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THL Citation Management

Tutorials provided by the Taubman Health Sciences Library on citation management programs.

Using Zotero with Large Projects

Working on a large project - that is, one where you expect to gather more than 100 sources? You may need to know:

  • How to export large batches of citations from a database directly into Zotero, 
  • How to de-duplicate your sources from multiple database exports,
  • How to organize your sources within a folder with tags.
  • How to free up space if you drag and drop a large number of PDFs into your Zotero program to retrieve the citation information from them.

Batch Export from a Database to Zotero

For some projects, you may be capturing so many sources from a database that it would be more convenient to batch export all of your search results than to save them one by one or even page by page with the web connector. Zotero allows you to import a file of as many sources as you want that you've saved from a database.

From the database:

The first step is to export a file from your database that is readable by a citation manager. This includes .ris, .txt, .nbib, and many more. Every database's export process looks different. For this example, I will be exporting from PubMed. 

From your search results page in PubMed, click on the words Send To located just beneath the search box. Choose Citation manager, then choose from the drop-down box if you'd like All results or All results on this page. Click Create File. A .nbib file should be saved to your computer.

Into Zotero:

Open your Zotero desktop program, click on the library that you want the folder to be in (either your personal or a group library), and then click on File from the top menu, and then select Import. 

When asked Where Do You Want to Import From?, choose A File, and click Next. Choose the file from your computer; it's probably in your Downloads if you didn't specify another location. Zotero will confirm that you want to create a new folder ("collection") for these imported sources. Even if you plan to move these into another folder, creating a new folder when importing is recommended so that you can easily review what you've just added. When you hit Next again, Zotero will import these sources into a new folder that has the same title as your file. Click Finish.

You should now see the imported sources in your Zotero.

Deduplication with Zotero

When you export sources from multiple databases, you will frequently end up with duplicate copies of the same source. To help you get these out of your library, Zotero will automatically find duplicates for you. It does so on the "My Library" level; it doesn't locate duplicates in individual folders. It also does not affect articles that you've copied into multiple folders. If you want to keep track of how many duplicates you're removing for a project (such as for a PRISMA flowchart), you should create a new group and move your sources there for a "clean" library in which to deduplicate.

Under each library you have in your Zotero desktop program (either your personal library or your group libraries), you'll see a folder titled Duplicate Items.

If this folder is empty, your library doesn't include any duplicates. If it isn't, Zotero requires you to review and merge each duplicate entry individual. (Unfortunately, there is not automatic deduplication tool.) To do so, click on a title in the center pane of your Zotero program, and Zotero will highlight the other title(s) that are duplications of that source.

You can compare the sources, and choose the version to keep on the right pane. Click Merge Items when you're ready.

Unfortunately, Zotero might not be able to identify all the duplicates in your library. I recommend spending a few minutes skimming through your library to see if you spot any yourself. If you do, select the two articles, then right-click over them in the center pane and choose Merge Items
Just like before, it will give you a choice on which one to keep. 


Because this process requires manually clicking through each set of duplicates, if you have thousands of duplicates and access to EndNote, I recommend exporting your library into EndNote, completing the deduplication there, and then importing the deduplicated library back to Zotero. 

Organizing Sources with Tags

You may want to organize your articles within folders. You can do so by tagging your articles.

Zotero auto-imports tags from the article's record in the database (usually from the subject headings or author-supplied keywords fields), but you can create your own tags as well.

Click on the title of your article in the center pane of your Zotero program. Then look to the right-hand pane, and click Tags, then Add. Start typing your new tag in the new field that appears. Tags are case sensitive. When you're finished, just click away.

To find the articles that you've marked with this tag, look to the bottom left-hand corner of your Zotero program, and type the tag into the search box there. Click on that tag as it appears in the box above the search bar, and you'll see your articles in that folder marked with that tag appear in the center pane.

I recommend using the tag format *0_[your tag text here], because that will make the tag appear at the top of the list of the autoimported tags. 

You can color-code your tags by right-clicking over them on their lower left-hand panel. Choose Assign Color.

Pick a color that makes sense to you, then click Set Color

You should now see colored squares beside the titles of the articles that you've tagged in the center column of your Zotero. This can be handy to remind yourself which articles you've reviewed and which you haven't. 

Freeing Up Space if Your Zotero Account Is Nearing Its Storage Limit

There is no limit to how many sources you save to your free Zotero account. However, attachments (like PDF files) do take up space. If you entered many sources into your library by dragging and dropping previously-saved PDF files of articles, then you might reach your space limit quickly. If this has happened to here, here's how you can delete those unnecessary PDF files. 

In your Zotero desktop program, use the All Fields & Tags search box in the top of the middle panel to search for "PDF". 

When you do so, you'll see all the PDF attachments you have visible under their citation entries. Click anywhere in the center panel, then hit Ctrl+A on a PC keyboard or Cmd+A on a Mac keyboard. This will select all the PDF attachments. Right-click over them and choose Move Items to Trash.

Right click over the Trash in your left-hand menu, and choose Empty Trash

When you go back to your original folder, you should now see all of your sources still there, just without the PDFs that were taking up all your account's storage space.

Downloadable Guide