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EndNote Library Management

Importing Directly from Databases Into EndNote

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Direct Importing Into EndNote

Direct importing is a quicker and easier method of getting citations into EndNote than entering references manually. Depending on the electronic resource you use, there will be different steps to follow in exporting and importing your references:

To export: Select the desired references and follow the instructions in the table in the EndNote Import/Export LibGuide.

To import into EndNote: Go to the File menu, then select Import... then follow the instructions listed in the table.

Note: Import filters must be saved in the c:\program files\endnotex9\filters. [Note: x9 would be replaced with the current version of EndNote]

Working with EndNote Import Filters

A filter is a file that contains instructions on how EndNote should import references from databases and online catalogs. The filter helps to place imported data into the appropriate fields in the reference window (authors end up in the author field, journal titles end up in the journal title field, etc.).
There is a variety of filters to accommodate the various database/information provider combinations. Any of the filters supplied with EndNote can be modified, and new filters can be created or downloaded from

Using existing filters

There are two parts to using filters: choosing the right export format and choosing the right import filter.
Below is a record exported from MEDLINE in a format called Refer. The codes (%M, for example) identify the data fields: %A = author, %T = title, %J = journal title, etc. The appropriate EndNote filter uses these codes to put the authors in the author field, etc.

Once the data file has been successfully exported from the online resource, the next step is to select the proper filter within EndNote. The EndNote Import/Export LibGuide contains a table that describes export and import procedures for the most commonly used resources at the University of Toledo.

An Import option must be selected whenever a data file is imported. The EndNote filter manager can be used to indicate which import filters are given as options for import.

From the Edit menu, select Import Filters, then Open filter manager…. Using the filter manager (see below), select the filters to be displayed as import options, then close the window.

Before creating a new filter, check the EndNote Import Filters List to see if the desired filter already exists ( Save downloaded filters into the filters subdirectory of the EndNote directory.



Creating new filters and editing existing ones

EndNote includes a filter editor that allows the creation of new filters for unsupported databases or customization of existing filters (in the filter manager window, select the filter to edit and click on the Edit button). For more information about working with the filter editor, consult Help in EndNote's toolbar.

Importing PDFs into EndNote

Existing collections of PDF files may be converted into EndNote records with minimal typing and copying by extracting Digital Object identifiers (DOI) from PDF files. Scanned documents will not be imported with the accompanying bibliographic content.

To import publisher-created PDFs or folders full of PDF files (no scanned documents):

  • Select a library
  • Select Import under the file menu
  • Set import option to PDF, or
  • Select folder option to import entire folder (If the selected folder lists sub-folders, click the Include files in all sub-folders radio button to include)
  • Click the Import button to add to the library


See also: Importing PDFs


Importing Folders:


Finding Full Text with EndNote

EndNote can be configured to allow access to OhioLINK subscription full text resources through the EBSCO Linksource.

To enable access, Go to EndNote -- Edit -- Preferences – Find Full Text – OpenURL Path. Select the OpenURL check box, and enter [for UToledo users] in the OpenURL path box.

Also, enter in the Authenticate with: URL box. Then, when you either invoke the automatic find full text or authenticate (References > Find Full Text > Find Full Text or References > Find Full Text > Authenticate), you will be asked to log in at the usual UToledo authentication screen.

Preferences can also be set to optimize searching in Web of Science (formerly Web of Knowledge) and PubMed, or searching for Digital Object Identifier numbers.

Find Full Text Preferences


Working with Connection Files to Search Remote Databases from within EndNote

Connection files allow the use of the EndNote interface to search remote databases. Searching databases through EndNote is not recommended because it relies only upon text word searching. The power of PubMed and CINAHL lies in their use of controlled vocabulary and features like the thesaurus, focusing, expanding, subheadings, and limits; searching with EndNote does not take advantage of these features. For more information, consult EndNote’s online help.

To search remote databases:


The right side of the search pane has additional features:

Importing Free Full-Text Articles Into EndNote

EndNote can be used to search for and download PDF files of articles.  Before doing this, go to the Edit menu >> Preferences… >> Find Full Text.  Click beside the box for PubMed LinkOut.  You will also want to enter in the field labeled Open URL path.

In your library, highlight the references for which you want EN to search for the PDF, then from the References menu, select Find Full Text >> Find Full Text.  This may take some time to search; follow the progress in the left hand pane.  When EN finds PDFs, it saves them to\PDF  (you may choose to keep all article PDF files in this directory.) and makes a link from the record in EN to its PDF file.  Note that this does not find all full-text articles, so you may still have to use the library catalog to find them.  Also note that by using this feature, you agree to follow copyright and licensing restrictions.