In this post, I want to share with you how to use Zotero effectively for organizing your references. Additionally, if you use R markdown for writing reports/ manuscripts, using Zotero is a must for citing references quickly and easily.

1. Install Zotero and related things

First of all you need to

• Install Zotero: https://www.zotero.org/
• Install Zotero connector (with the brower you use): https://www.zotero.org/download/
• Install useful plugins (Zotfile, Better BibTeX): https://www.zotero.org/support/plugins

2. Organize your Zotero

I highly recommend you to set-up your Zotero before you start adding references.

• Creating groups in your Zotero library according to your projects.

• Set location of pdf files and their (new) names: This step is very important. When Zotero download pdf files, it will store those files in separate folders (one article in one folder) in the C:\User\admin\Zotero with random & non-sense names. However, I’m sure that you want to locate all those pdf files in folders where you can easily find and work with. You click Tools -> Zotfile References…, then:

  • In the General settings tab, the lower part (Location of file), choose “Custom Location”, then choose where you want to keep your pdf file. I highly recommend you choose an online path (Google drive/ OneDrive), so you can access to your pdf files anywhere.

  • Then check the underneath line “Use subfolder defined by:…”. This is to organize your pdf files into different folders. In the box next to it you can indicate how you want to name your subfolder: %y: by year; %w: by journal; and importantly %c: by name of your Zotero group. Before % sign, you need to put \ (for Window) or / (for Mac). For example, I use Window so I would add: \%c

  • In Renaming rules (will automatically remain the pdf file according to the rule you set): set the rule as you like

  • Other tabs: you can check if you want to change anything. Otherwise, we’re fine as it is now.

DONE! Now we are going to ask Zotero to work for us…

3. Make use of Zotero to improve your workflow

3.1. Easily add your references

There are multiple way that you can add your reference to Zotero. Regardless of the way you do, the citation will be added automatically.
Zotero can find PDF files for you if you want and if PDFs are openly available, or you can always add PDF later. This feature is similar to EndNote.

3.1.1. Add individual citation:

• Directly from the website: just click to the Zotero add-in icon on the right corner of your webpage. When you only have 1 paper on the webpage, Zotero-add-in icon looks like a paper-icon
• Indirectly via identify number (PMID, DOI,…): Click to the icon “Add item(s) by identifier” in the tab-bar of Zotero
• Drag and drop the pdf file to Zotero

3.1.2. Add multiple citations:

• Directly from the website: Same as above. When you only have 1 paper on the webpage, Zotero-add-in icon looks like a folder-icon. This is super useful when you do a systematic review, you run your search, PubMed or EMBASE returns a list of retrieved papers, you just need to add all of them to Zotero folder :)
• Via identify number (PMID, DOI,…): Paste multiple identifiers to the box “Add item(s) by identifier”. Zotero can identify a few hundred of DOIs per time, but much less with PMID.
• Drag and drop the pdf files to Zotero. If you want, you can use Zotero to rename (i.e., author_year_title) your pdfs
• Import your existing library (BibTeX, RIS, Zotero, Mendeley, or Endnote file): In Zotero, choose File -> Import. If you want to download available pdf: Select all citations (Ctrl A) -> right mouse click -> Find available pdfs.

3.2. Easily fix your previously poor-organized setup

If you have been using Zotero for a while but in an unstructured way, you can still fix it. You can start with setting location for pdf files, then:

• Rearrange your Zotero library’s structure: Create (sub)groups. Moving references to the right (sub)groups
• Relocate your pdf files: select all citations in your chosen (sub)groups -> right mouse click -> Manage attachments -> rename and move. Zotero (+Zotfile) will rename your pdf files, cut and paste them to the new location that you’ve just set. Amazing!!!

3.3. Deduplication

Zotero can recognize duplicates and merge them when you want. On your left hand side, click “Duplicate items”, click to one of the duplicated items, on your right side, select the item that you want to keep, then click “merge”.

3.4. Edit your references:

3.4.1. Edit the citation

• You can change the title to “Title case” or “Sentence case” by selecting the citation -> right click to the title -> choose the option you want
• Add note/tag: Choose the action you want on your right hand side. It’s useful when you work in a shared project, you can add your name to the tag to mention you’ve added the ref, or add the status of your work on that reference

3.4.2. Edit the pdf

• Highlight: use different color for different purpose. For example: yellow for evidence, blue for refs, …Then you can choose to only show blue or yellow highlighed parts
• Export your highlighted parts: Right click to the pdf file (underneath the reference), choose “Add notes from annotations”

3.5. Zotero suggests keywords for your manuscript/report

On the bottom left corner, you see a list of automatic tags in your library. You may want to select some of those for your manuscript :D

3.6. Collaborate with your colleagues in Zotero library

You can share your Zotero library with your colleages easily. Your team members can add/edit references. By adding your/ your colleagues’ name in tags/notes, the team knows who added/edited the refs.

3.6.1 Create a new Zotero group:

• You create an account on https://www.zotero.org/
• Log in to your account
• Click to “Group” tab -> create a new group -> Set a name and choose “public” or “private” as you like.

3.6.2 Move your existing library (folder) from personal library to group library:

Drag and drop your existing folder from personal library to group library. However, doing that way will not move all pdf attachments. That’s why I highly recommend that you organize your group library well at the beginning.

Then you/your team members can work with the group library in the same way as personal library.

Note: There are thousands of hacks out there so I will update this post every now and then. That’s it for now, I hope that you find this post useful!

Additional materials:

1. https://ikashnitsky.github.io/2019/zotero/
2. https://www.youtube.com/@research_craft