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Research Guides@Tufts

Laboratory Animal Medicine: EndNote FAQs, Help, & Training

Resources for students in the Cummings School MS Laboratory Animal Medicine program and people submitting IACUC proposals.

EndNote Help & Support Options (EndNote website)

*Tufts does not subscribe to all the databases shown on the lists for import filters and connection files

Frequently Asked Questions (FAQs)

Importing References

See also this guide's page on Importing References into EndNote

Can I import references from an existing bibliography that I have composed in Microsoft Word or another word processor?

The only way to import references from a Word document or any other text file is if the contents can be "tagged" for standard bibliographic fields such as author, title, journal, and date.  You then must save the file as a text file.  For details, see the EndNote Manual section on Creating Structured Text Files that EndNote Can Import. For references which can be found in online catalogs or databases, importing references from those sources may be less time-consuming while offering the advantage of providing additional data for your records.  Other options are to copy and paste data from the original document into EndNote records.   Several attempts have been made to try to import untagged references from text documents into bibliographic databases. Examples include cb2Bib, the CrossRef Simple Text Query, the HubMed Citation Finder, and Makino Takaki's Conversion tool for BiBTex.

Can I import citation information from an Acrobat PDF document?

The more recent versions of EndNote offer the ability to import basic citation information from a PDF that has been downloaded to your computer. This feature allows you to convert existing collections of PDF files into EndNote references with minimal typing and copying by extracting Digital Object identifiers (DOI) from PDF files. This feature only works with PDFs which contain a valid DOI and can link to a website which contains the citation information in a compatible format. For details, see the EndNote Manual's section on Importing PDF Files to Create New References.

When importing from a literature database which contains multiple indexes, which import filter should I use?

Certain of our literature databases are comprised of multiple index files from many sources.  One example is CSA (Cambridge Scientific Abstracts), now part of ProQuest, which offers AGRICOLA, ERIC, Econlit, and PsycInfo, among many others.  Another is Thomson's ISI Web of Knowledge, which includes Science Citation Index, Current Contents Connect, Derwents, and MEDLINE.  Each index file uses a different database structure; consequently, EndNote provides separate filters for each one in order to enable you to import the maximum number of data fields possible.  If you have collected references from multiple databases, you can experiment with using any of the filters provided by the same vendor but you will lose some of the metadata beyond standard fields such as author, document title, source title, or publication date.

How can I view the full text of articles I've cited in EndNote?

EndNote offers three methods.  For more information, review EndNote's online help or manuals. For subscription-based journal collections, access depends on whether Tufts subscribes to the journal.

  1. Click the URL link (where available) in the URL field of any EndNote reference record.  Depending on the origins of this link, it may take you directly to an Acrobat PDF or HTML page or else to a Tufts Catalog page that will provide links to the source. 
  2. If you have downloaded a PDF or other document containing the text of your article to your hard drive or a networked server, link to the file through the File Attachments field within the appropriate Reference record.  Then click the resulting file icon to open the text.
  3. For the most recent versions of EndNote X, in the Browse window of EndNote, select one or more references and right-click to select the Find Full Text... menu option.  For this to work with Tufts' subscriptions, first go to Edit Menu > Preferences > Find Full Text.  In the resulting screen, make the following selections:
    • Select all four checkboxes for Find Full Text.
    • In the OpenURL Path field, enter:
    • Click OK
      This feature works ONLY with databases which are either open access or to which Tufts has a subscription AND which support the OpenURL protocol.  It may not work reliably when using EndNote from outside the Tufts network.

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Creating Bibliographies

See also this guide's page on Creating Bibliographies in EndNote

How can I print ALL the fields from one or more EndNote references?  The typical output styles only display selected fields.

Two options:

  1. Use as the Bibliographic Output Style the default Show All Fields style. This will display any field in an EndNote record which contains some content.
  2. Create a new Output style which includes all the fields.  You must specify all the fields for each reference type you are using and make sure the fields are appropriately separated by commas, line breaks, and other punctuation.  For details, see the EndNote Manual's section on Modifying Style Templates.

What is an Annotated Bibliography and how do I create one in EndNote?

In addition to presenting a set of references in a specific citation output style, an annotated bibliography also includes additional information.  This usually is a commentary by the person producing a bibliography but it could also contain abstracts for each reference or research notes.

Two options:

  1. Use as the Bibliographic Output Style the default Annotated style. This will display the contents of the record's Abstract field.
  2. Create a new Output style which includes the field(s0 which contain your annotations. You must specify these fields for each reference type you are using and make sure the fields are appropriately separated by commas, line breaks, and other punctuation.  For details, see the EndNote Manual's section on Modifying Style Templates.

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Formatting Issues

When I preview my bibliography in my selected output citation style, the citation formatting in some of my references appears incorrect. Why?

