IMPORTING PDF FILES ON WINDOWS
EndNote can import PDF files containing a Digital Object Identifier (DOI) in the metadata or on the first two pages of the PDF. EndNote sends the DOI to PubMed and CrossRef, online databases capable of looking up reference data by DOI. The online databases send back the bibliographic information, EndNote imports it, then attaches the PDF to the record created. This means the PDF must have a DOI and EndNote must have access to the Internet during the import.
3.1.1 Importing a Folder of PDF Files on Windows
- Select 1) Import from the File menu, then 2) Folder.
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1) Click the Choose button, navigate to the folder you want to import, and double-click on it. It will appear in the Import Folder: field. 2) If you wish to include subfolders within that folder, mark the box labeled Include files in subfolders. 3) If you want EndNote to create a separate group set for the main folder and groups within it for the subfolders, mark the box labeled Create a Group Set for this import. Leave the other settings at their defaults. (Note that in EndNote X7 or above, the program will attempt to attach PDFs to matching records that already exist in the library instead of creating duplicate records.) 4) When all your options are set, click the Import button.
The PDF files are imported. Below you see an example of the group set and groups that would be created for a folder called New PDF Examples that contained a folder called Bats and a folder called Birds.
Source : Little EndNote How-To Book.