Overview of how to organize your library
A tidy library makes it easier to spot what you need, share references with collaborators, and keep your research organized. Paperpile gives you five built-in tools—folders, labels, starred, duplicates, and trash—so you can sort papers quickly and find them just as fast.
Below is a quick tour of each one, when to use it, and how they work together.
Organize at a glance
| Tool | What it is | Why use it | How to use it |
|---|---|---|---|
Folders | Containers that live in the sidebar under My Library (works like folders on your computer). | Useful for hierarchical organization of references. Mirror projects, grant proposals, or thesis chapters; share entire folders with collaborators. | Click the plus button in the sidebar to create a new folder, name it, then drag references in. You can create subfolders within folders for deeper structures. |
Labels | Color-coded tags you can stick on any reference and can be accessed in the sidebar. | Helpful for organization of references by topic. Add flexible categories (“Methods,” “Read next,” course codes) without moving references. | Click the plus button in the sidebar under Labels to create a new label. Drag a reference onto a label—or the other way around—to apply it. |
Starred | A one-click bookmark for anything important. | Keep papers you cite frequently, “to-read” references, or articles you need to read again within reach. | Click the star in the reference list to star or unstar a reference. Click Starred in the sidebar to view them. |
Duplicates | An automatic list of references with matching titles or DOIs. | Merge duplicates to avoid citation errors and clutter. | Open Duplicates in the filter menu and select the references you’d like to merge. |
Trash | A safety net for any reference you delete. | You can trash references that you don’t need anymore. Restore references or clear space from your personal or shared libraries with confidence. | Click Trash in the sidebar to show all trashed references. You can empty the Trash, permanently delete selected references, or restore references from the Trash to bring them back to your library. |
Folders
Folders are the most common way to organize your references in Paperpile. Think of them like filing cabinets for your research—each folder can contain references related to a specific project or topic. Folders can have one or more subfolders for hierarchical organization.
Use folders for major categories like research projects, courses, or broad topic areas. For example, you might have folders for "Dissertation", "Coursework - Biology 301," and “Journal club”. See Organize your library with folders.
Labels
Labels work alongside folders to add flexible tagging to your references. While folders represent where your references "live," labels are like sticky notes you can attach to flag specific characteristics or topics.
Labels are perfect for cross-cutting themes and status tags that span multiple folders, such as "Methodology," "Read next", “Annotated”, or "Cite in introduction", or topics such as “Machine learning” or “DNA sequencing”. See Organize your library with labels.
Starred references
Star important references to mark them for quick access later. Starred references appear in a special "Starred" section in your sidebar, making it easy to find your most crucial sources.
Use starring for references you cite frequently, foundational papers in your field, or articles you want to revisit soon. See Star references.
Managing duplicates
Paperpile automatically tries to prevent duplicates when you add new references, but duplicates can still occur when importing from different sources or bibliography files.
Use the filter menu to show Duplicates in your library. You can merge selected duplicates, trash duplicates, or mark references as Not a duplicate. This keeps your library clean and prevents citation errors in your documents. See Duplicates explained.
Trash
When you delete references, they move to the Trash where you can restore them if needed. References in the Trash don't appear in your regular library views, searches, or exports.
Important: References remain in the Trash until you choose to permanently delete them or empty the Trash. This gives you a safety net if you accidentally delete something important. See Trash and delete references.
Organization strategies and best practices
Start simple. Begin with a few broad folders and add more specific organization as your library grows.
Combine approaches. Use folders for projects and labels for topics. For example, put references in a "Manuscript" folder and tag them with labels like "Background," "Methods," or "Results." See Folders and labels explained.
Organize as you go. When you save references to Paperpile with the browser extension, you can add them to folders and labels. See Save to Paperpile with the extension popup and Save from supported databases and websites with the Paperpile buttons.
Merge early, merge often. Regularly clear the Duplicates list to keep your citations unique and prevent issues when adding citations to your documents. See Find and merge duplicates automatically.
Regular maintenance. Periodically review your organization system and adjust as your research evolves.