Several reasons can account for this:

  • Your references aren't coded for the proper Reference Type, such as Journal Article, Book, or Conference Proceeding. Some references import into EndNote as a "Generic" document type. Try changing the reference type in the problem references and then preview the bibliography again to see if the changes resolved the issue.
  • You are using the wrong version of a particular style.  Some citation styles have multiple versions or variants, for example, Chicago has a Notes & Bibliography and an Author-Date style.  APA and MLA recently introduced new versions of their styles .  Experiment with different versions of an output style family by selecting on various styles in the style pull-down menu.  Check the Access Output Style Manager... option at the bottom of the Output Style menu in the Bibliography window  for additional output filters ((you may need to download additional styles from the EndNote Support website).
  • If the references were imported from databases rather than created manually, the source database may have exported data in a format that conflicts with your selected citation style.  For example, you might need to use the full author name, but the data source only exports the first letter of the author's first name.  In such cases, you either have to edit the references manually or else see if the references you are using are available in another database that uses a different export format.
  • Your selected output style has requirements that EndNote finds difficult to comply with (often this reflects some murkiness on the part of the style's requirements).  Possible work-arounds:
    • Modify troublesome references so that they appear in the proper format.  This may entail changing the Reference Type, moving data into different fields, or changing the contents of a field.
    • Clone the output style and modify the defaults for particular fields within particular reference types.
    • Export your bibliography or citations into an editable document and make the edits in that document.  While that is not an optimal solution for ongoing citation management and running multiple versions of a bibliography, it is necessary with some styles.

Why does the casing (titling) in my citations appear incorrectly?

For titles of articles and journals and for author names, citation styles provide general rules about the casing.  The EndNote Output filters apply either title casing or sentence casing, or enables the citation record's approach determine the casing.  These approaches can be controlled by selecting an import filter in the Edit Menu > Output Styles and then editing the Title Capitalization options. The filters cannot, however, make exceptions to these rules for specific words or types of words such as proper nouns.  For that, use the Edit Menu > Preferences > Change Case feature; here you can specify all words which case must remain as entered in the records (these rules will be applied to all output styles).

Why do some of my imported references show peculiar characters?

The presence of peculiar characters in EndNote references usually is caused by a conflict with character sets.  The newest versions of EndNote default to Unicode (the universal character set) but some databases may use other encoding such as ANSI or ISO character sets that only contain a character subset, usually to accommodate non-Roman alphabets.  One workaround is to check the encoding that is used in the database you are trying to import records from (this usually is a command in your browser's pull-down menu).  Take note if it is not Unicode (UTF-8) compliant.  Then experiment with importing the records using the character encoding used in the source database.  You can specify the encoding in the EndNote File Menu > Import screen, in the option for Text Translation.

Note: Records in the Tufts Library Catalog which contain specific character sets, such as those used by Slavic languages, seem to cause generate character translation errors regardless of the Text Translation filter used. Once imported into EndNote, these records need to be modified on a case-by-case basis or by using (carefully) using the EndNote Change Text command.

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Working with Word Processors

The Cite-While-You-Write (CWYW) Utility isn't working properly.  Why?

Several reasons can account for this:

  • CWYW isn't installed properly on your computer.  Make sure that your Word configuration has the CWYW components loaded.
  • The version of CWYW you are using is incompatible with your version of Word or you haven't installed the most recent updated version of EndNote.  Check the EndNote website for current installation requirements and download new updaters for EndNote as necessary.
  • Your method of inserting citations is incompatible with your selected output style, for example, you are inserting in-text citations for a style that calls for footnotes.  Try stripping the document of all existing references and then re-inserting them.

If none of the above methods work, contact EndNote Technical Support

I've split my thesis (or book project or other lengthy document) into separate Word files.  From these files, I want to generate a composite bibliography with continuously-numbered endnotes or footnotes.  Is this possible with EndNote and CWYW?

You can generate a composite bibliography if you use Word's Master Document feature, which requires embedding multiple documents as Sub-documents within a Master document.  For instructions, see the section within the EndNote manual on Creating a Bibliography from Multiple Documents.  Alternatively, once your document is essentially complete, you can combine all the Word files into a single and then generate the bibliographies and citations from that.

I am using a single Word document, the content of which is divided into multiple chapters.  I want to generate separate bibliographies at the end of each chapter.  Can I do that with EndNote and CWYW?

Yes.  First, you need to use the Word Insert Section command to specify the start of each chapter.  Second, you need to ensure that the EndNote filter for your selected output style (APA, MLA, etc.) knows to generate multiple bibliographies.  Some styles do this automatically.  Others require that you modify the existing output filter to do this. For instructions, see the section within the EndNote manual on Creating Multiple Bibliographies in a Single Document.

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EndNote Online (EndNote Web)

What is EndNote Online and how do I access it?

EndNote Online (previously known as EndNote Web) is a subscription-based, web-based offspring of EndNote.  It is less powerful than EndNote, offering fewer customization options, utilities, and functions, and only supports 10,000 records whereas EndNote libraries can be unlimited in size (a comparison of the two products is available on the EndNote website). It is handy for situations where EndNote users cannot easily access their EndNote installation (for example when traveling) and offers strong integration with ISI Web of Science and Researcher ID (which, like EndNote, are provided by Thomson Reuters). It also can be used as a collaboration tool.  If you are interested in a web-based citation manager, you may also want to consider Zotero or Mendeley (see our comparative matrix).

Licensed users of EndNote may set up an EndNote Online account for free.  EndNote Online is also available for current Tufts students, faculty, and staff who can access Web of Science; online accounts are created by clicking the EndNote link in the top of the Web of Science screen.