AI in Science
Writing & Reference Management⏱ 2–3 hours to set up; pays off across months of use

Setting Up a Zotero + AI Annotation Workflow

How to use Zotero as the foundation of a research reading system, combine it with AI tools for synthesis, and maintain a citation library that actually stays organized.

AudienceResearchers who want a durable, organized system for reading, annotating, and citing papers
Tools coveredZotero, NotebookLM, Semantic Scholar
Published July 2026

Why Zotero is the right foundation

Before AI tools can help you synthesize literature, you need your literature in one place. Zotero is the right foundation for most researchers because it’s free, open-source, syncs across devices, integrates with every major word processor, and stores your PDFs alongside your references — so you’re never hunting for a paper you’ve already read.

The goal of this tutorial is a system where: papers flow in from databases → get organized in Zotero → PDFs get annotated in Zotero’s reader → collections export cleanly to NotebookLM or other AI tools → citations insert directly into your manuscript.

Step 1: Install Zotero and the browser connector

  1. Download Zotero from zotero.org — available for Mac, Windows, Linux
  2. Install the Zotero Connector browser extension (available for Chrome, Firefox, Safari, Edge)
  3. Create a free Zotero account for sync — go to zotero.org/user/register

With the connector installed, a small save icon appears in your browser toolbar. When you’re on a paper page (PubMed, Google Scholar, journal website, arXiv), clicking it saves the full citation metadata — and the PDF if it’s accessible — directly to Zotero.

Step 2: Organize with collections and tags

Collections (the left sidebar in Zotero) work like folders but are non-exclusive — one paper can live in multiple collections without being duplicated. Structure by project, not by topic.

Suggested top-level structure:

My Library
├── Project A
│   ├── Background
│   ├── Methods
│   └── To Read
├── Project B
└── Inbox (uncategorized saves)

Tags complement collections for cross-cutting attributes:

  • to-read / read — reading status
  • key-paper — papers central to your argument
  • disagrees-with-consensus — papers worth flagging for closer reading
  • cite-in-intro / cite-in-methods — where you plan to use this

In Zotero’s left sidebar, click Tags to filter your library by any combination of tags.

Step 3: Use Zotero’s PDF reader for annotation

Zotero has a built-in PDF reader that stores annotations in your library — not embedded in the PDF file, which means they sync with your Zotero account and are searchable.

Annotation types:

  • Highlight (yellow, red, blue, green) — color-code by theme
  • Note — free-text annotation anchored to a passage
  • Image — capture a figure or table

Recommended color convention:

  • Yellow = key claim or finding
  • Red = I disagree or need to check this
  • Green = methodology I might adopt
  • Blue = definition or concept to add to glossary

After reading a paper, right-click the PDF in your library → Add Note from Annotations to extract all your highlights into a searchable note item.

Step 4: Export to AI tools for synthesis

Export a collection to NotebookLM:

  1. Right-click a collection in Zotero → Export Collection
  2. Choose format: Zotero RDF (preserves full metadata) or just export PDFs
  3. For PDFs: select items → right-click → Show File to locate the PDFs, then upload to NotebookLM

Export citation data:

  • For BibTeX (LaTeX users): right-click collection → Export → BibTeX
  • For Word/Google Docs: use the Zotero word processor plugin, which inserts citations directly and auto-generates a bibliography

Tip: Keep NotebookLM notebooks aligned with Zotero collections. When you add new papers to a Zotero collection, update the corresponding NotebookLM notebook.

Step 5: Cite directly from Zotero in your manuscript

In Microsoft Word:

  1. Install the Zotero Word plugin (installed automatically with Zotero on most systems)
  2. In Word, go to the Zotero tab → Add/Edit Citation
  3. Search by author, title, or year → insert
  4. When finished, click Add/Edit Bibliography to generate a formatted reference list

In Google Docs:

  1. Install the Zotero Connector (same browser extension from Step 1)
  2. In Google Docs: Extensions → Zotero Connector → Add/Edit Citation

In Overleaf/LaTeX:

  1. Export your library as BibTeX from Zotero
  2. Upload the .bib file to your Overleaf project
  3. Use \cite{key} as normal — the key matches Zotero’s citation key format

Keeping your library healthy

A Zotero library is only useful if it stays organized. A few habits that help:

  • Save to Inbox first, sort weekly. Don’t try to file papers perfectly at point of capture. Save everything to an Inbox collection and do a 5-minute sort once a week.
  • Merge duplicates regularly. Zotero’s duplicate detection (in the left sidebar) catches most cases. Review monthly.
  • Keep PDF storage in check. Zotero’s free sync plan includes 300MB of file storage. For larger libraries, either store PDFs locally (without syncing them) or use a WebDAV service.
  • Attach notes after reading. The annotation-to-note workflow (Step 3) creates a searchable record of what you thought about each paper — far more useful than re-reading a highlighted PDF six months later.

Related tools and content

← Back to Learn