date: 2014
        Follow the steps below to configure EndNote to use UC-eLinks to find full text:
      • 1) Open EndNote
      • 2) On the top menu: PCs: Select: Edit | Preferences | Find Full Text (tab) or Macs: Select: EndNote | Preferences | Find Full Text
      • 3) In the OpenURL Path text box, enter: http://ucelinks.cdlib.org:8888/sfx_local
      • 4) Check all 4 boxes
      • 5) Click OK
  • EndNote Webinars
    • Sign up for free one-hour to 1.5 hour sessions offered on all major areas of EndNote and EndNote Web. Sessions often have less than 10 attendees and there is plenty of opportunity to “chat” with the expert instructor. Excellent Pacific time schedules are offered 2-3 times/month for each topic. Register online and confirmation will be sent. If you need to cancel, follow the link located *below* the training steps info in your confirmation email to easily cancel.
  • UCD Librarians — EndNote Help Form

EndNote Online or my.endnote.com (formerly called EndNote Web) is complementary to your downloaded copy of EndNote but cannot replace the most powerful features of the software (desktop) version of EndNote. Use the Online version to quickly import references when not using your own computer or to share your EndNote groups or references with other EndNote users.

NOTE: See link below on EndNote versions to compare various features in EndNote Desktop, EndNote Online & EndNote Basic

CLASS EXERCISE: If you don’t already have one, set up a new EndNote Online account.

  • EndNote Online or my.endnote.com
    • EndNote Online (formerly EndNote Web) facilitates collaborative work and using EndNote Web from any internet-accessible location in the world. You may easily transfer references from your EndNote Web to your desktop Endnote or vice-versa. You can “Cite While You Write” from this Web version or your desktop version although CWYW works best from the desktop version.
    • NOTE: EndNote Web X5 is the first version to enable PDF attachments.
  • EndNote Versions — Comparison Table
    • Scroll down to gray section labeled “Compare features and capacity” to find table comparing features available in EndNote Basic versus EndNote X8
  • EndNote Online – Quick Reference Guide (PDF)

    • Author: Thomson Reuters
    • 8-page PDF of the EndNote Online booklet.
    • Date: 2015
  • EndNote Online FAQs
    • The majority of the EndNote Online (formerly EndNote Web) FAQs deal with Cite-while-you-write (CWYW), MS Word compatibility questions and Transferring References to/from EndNote Web. Additional FAQs cover importing and installation problems.
    • Related:


EndNote iPad was just released in early 2013. This is still a first generation of the iPad version but it is worth exploring for iPad users. As of June 2014, there are several iPad specific FAQs (from the first link below) and are only a few articles in the EndNote Knowledge Base. PLEASE NOTE: since EndNote is not affiliated with Apple, you will need to pay the app download fee at the iTunes store. Currently this is $3.99 (July 2014).

iPhone ALERT: If you have your EndNote Web/Online account set up, you can download an EndNote iPhone app.

  • EndNote for iPad App
    • Author: Clarivate Analytics (was Thomson Reuters before 1/2017)
  • EndNote iPad Training [YouTube Channel]
    • There are four videos on the iPad playlist 07: EndNote iPad: Sync and Settings; EndNote iPad: Importing References Using the In-App Browser; EndNote iPad: Importing Records Using Safari; EndNote iPad: Working with PDFs and Searching the Library