How to organize your references for free.

Discover simple and free methods to add, organize, and grow your research paper collections.

A black and white photo of a bookshelf with old books.

How to organize your references for free.

Discover simple and free methods to add, organize, and grow your research paper collections.

A black and white photo of a bookshelf with old books.

About scienceOS


The AI research agent for scientists with high standards and little time.

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Organizing an ever‑growing list of citations and PDFs can feel like a full-time job. Grouping articles by topic, finding related studies, and generally managing your citations is time-consuming. The AI personal library of scienceOS brings together automatic metadata extraction, bulk imports, and intuitive collections to organize your literature by topic or project.

Adding papers to your scienceOS library

The literature organization and discovery tools require you to manage your citations and PDFs in the AI reference manager – this starts with uploading up to 4,000 research papers. As an addon, organizing your references in scienceOS also allows you to chat with all your full-text papers yourself and create shared projects to let your colleagues work with your literature.

Organizing your references and PDFs in scienceOS is simple:

  1. Open the library: Click on ‘My library’ in the sidebar to go to your library.
  2. Start the upload: Click the pink plus button and choose from the options.
    • “Upload PDFs” for directly adding PDF files
    • “Import from folder” to import a folder of PDFs
    • “Import from Zotero” to add collections from Zotero web library or Zotero desktop app
    • “Provide DOIs” for importing DOIs (and abstracts) from BibTeX and RIS export files
  3. Upload your references: Follow the instructions of the upload manager.
Click the image to play the video.

Upload PDFs to your library. A short video showing that you can also drag-and-drop PDFs into the AI reference manager to organize your research papers.

During the import of your references and PDFs, scienceOS automatically parses their metadata to create citation entries and the built-in deduplication protocol makes sure to not create duplicates in your library. Further, when chatting with the AI research agent, any time it cites a source from the scienceOS database or a specific paragraph when chatting with a PDF, you can click “Add to library”. This helps you manage and organize your research papers in one central space.

Creating and managing collections

Once you have built up your library with your PDFs and citations, you can organize your research papers by adding them to collections. Group your references into topic- or project-specific sets (e.g. “CRISPR gene editing”) that mirror your active research or topics of interest. Additionally, by organizing your references into collections, you can set up projects to chat with specific collections from your library for a more focused approach.

  1. Select sources

    Browse your library or use the built-in search function to identify and select relevant sources in the reference manager.

  2. Add sources to collections

    Click “Add to collection(s)”, then create new collection tags or choose from existing collections; confirm your selection to finish the process.

  3. Manage collections

    Each collection is assigned a random color automatically. To change a collection’s color or rename it, click the three-dot menu next to the pink plus button.

Click the image to play the video.

Create collections in your library and chat with them. A brief video that demonstrates the full workflow from uploading PDFs and adding them to a collection to creating a new project from the collection and writing a literature review based on the sources in the project.

Organize your references with scienceOS

The scienceOS AI research agent provides you with trustworthy tools to manage and organize your citations and PDFs – all within one, free and AI-powered reference manager. Automatic metadata extraction and deduplication, bulk imports, und intuitive collections – it helps you manage your papers and grow your library at no cost. With organized references, you are well-positioned to draft literature reviews, generate structured summaries of your PDFs and drive your research forward.

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