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Veterinary Medicine

Resources to support study and research in veterinary sciences.

Moving from files of PDFs to citation management

Many researchers who wish to begin using a citation management tool need a way to transition from a collection of PDFs on their computers.  The desktop versions of both EndNote and Zotero can assist with this by importing PDFs and extracting citation information from at least some of them.

Zotero is generally more effective at this task.  Instructions are given below for importing PDFs using EndNote, Zotero, and a combination of both tools.

Importing PDFs using EndNote Desktop

  1. In EndNote, Select File > Import
  2. Choose File to import a single PDF, or Folder to import all the PDFs in a folder.
    1. To import a single PDF file, click Choose then navigate to the location of your file or folder on your computer.  Choose PDF as your import option.  Click Import.
    2. To import a folder of PDFs, click Choose then navigate to the location of your file or folder on your computer.  Select “Include subfiles in folders” if you want to import files from multiple, nested folders.  Click Import.
  3. If the PDF has metadata that EndNote can identify, it will import the file as a citation with an attached PDF.  If EndNote cannot parse the PDF file, it will import just the PDF.  You can add citation information to this record by hand.
  4. Double-check the automatically added citation information for accuracy.

Importing PDFs using Zotero

  1. In Zotero, select the collection (folder) to which you want to add your files.  Drag and drop your PDF file(s) from your computer into Zotero.
  2. Select the PDFs in Zotero, then right-click (command-click) to get the context menu. 
  3. Select “Retrieve metadata for PDF(s).”
  4. If the PDF has metadata or text that Zotero can identify, it will convert the PDF to a citation with the PDF attached.  If not, it will retain the PDF, and you can add citation information to this record by hand.

Importing PDFs using Zotero, then transferring the citations to EndNote

This option often results in more PDFs successfully converted to citations than importing to EndNote directly.

  1. Follow the instructions above for importing PDFs in Zotero. 
  2. In Zotero, select the citations you want to export, right click (command-click), and choose Export Items from the context menu.  (If you want to export your whole Zotero library, you can go to File > Export Library instead of selecting specific citations.)  Choose RIS as the file format, and save it somewhere on your computer where you can find it.  
  3. Choose whether to import to EndNote Desktop or EndNote Online.  Either:
    1. In EndNote Desktop, choose File> Import > File.  Choose the file you just exported from Zotero.  Choose Reference Manager (RIS) as your import option. 
    2. In EndNote Online, choose Collect > Import References.  Browse to the file you just exported from Zotero and choose Reference Manager (RIS) as your import option.
  4. The attached PDFs will not transfer with the citations.  To get PDFs attached to your citations in EndNote:
    1. Let EndNote Desktop try to find copies online.  Select your citations (no more than about 20 at a time to prevent publisher websites from mistaking you for a bot.)  Click “Find Full Text”.
    2. If you use EndNote Online, or if EndNote Desktop did not find PDFs for all citations, drag your PDFs over to the citation in EndNote from the corresponding citation in Zotero.