Covidence

How to Organize PDFs Into a Single Folder

After you have located the full text for every reference in EndNote, the next task is important, as it allows you to upload your PDF files in bulk at one time (Step 3). You can watch the video or follow the written instructions below on how to organize your PDFs into a single folder using a Windows or Mac computer. 

Organizing PDFs Into a Single Folder on Windows

1. First, open your file explorer window, and locate your EndNote library. On a windows computer, your EndNote library will most likely exist in your documents folder.
2. Once you have located your EndNote library project, open the folder and click My EndNote Library.Data and then click the PDF folder.
3. In the top right hand corner, type *.pdf in the search bar and press enter.
4. This search gathers all of the full text articles that you have retrieved. Select all of the PDFs from this screen and then copy them.
   • To select all on a windows – hold down control + A
   • Note the timestamp of the PDFs to make sure you select the articles from your most recent search.
5. Create a new folder with an easy-to-remember name and paste the copied PDFs into your new folder.
   • Make sure to name the folder so you remember which one has full text. This will make it easy to bulk upload your PDFs back into Covidence at the full text screening stage.   

Organizing PDFs Into a Single Folder on a Mac 

The default settings on a mac automatically searches your whole computer when you use the search bar in the finder window. 

1. First, navigate to your Finder and then access your Finder Settings.
2. Under advanced, you will see the option to choose When performing a search. Click Search the Current Folder.
   • For more help on how to complete this step, click here.
3. After you have completed this step, locate your EndNote library project, open the folder and click My EndNote Library.Data and then click the PDF folder.
4. In the top right hand corner, type .pdf in the search bar.
5. This search gathers all of the full text articles that you have retrieved. Select all of the PDFs from this screen and then copy them.
   • To select all on a mac – hold down command + A      
   • Note the timestamp of the PDFs to make sure you select the articles from your most recent search.
6. Create a new folder with an easy-to-remember name and paste the copied PDFs into your new folder.
   • Make sure to name the folder so you remember which one has full text. This will make it easy to bulk upload your PDFs back into Covidence at the full text screening stage.   

How to Import the File Back Into Covidence

Now that your PDFs are in a single folder, you can import them back into Covidence. In EndNote, select or highlight the list of references with newly added PDFs. Click File and then click Export.

Save your file type as XML and for output style, select Show All Fields as the output style. The box at the top of the photo below indicates where the file will be saved. Remember where you save your file, as you will need to remember to follow the steps below to import the file back into Covidence.

Navigate back to the Bulk Uploads page in Covidence and click Choose XML File to search for the XML file you just exported from EndNote.

After you have completed your bulk upload, browse your references to ensure that the full text for each article was uploaded. If there are any missing, you can easily do a single article upload, by clicking add full text below the reference.

• In some cases, references will have the DOI link below the title, which can sometimes link directly to the full text of a reference.