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Publishing Resources for STEM Authors: EndNote online

A guide with resources to accompany the workshops on publishing for gradute students and post-doctoral researchers.

EndNote online

EndNote online (

The online version of EndNote, while significantly less sophisticated and powerful than the parent EndNote software has the advantage of being free to any user, (Note: Institutional subscribers to Web of Science obtain access to a somewhat more powerful version.) and so a reasonable choice for students and others who may not need all the features but would like to use a PBS package, and, since it is based on Thomson's servers you can access it anywhere on any computer connected to the Web. Moreover, it is a very useful tool for collaborative research efforts: multiple users can share libraries of references, and cooperatively edit Word documents.

In addition to the information below, you may wish to consult some of the excellent online tutorials at provided by Clarivate Analytics. Tutorials are available in a variety of formats (including MP4 and WMV), and require a current Flash player for viewing.  You may also want to look at the EndNote Web help pages ( and the UCSB Library's guide to EndNote ( and the PDF guide to EndNote Web.

Creating an EndNote online account

  • Note that an account created for EndNote online also serves as an account for ISI's Web of Science databases (e.g. Web of Science, BIOSIS) for saving searches and setting up alerts and as an account for ResearcherID, and vice versa. Note, too, that EndNote online has very specific requirements for the number and type of characters in a password.
  • From the login screen (see below), if you are not already registered, click on the  Sign up link and follow the instructions.  If already registered, just log in.  (Note: UCSB does not yet have Shibboleth identity verification set up.  When we do, you would be able to log in using your UCSBnetID and password.)
  • You will first be prompted to enter and confirm an e-mail account.  Note that you do not need to use a UCSB e-mail account; indeed, if you want to keep the same EndNote account after graduation, you are better off using a commercial e-mail account. If you have already created an account using that e-mail, you will be notified, and prompted to login or reset your password.
  • Note that you can both sign up and log in  using a Facebook or LinkedIn account.  Your EndNote account will then be connected to the email address you used on that account.

EndNote web login screen


The EndNote online library screen

  • Here's an example (below) of the screen displayed after login, for a user who already has some collected references.
  • In the band at top, there is a "Welcome, <user's first name>" message, links to Web of Science, ResearcherID, Welcome *User* and Help.
  • Below that, there are tabs for the different functions of EndNote Web: My References (the opening default screen), Collect, Organize, Format, Match and Options. Further right are tabs for Connect, the online EndNOte user community, and Adminstrator Options.
  • On the My References screen, note the panel at left which allows you to select which group of references you wish to display, and to do a quick search of the references.  Note that if you have used ResearcherID to identify articles you have authored, the ResearcherID groups are listed there.
  • In the body of the screen, the brief records in the group are displayed.  One dropdown menu allows you to control the number of records displayed per page; another allows you to control the sort order (default is alphabetical by First Author; others are Year (of publication), Title, Source Title, Times Cited, date Added to Library and date Last Updated. Other links allow you to move between screens.
  • Each brief record displays the first author, year of publication, document title (linked to the full record), journal name (if applicable), the date the record was added to the EndNote library, and the date it was last updated, a link to the Web of Science record for the item (if available), and, for UC users, a UC-e-Links button. Note: if off campus, log into the Off-Campus Access (proxy server) before goint to EndNote to make best use of this feature.


EndNote basic personal home page


  • Below is an example of a full document record for a journal article from EndNote Web.  Note that the fields displayed will vary depending on the type of document and the information available when the record was entered
  • If you hover your cursor over a field in the full record, it becomes highlighted.  Click on the field to edit it. Note the link on the right-hand side of the screen that enables you to display currently empty fields for viewing and/or editing.
  • Note the magnifying glass by each author's name.  Clicking on it will search your EndNote Web files for that author.

EndNote online full record, pt. 1

EndNote online full record, pt. 2

EndNote online full record, pt. 3

Collecting References

  • Hovering the cursor over the Collect tab, or clicking on it displays the three options for adding records to your EndNote Web library: Online Search, New Reference and Import References.
  • The Online Search option allows you to search online databases using EndNote basic itself as the search interface.  I do not recommend this option for the following reasons:
    • Not all databases are available for searching through EndNote basic. That long, long list on the drop-down menu is composed mainly of library catalogs from universities around the world -- not usually a prime source for chemistry, biochemistry and other science and engineering searching.
    • Also note: in the vast majority of cases, the EndNote user interface will be less sophisticated and less powerful than the normal user interface of the index in question which may negatively impact your search results.
  • New Reference lets you create a reference record manually.  See below for a representative screen shot
  • Import References lets you take a downloaded answer set from an electronic database and import the entire group of records into EndNote Web.
  • Note that Web of Knowledge databases (as well as a handful from other vendors) allow you to export answer sets directly to EndNote Web, skipping the import step.

New References

  • This is the option for manually entering references.  Note the drop-down menu for Reference Type.  If you select a reference type, EndNote Web will display the fields that are most relevant for that reference type (journal artilce, patent, dissertation, etc.)  Note that there are separate reference types for articles and electronic articles, books and electronic books, etc. The screenshot below is the Generic record type.
  • Click on a field box to open it for enttry.  In the example, I have filled several fields, and opened the Number of Volumes field for entry. When you have entered data, the Cancel and Save buttons will appear at the bottom of the screen.
  • Once saved, your new reference can be manipulated just like an imported reference.

