Zotero: Manage & Organize

After you begin adding references to Zotero, here are some suggestions and tools to help manage and organize your library.

• Collections and Subcollections
• Duplicates and Merging Items
• Finding, attaching, and annotating PDFs
• Migrate a Library: EndNote > Zotero

Items in Zotero libraries can be organized with collections and subcollections.

Collections

Collections allow you to organize your library based on what makes sense to you. You might have a collection on a particular topic, assignment, course, scholar, etc. However, it is important to remember that items in a collection or multiple collections are not duplicated. Zotero likens collections to music playlists. A song could be featured in multiple playlists, but there is only one copy. So if you delete an item from a collection to will be deleting it from your library! Instead of deleting an item, simply right click on the reference and select "Remove from Collection".

To create a collection:

1. Open Zotero
2. Select File > New Collection
3. Give your Collection a name.

4. 

   Alternatively:

5. right click on "My Library" 
6. Select  New Collection
7. Give your Collection a name.

8. 

Subcollections 

To create a subcollection within an existing collection:

1. Right click on the collection
2. Select “New Subcollection…”

Or

To make an existing collection a subcollection:

1. Select the collection folder in the left panel 
2. Drag and drop the folder into another collection

The default setting is to import all citations.

1. If you want to merge or delete duplicate citations in your library select Duplicate Items in the left hand navigation menu. Once in the Duplicate Items area, you will see which articles have been imported multiple times.  You can either delete the items or merge them. ​
2. To delete an item, you can either drag and drop it into the Trash or right click on the item and select Move Item to Trash.
3. Or you can Merge items. Merging items may be useful for combining citations that differ slightly. To merge items, select two or more items. Next select which copy you would like to be the 'Master' copy and the click Merge in the upper right hand corner. 

To find PDFs based on a reference:

1. Right click on a reference entry that does not have a PDF.
2. Select Find available PDF 

NOTE: Items without DOIs, PMIDs, or a URL may not be found. Additionally, some items may be inaccessible if it is not Open Access or accessible via MBKU Library. If this happens, try searching for the item in MBKU Discovery or making a Interlibrary Loan (ILL) request.

To attach a downloaded PDF (or other file type) to a reference:

1. Select the reference in your library.
2. Select the paperclip icon  in the toolbar at the top.  or right click on the reference and hover over "Add Attachment".
3. The paperclip or right clicking on the reference will lead you to three options, shown in the image below. 
4. To attach a PDF or other file type, select "Attach Stored Copy of File..."
5. Choose the PDF on your computer. 

NOTE: Users can also attach links to references. For example, if you would prefer not to download an article you could link to the item online instead or you could link to a data set or image.

To annotate the PDF:

1. Select the reference
2. Double click on the reference
3. The PDF will be displayed in your default PDF reader, such as Adobe Acrobat.
4. Using the toolbar above the PDF, you can add sticky notes, highlight, underline, and strikeout text. You can also search the full-text of the article.
5. Once you close out of the PDF, you’ll be prompted to save your changes.

NOTE: If the PDF is older, or if it's from a scanned image, some of the annotation features may not work.

Exporting Your EndNote Library

The best file format for exporting and importing data between EndNote and Zotero is XML. Although RIS can also be used. Also, note that you can export a selected number of citations or you can export the entire library.

Follow these steps to export your EndNote Library:

1. In EndNote, go to File > Export 
2. A dialog box will appear. Double check that you are exporting the file to your EndNote data directory, most likely the location will be something like My Documents\endnote.Data. If you are not in the endnote.Data area, navigate to it. IMPORTANT: This step is important because it will help Zotero locate any attachments and notes related to your EndNote citations. Do not move or edit the PDF related folder or place the data file in another subsection.
3. Save the the export file as XML 
4. If you are only exporting a selection of references, select Export Selected References. If you are exporting your entire library leave this unchecked.
5. Click Save

Close EndNote.

Importing Your EndNote Library

IMPORTANT: If you are not starting with an empty Zotero library make a back up file of your existing Zotero library. See directions here. In case there is an issue with the import you will be able to restore your original library.

Follow these steps to import your EndNote library:

1. Disable automatic sync. Go to Zotero > Preferences > Sync and Unlink your account. This prevents the import from affecting your cloud storage or synced libraries on other computers from changing until you are satisfied with the import and organization of your EndNote import.
2. Select the File tab from the menu and choose Import 
3. A new box will appear. Navigate to the location of where you exported your EndNote XML file. If you followed the steps in the previous section the the location will be something like My Documents\endnote.Data.
4. Select this file and click Open
5. Review your uploaded material and double check that items are organized as you'd like and that the data is displaying correctly.
6. If you disabled the automatic sync, go back to Zotero > Preferences > Sync and sign in to your Zotero account.

NOTE: If Zotero identifies any fields or notes that it cannot slate into existing fields the data will be noted in a note that will be attached to the item and will be tagged with “_EndnoteXML import”. If there are too many of these types of notes, the import may get bogged down. Additionally, review these notes after the import and determine whether the information could be added to any of Zotero's existing fields or notes sections. 

Alternative EndNote Export Format

Instead of exporting your EndNote library using XML, you can export the data using RIS (.ris). The main benefit of exporting in RIS is tht you can retain the EndNote database ID. If you are interested in this, please see Zotero's help guide and review the section entitled RIS format (alternative). 

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