PDF bulk uploading into Rayyan or Covidence from Endnote

Leeds Institute of

Health Sciences

FACULTY OF MEDICINE AND HEALTH

AUHE Information Specialists

Once you have selected the studies you wish to include in the full text screening stage of a review the

EndNote Find full text feature is an efficient way to source journal articles freely available on the web. These

PDFs can then be loaded into the screening software (e.g. Covidence or Rayyan).

1. Find full text in EndNote

• Create a new group and add all the records you wish to screen

the full text.

• Select all the records in the group using the keys CONTROL+ A.

• Go to References → Find Full Text→ Find Full Text

or press the find full text icon.

• EndNote will search the internet to find a PDF for the selected

records. The left hand panel shows how many articles it

found. Records containing a PDF attachment will display a

paperclip symbol.

Note: EndNote can only find PDFs that are free on the web. If EndNote didn’t find your reference, check the

Library catalogue to see if you can locate and download the PDF from there.

Update references for improved full text finding

Some journal articles are free but not located by the full

text finder because their record is incomplete. To

increase the likelihood of retrieving more PDFs, select

the records that EndNote did not capture the full text.

• Go to References → Find Reference

Updates…

• Click Update Empty Fields to ensure that the

references are as up to date as possible before you

run the full text finder. Fields highlighted in blue will

be updated.

• Once complete rerun Find Full text on the

records.

Notes:

1. It is best to avoid updating records with a blank Author field as sometimes EndNote finds a

completely different reference

2. Using Update all fields searches Web of Science and Pubmed. It can overwrite notes you have added

to the original records or indexing from different databases but will not affect any of the blank fields

(eg Custom 1-8, Research Notes, Name of database). Check the blue highlighted fields to see what will

be changed.

2. Extracting PDFs in bulk from EndNote

STEP 1: Merging folders to extract PDFs

EndNote saves and stores the PDF from each record in a separate folder. The PDFs are labelled with the

Author details and record number (e.g. Anwar-2013-{#3820} Randomised controlled tr.PDF). To load these

into Rayyan the quickest way to do this is merge the PDFs into a new single folder

https://itstillworks.com/make-one-folder-out-multiple-folders-26192.html

1. Create a new folder to merge your PDFs.

2. Select and copy the entire contents of the PDF folder contained within the EndNote library data folder

(eg ...\Project Name\08-Literature\Searches\AKI MALDI.Data\PDF)

3. Paste them into the new folder for merging

4. In the search bar at the top right of the screen type *(fullstop)* and click the search arrow

5. Sort the folder by file type and select all the PDF files

6. Cut and paste all the PDFs into a new project PDF folder ...\Project Name\08-Literature\PDFs

7. Delete the empty folder used for Merging

Note: this will extract most PDFs but I have found some occasionally go missing. You can manually copy

these individually into your PDF article folder

STEP 2A: Load PDFs into Rayyan

To date (Nov 2020) there is no way to bulk upload into Rayyan – the PDFs need to be added manually to each

record

1. Create a new Rayyan library for the full text screening review

2. Select and export the entire full text screening group as a ris file (we use a style that adds the record

number to the title– see Rayyan.enl) and load the records into Rayyan

3. Click on Upload PDF full-texts and navigate to your PDF folder

STEP 2B: Load PDFs into Covidence

• You can bulk import PDFs from EndNote into Covidence using the instructions described here

https://support.covidence.org/help/bulk-PDF-import-9cd5e1b4

• If redirecting to the EndNote PDF folder doesn’t work, merge the PDFs into a single folder as described

in Step 1 and direct to your new PDF folder.

• For PDFs that haven’t loaded, Click the Filter button to select "Only studies without full text".

Manually upload any PDFs missed by bulk import into these records.

This work is made available for reuse under the terms of the Creative Commons Attribution-

NonCommercial-ShareAlike 4.0 International Licence.