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Covidence

The purpose of this guide is to provide tutorials and resources for the standards based review tool, Covidence. This guide is aimed at graduate students, faculty, and others involved in the process who are interested in utilizing Covidence.

Full Text Review

In the Full Text Review stage, you screen articles, make final inclusion/exclusion decisions on relevant articles and assign exclusion reasons (if applicable). Before you can screen by full text, you'll need to upload the corresponding PDFs into Covidence.

Below, you can find information on using LibKey Nomad to find full text PDFs, an overview of the process to upload into Covidence, and step by step instructions on how to upload full text into Covidence.

LibKey Nomad

Duquesne University affiliated students, faculty, and staff can use the browser extension LibKey Nomad to get access to full text articles. When you see this symbolit means LibKey Nomad has found the full text PDF and you're able to access it. After installing, LibKey Nomad will integrate into Covidence for Duquesne users. 

 

For more information, view our LibKey Nomad libguide.

Upload Full Text - Single PDF

For instructions on how to upload a single PDF, follow the steps below.

Find the full text article PDF and save it to your computer. On the Covidence homepage, click Full Text Screening and then click Continue.

Click Add Full Text for the article. Click Browse then find and upload the previously saved PDF file from your computer.

Alternatively, may also see the LibKey Nomad symbol underneath the article. Click the Download PDF icon and then save it to your computer. Click Add Full Text for the article and then click Browse. Upload the PDF you just saved. You will now see the option to View Full Text.

Additional information on finding full text can be found on our libguide.

Bulk Upload Full Text

Uploading full text PDFs in bulk is only available for Duquesne Covidence accounts. There are multiple ways you can find full text for your review. One way is utilizing LibKey Nomad - see the above instructions for more information. Using EndNote's "Find Full Text" feature is another way to get PDFs. If you choose to use EndNote for this process, follow the instructions below.

 

Step 1: Export References from Covidence

The most efficient way to bulk upload full text is to export the references from Covidence into EndNote, run a full text search, and then import back into Covidence. Follow the instructions below on how to complete this process:

 

In Covidence, click Export in the top right hand corner.

The blue "export" button in Covidence

Go to the References box. Under Options, select Full Text Review and for Format, select EndNote. Click Prepare File. Your file will begin to download below. Save your file in a location you will remember (for example, your Downloads folder), as you will need to access it in the following steps.

        

Go back to the main menu. Under Full Text Review, click # studies to review, then click Bulk upload missing full texts in the top right hand corner.

Here you will see a list of steps.

Click Download studies. Covidence will create a file containing the references for studies that still need full text PDFs. Save your file where you will remember, as you will need to access it in the following steps.

 

Step 2: Import Covidence File into EndNote & Retrieve Full Text

Import File into Covidence

In some cases, your download will automatically export from Covidence into EndNote. If this doesn't happen, in EndNote, create a new group to store your references. You can do this by clicking File > New.


Navigate to File and click Import.

 


Locate the file you downloaded and saved from Covidence in the previous step. When you select your file, it will give you an Import Option. You must select Reference Manager (RIS).

Note: Mac users should follow the same steps, but will need to click the Options button on the bottom left side of the box when importing the file, to select the RIS option.

Retrieve Full Text in EndNote

Select the references you want to find full text for. Navigate to the menu bar at the top and click References. Then click Find Full Text. Alternatively, once your references are selected, you can right click and then select Find Full Text.

Note: If you are off-campus, you may have to confirm authentication by entering your Multipass credentials. If you haven't confirmed authentication, visit our EndNote guide for more steps on how to edit full text preferences.

If EndNote says "Not Found" when searching for full text - use our tutorial for more guidance on how to find full text.

If you need additional assistance, Covidence also has resources on how to use EndNote to upload full text.

Step 3: Organize PDFs into a Single Folder

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

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.
    1. To select all on a windows - hold down control + A
    2. 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.
    1. 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.
    1. For more help on how to complete this step, click here (insert link).
  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.
    1. To select all on a Mac - hold down command + A
    2. 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.
    1. Make sure to name the folder so you remember which one has a full text. This will make it easy to bulk upload your PDFs back in Covidence at full text screening stage.

Step 4: Import EndNote XML File and PDFs Back into Covidence

After you've chosen and uploaded your XML file, you will then be prompted to upload the folder that you created containing your PDFs. Click Choose folder and then locate the folder you created in Step 3.

How to Import the XML 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 with 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 review homepage, on the full text screening stage, click Continue. At the top of the page, click the Bulk Upload PDFs button.

     

 

Click Select File. Search for the XML file you just exported from EndNote.

When the XML file is finished uploading, click Select Files and upload the PDF files you previously saved into a single folder.

 

After you 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 (link) 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.
Upload PDFs into Covidence

 

 

Once you've selected the correct folder, your PDFs will upload into Covidence. You will see a green check mark if the upload has been successful. Once complete, click the Return to full text screening button to be redirected back to that review stage.

 

Back in full text review, entries that now have a PDF will indicate that full text has been uploaded and by which user.

 

Covidence Videos

For additional help, Covidence has created video tutorials of varying lengths. "Quick Tip" is a short overview, while "Long Tutorial" is an in-depth, hour long recorded webinar on the entire full text retrieval stage.