If you have multiple folders in Mendeley Desktop, you will have to export each folder separately. The only alternative is to export your entire library (all your references) and rearrange them in EndNote.
Moving your PDFs to EndNote
Step 1
The first thing you should do is to move your PDF files from Mendeley to EndNote. To do this, open EndNote. Click on File>Import>Folder: (To find out where Mendeley has saved your PDF files, first skip this step and proceed to Step 2)
At Import Option, select PDF:
At the Import File bar, click on Choose and then navigate to where Mendeley has stored your files:
Step 2
Mendeley Desktop:If you are unsure where your files are saved, open Mendeley Desktop and click on Tools>Options:
Then click on the File Organizer tab. The path at the top indicates where your PDF files are stored:
Mendeley Reference Manager:
Please note, most of your PDF files are very likely to be stored online and are not stored on your hard drive. To download all of your PDF files, first take the following steps:
In Mendeley Reference Manager, right click on All References and select Make available offline:
It will take some time to download your PDF files, depending on how many you have.
With Mendeley Reference Manager, your PDF files are usually stored here:
C:\Users\YOUR USERNAME\AppData\Roaming\Mendeley Reference Manager\userfiles
EndNote will automatically import all of your PDF files and generate references with the information stored on each file.
In Mendeley:
Select the records you wish to export. You can click Edit > Select All if you want your entire database.
Click on the File menu > Export
Change Save As Type option to "RIS - Research Information Systems"
Pick a name and location for the file and Save.
You will end up with a file titled "My Collection.ris."
In EndNote:
Click the File menu > New to create a new library.
Click on the File menu > Import File.
Click Choose and browse to the "My Collection.ris" file you downloaded and click Open.
Change the Import option to Reference Manager (RIS).
Click Import.
This will import your Mendeley records into this new EndNote™ library.
You can also try the following steps instead:
In Mendeley:
Select the records you wish to export. You can click Edit > Select All if you want your entire database.
Click on the File menu > Export
Change Save As Type option to "EndNote XML"
Pick a name and location for the file and Save.
You will end up with a file titled "My Collection.xml" and a folder titled "My Collection.Data."
In EndNote:
Click the File menu > New to create a new library.
Click on the File menu > Import File.
Click Choose and browse to the "My Collection.xml" file you downloaded and click Open.
Change the Import option to EndNote generated XML.
Click Import.
Click the File menu > Exit
Open the "My Collection.Data" folder.
If there is a PDF folder, copy it to the new .Data folder created with your EndNote Library. If you created a library titled "My EndNote Library," there will be a "My EndNote Library.Data" folder.
When you open the library in EndNote again, you will have the working attachments.
Please Note: The steps below will work with Mendeley Desktop only and cannot be used with the Mendeley Reference Manager or for documents used with Mendeley Cite.
Document Conversion:
In order to convert a document created using Mendeley's "Cite-O-Matic" tools, it needs to be formatted in a custom style. You will find a copy of the custom style in the Attachments section at the bottom of this article. Download the "Mendeley-to-Endnote-Title.csl" file:
Now add the custom style to the Mendeley program.
Adding the custom style to the Mendeley program:
Open Mendeley and click View > Citation Style > More Styles.
Under the Installed tab, please drag and drop the custom style.
In Word follow the steps below:
Open Word, click the References tab, click on Style dropdown > More Styles.
Select Mendeley-to-Endnote-Title and click OK. Now references will display only the title in the open and close curly braces: {Title}.
Open the EndNote library and the document formatted using the "custom" style.
Save the modified document with a new name.
Press [Ctrl]+A on the keyboard to highlight everything.
Press [Ctrl]+6 (above the "T" and "Y" key) to remove any field codes.
Remove any Bibliography present in the document.
Save and close the document.
Remove Mendeley Cite-o-matic from Word
Open Mendeley Desktop
Click on Tools>Uninstall MS Word Plugin
Open the document and update it with the appropriate style using the EndNote tools. See EndNote: Changing Output Styles Within a Document for more information.
Once you have converted all your documents, you can uninstall Mendeley Desktop.
Please note that you may get the "EndNote Select Matching Reference" dialog box when formatting the bibliography, please click at EndNote: Select Matching Reference for information on how to resolve this and in case if we get a Cannot Edit Range message then refer to this: EndNote: Cannot Edit Range or A COM exception has occurred
