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Zotero: Working with Large Sets

Zotero is a free extension for your web browser that acts as a citation management system. You can save, organize, format your citations in your paper, and more.

Use a batch file

What if you are working on a project such as a literature review article which requries managing large sets of citations? In that case, Zotero's usual options for downloading one citation at a time, or all the citations on a single page of results, may not be enough for your needs.

Most library research databases have an option for exporting large sets of citations in a standardized bibliographic format. There are several format options, but two of the most common are RIS/RefMan and BibTeX.

You can import such files into Zotero in order to do a batch uploads of citations. 

Imports Citations, not Full Text!

WARNING! Batch exports and imports to Zotero will NOT include the full text of the articles. They will have CITATIONS ONLY.

EBSCOhost

If you need to import a large number of citations from a database on the EBSCOhost platform, check our handout below for instructions:

PubMed

To export large sets from PubMed, choose Send to > Citation Manager

Options are Save, Email, or Send to. Under Send to, choose the last option, Citation Manager.

Choose which results you want to save: All results on the current page, all results in the search set, or only the results you have marked to select.

Create a file for external citation management software. Choices are All results on this page, All results, or Selection

Then press Create File and save it to your desired location.

The resulting file will be in the .nbib format, which can be imported into Zotero just like RIS or BibTex files. 

Add from DOI, PMID, etc.

The Add Items by Identifier option (the "magic wand" icon) accepts long lists of DOIs, PMIDs, and other standard numbers so long as they are on separate lines. For example, if you have a spreadsheet with a column of such numbers, you can copy-paste the column into the blank:

Snippet of the "add items" option showing multiple DOIs, with each one on separate line.

 

Exports from Google Scholar: Special Considerations

Unfortunately, Google Scholar does not have a function for exporting citations.

If you need a relatively small set, you can save them to your Google Scholar account, then use Zotero's "all on page" function to capture the list.

For large sets, you can use a helper program called "Publish or Perish" to save up to 1000 Google Scholar results. This software is free!

Be aware that Google Scholar citations may be incomplete or have other errors. For clean metadata, there are better databases to choose from. 

Export results with Publish or Perish

Open Publish or Perish.

Select the Google Scholar option.

snippet of the search sources in Publish or Perish. Google Scholar is the second button.

Enter your search terms just as you would at the Google Scholar site.

  • The Maximum Results option defaults to 200. You can change it; the maximum is 1000.
  • You may want to uncheck the Patents option. 

Click Search.

snipppet of the Publish or Perish Google Scholar search options, with highlights on Keywords, Maximum Results, Patents, and Search

Google Scholar will probably sense the mass download and ask you to prove that you are human by completing a Captcha. To avoid being blocked, be cautious about downloading too many result sets at the same time. 

Once you have the result set, choose Save Results. For importing citations into Zotero, choose either BibTeX or RIS/RefManager.

The Save Results button has numerous file format and citation style options.

Save the file to your preferred location.

Import result set file to Zotero

  1. Open your Zotero client.
  2. Choose File > Import
  3. Use the option for "A file (BibTeX, RIS, Zotero RDF, etc.)"
    The import box asks, "Where do you want to import from?"
  4. Choose Next
  5. Select to file you want to import, then click Open.
  6. Zotero will ask how to handle the imported items. The default choices are fine for most users.
    The Import Options box assumes you want to place imported collections and items in a new collection.
  7. Assuming you kept the option to place the imported items in a new collection, you will now have a new folder in Zotero with the same same as the file.

Deduping One-by-one

Zotero has an automatic tool for deduplicating citations within your Zotero library. Just click the "Duplicate Items" option in the left Zotero panel.

Bottom of the Zotero library panel showing My Publications, Duplicate Items, Unfiled Items, and Trash. Duplication Items is highlighted and has a figure next to it: 5/10

In this example, Zotero has dectected 5 duplicate items with 10 total citation entries.

To merge the duplicates, click each duplicate set in the middle panel, then choose the "Merge" option in the right panel. You can select which version of the citation you want to keep, if one is more complete than the other, and even which specific fields you want to keep.

Snippet of middle panel showing duplicated titles. The top set has been selected, so the button "Merge 2 items" appears in the right panel.

However, Zotero assumes that you will be deduping one by one, and this might not be practical if you are dealing with large sets.

Batch Deduping

If you need to batch dedupe in Zotero, you may want to try a free Zoter plug-in called Zoplicate.

To install Zoplicate:

  1. Download the latest .xpi file
  2. Open your Zotero client
  3. Choose Tools > Plugins
  4. Drag the .xpi file into the Plugins window. 
  5. The file will automatically install. It will look like this:
    "Manage Your Plugins" window showing Zoplicate enabled.

Once installed, Zoplicate adds two buttons to your Merge Duplicates panel. Choose Bulk Merge to automatically merge all duplicates, rather than approving them one by one.

Snippet of the right panel, highlighting the Zoplicate buttons, "Bulk Merge All Duplicate Items" and "They are NOT duplicates."