EndNote Web new reference entry, part I
EndNote new reference entry, part II
EndNote Web new reference entry, part III

Importing References

  • The Import References option is used to bring in sets of references from downloaded files.  Note that most databases will have some sort of export option.  Choose the one most appropriate for exporting references to EndNote, and save the file.
  • The file window allow you to enter the name and location of the file you wish to import.  The Browse button lets you look through the directories available on your computer for the desired file.
  • The Import Options drop-down menu lets you specify which database and vendor you are importing from.  EndNote and EndNote Web have extensive lists of possible database/vendor combinations - make sure you choose the one that corresponds to the answer set you are importing.  The Select Favorites link lets you create a list of the databases you use most frequently to save time.  If you have selected one or more "favorites", only those databases will show up in the drop-down menu.  If you need a different database, use the Select Favorites option to add it to your favorites list at least temporariy.
  • Note that many database vendors (including SciFinder) now allow you to export references as a .RIS file, so it's a good idea to have RefMan RIS on your favorites list.
  • The To: dropdown menu lets you select which of your EndNote Web folders you'd like the reference(s) to be placed in.  For creating folders, see the Organize section below.

EndNote Web import references screen

Organize References

  • Hovering your cursor over, or clicking on Organize reveals the organzing options: Manage My Groups, Others' Groups, Find Duplicates and Manage Attachments.
  • Manage My Groups allows you to add or delete groups, and, if desired, open up groups for sharing with other EndNote Web users.  To share a group, click the check box under Share, then click the Manage Sharing button.  From the next screen you can add or delete the e-mail addresses of thoe you wish to share references with.  Sharing may be "read-only" or "read and write". Note that you can have different sharing arrangements for each folder if desired.  In the example below, I've elected to share the "My Publications" folder from ResearcherID.  The "group" icon to the left of the folder name indicates that it's being shared.
  • Others' Groups is only relevant if other users have elected to share with you.
  • Find Duplicates searches your EndNote library to determine whether you have duplicate reences entered.  If it detects them, you have the option to delete selected duplicates.
  • Manage Attachments refers to PDF copies of documents and other files attached to your EndNote records.  Note that this option only works if you also own a registered copy of the desktop version of EndNote.

EndNote Web manage groups screen

Formatting References

  • Hovering your cursor over, or clicking on the Format tab displays the options: Bibliography, Cite While U Write Plug-In, Format Paper and Export References.
    • Bibliography lets you create stand-alone bibliographies from selected references in your EndNote library in a selected citation style (see below.)
    • Cite While U Write Plugin has links for downloading a plug-in (for either Windows or Mac OS) which links your EndNote library to Microsoft Word, allowing you to insert "live" footnotes into and bibliography into a Word document, which will, for example, automatically renumber footnotes if you rearrange your document. For more information on using Cite While U Write, see the EndNote tutorials or the Cite While U Write section of the UCSB Library's EndNote Desktop guide.
    • Format Paper allows you to take an RTF format document containing partial citations and convert it to fully formatted footnotes and bibliography using your chosen citation style from within  EndNote Web.  For more intfomation on using Format Paper, see the relevant EndNote Web help page.
    • Export References allows you to export selected references in a variety of file formats (EndNote, BibTeX, RefMan, Refer, and tab-delimited.)


  • This option allows you to save as a file (HTML, RTF or TXT), e-mail or print a formatted bibliography.
  • To use, first select the references in your EndNote library you wish to include using the upper drop-down menu.
  • Then, select the bibliopgraphic citation style you wish to follow.  Since there are hundreds of citation styles to choose from, it is advantageous to create a "favorites" list, using the "Select Favorites" option.  Once you have done so, only your "favorites" will appear in the main drop-down menu.  You can always add or delete favorites from your list by using the "Select Favorites" link.
  • Then, select the file format you wish to use, and click Save, E-Mail or Preview and Print.  It is usually a good idea to preview your bibliography before printing, e-mailing or saving it, to make sure you have the right references, are using the correct format and have all the requisite information in your records.

EndNote online create bibliography


  • When downloaded and installed to a computer with Microsoft Word, the Cite-While-You-Write plugin adds a menu item to the top menu bar in Word.  Note for Macintosh users:  You may need to go into the Preferences for Word and select EndNote online as opposed to EndNote.  If this is not done, the plugin will search for the EndNote desktop software on your computer, and, unable to find it, give you an error message.
  • Clicking on the EndNote Web menu tab will open a login screen.  Once you have logged into your EndNote online account, a new menu bar will become available.

EndNote CiteWhileUWrite menu bar for Microsoft Word for Windows

EndNote CiteWhileUWrite menu bar for Microsoft Word for Windows

  • While typing a document, the Insert Citations button will open a window allowing you to search your EndNote Web database and select a citation to insert.  It will appear in the style selected in the drop-down style menu.  Note that the style menu contains those styles which you have added to your Favorites list in EndNote onlne. You may search by author, year of publication or title keyword.  Select the desired citation and click Insert to enter the footnote and add the reference to the bibliography.

Cite-While-You-Write reference search

  • To change citation styles, simply select a new style from the dropdown menu.  If you edit the document (e.g. cutting and pasting sections), clicking the Update Citations and Bibliography link will rearrange and renumber (if necessary) both the citations and bibiliography.


  • This new feature does not relate directly to creating a database of bibliographic references.  Rather, it is designed to help scholarly authors select potential journals in which to publish their research.
  • To use Match, enter the title and abstract of your paper.  If you will be using references from your EndNote database for the paper, select the folder containing the references, and click Find Journals
  • Comparing your keywords and refeences to papers in the Web of Science database, the system will suggest likely journals. See example, below.  (Note: the journals suggested are *not* the journal in which the article was actually published!)

EndNote online Match entry screen

EndNote online Match results, pt. 1

EndNote online Match results, pt. 2

  • Links from this screen will take you to the journal's submission page, and/or to information about the journal from the publisher's website.


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