Zotero

This page is intended to provide step-by-step guidance to using Zotero's bulk upload feature to help with Covidence's full-text retrieval process. Covidence is a software designed specifically to assist with systematic and scoping reviews. For more information on Covidence, check out our Covidence Guide. Please note that this process will locate only 20-40% of all articles. If you want to add PDFs of full text but prefer to not use Zotero, information to assist with that process can be found here:  Locating PDFs and Attaching Full Text.

Some things to keep in mind before you start:

• Zotero's full-text bulk upload feature will only work on Zotero's desktop version
  • If you haven't already installed Zotero's desktop version, go ahead and do so. You can check out Installing Zotero Desktop Version for guidance on how to do so. 
• For the bulk-upload to work, citations need to have a DOI or PMID associated with it.
  • If the files were exported from a database like PubMed or they were imported into Covidence by Rush's librarians, they should have the DOI associated with each citation.

Bulk Uploading PDFs from Zotero into Covidence

At this point, Covidence users should have screened all articles in the Title and Abstract stage. You should have articles in the Full Text screening stage. These articles need to have full text PDFs attached to them.  You will probably notice that some of them do, as Covidence automatically locates and attaches open access articles.

Create a file of full text articles that need PDFs

Step 1: To start, log into your Covidence account, open your review, and expand the Full Text Review stage. Click Continue. On the Full Text Review page, click the Bulk upload missing full texts link in the upper right. On the following page, click the Download Studies button and save the resultant RIS-formatted file to computer. Make a note of the name of the file so you can easily find the file for the next steps in Zotero. It will probably be the top item in your downloads folder.

Import the Covidence file into Zotero, which automatically creates a new Zotero folder

Step 2: Once in Zotero, click “File” and then “Import”.

Step 3 : Upload the PDF folder. Choose the first option (for RIS).

Step 4: Once the import is complete,a new collection will be made in Zotero. The new folder will appear under My Library.  Note:  if you have already created a Zotero folder and have additional citations (besides those you just imported from Covidence) – DO NOT USE THAT FOLDER. Let Covidence create this folder and then import your additional citations into it.

Find and attach PDFs

Step 5: Highlight all the studies by clicking on the top study, clicking "Shift" on your keypad and clicking the bottom study, or use Control A (or CMD A). Then RIGHT CLICK. Then click "Find Available PDFs." 

Step 6: Zotero will then try to find as many PDFs as possible. If the progress bar stops moving while this is underway quit Zotero, re-open it, and repeat step 5. This process takes many minutes, maybe even a half hour. When it is finished, you do not receive a message but the bar is now completely filled in. Please note that sometimes the green bar will freeze mid-way and not reach the end, even after quitting Zotero and re-opening it. If this happens, you should still see some of the full texts. 

Export the file 

Step 7: Now you need to export the files. Highlight all the studies by clicking on the top study, clicking "Shift" on your keypad and clicking the bottom study, or use Control A (or CMD A). Then RIGHT CLICK and choose "Export items."

Step 8: Make sure you select the "Endnote XML" format and tick "Export Notes" and "Export Files".

Step 9: Name the folder something you will remember and make a note of the location, because you will need to find this folder when uploading the XML into Covidence. It should be the top file in your Downloads folder. If you choose not to rename it, it will default to "Exported Items."

Step 10: If you open your Downloads folder documents you will see that the folder has been downloaded. Within the folder you should have an XML file and a "PDF" folder. There is no need to rename the pdf files or manipulate your folder structure after exporting out of your reference manager and, in fact this will cause issues when uploading to Covidence.

Step 11: Now you are ready to upload the XML file into Covidence at step 3 on the bulk upload page. 

Import the Zotero file into Covidence 

To get to the file, go to Downloads, click on Exported Items (or whatever you named it). This will open up more subfolders. You want to click the Microsoft Edge file type. 

Clicking on that will give you the message below

Click Choose Folder. You will get an image similar to the one below, with each PDF shown individually.  Do not select PDFs, just  (click? )

Confirm, as per the message below.

Done!

To check, go back into your Full Text Screening and click "Filter," then "Has Full Text," then "Filter." You’ll get a number that is likely larger than what you just imported.  That’s because Covidence automatically locates and attaches articles that are free to access.

To find PDFs of the rest of the articles, go to our guide on using Covidence: Locating PDFs and Attaching Full Text

Zotero | Your personal research assistant  click that link to see how much storage you've used and how much you have left. Looks like it  needs to be cleared after each export?