Holubar Lab — Research Toolkit

Which Reference Manager?

Side-by-side comparison of Zotero, Mendeley, and EndNote for clinical research fellows and students.

Lab default: Zotero. Per-project profile architecture, local-only library (no cloud lock-in), free, open-source, scriptable via the local HTTP API. See Why Zotero won below for the rationale. EndNote remains available read-only via Cleveland Clinic institutional license for legacy libraries.

● Zotero — lab default ● Mendeley ● EndNote

Quick verdict

If you're starting fresh: use Zotero. Free, open, syncs across all your devices via Zotero's own server or self-hosted WebDAV, and has the strongest open-source ecosystem (Better BibTeX, ZotPilot, GPT4Bib).

If your PI uses EndNote: match their tool to share Group Libraries — EndNote's institutional license at most academic medical centers (including CCF) covers desktop installs.

If you came in on Mendeley: export to Zotero. Mendeley's 2024–25 product direction has been to push users to its Elsevier-owned Mendeley Reference Manager (rebuilt from scratch, narrower than the legacy desktop client). Migration is straightforward via RIS/BibTeX.

Full comparison table

Feature Zotero Mendeley EndNote
Cost Free (open source, AGPL) Free (Elsevier-owned) $249.95 one-time (or institutional license — CCF has one)
Storage — free tier 300 MB cloud (unlimited local + WebDAV self-host) 2 GB cloud (Elsevier servers only) 2 GB cloud (EndNote Online); unlimited local
Storage — paid tier $20/yr (2 GB) · $60/yr (6 GB) · $120/yr (unlimited) Up to 100 GB via Elsevier subscription Bundled with desktop license; extra via institutional
Open source Yes — AGPL, GitHub No — Elsevier proprietary No — Clarivate proprietary
Cloud sync Zotero.org (paid) · WebDAV (self-host) · local-only is fully supported Elsevier cloud (mandatory for sync) EndNote Online (Clarivate); requires account
Local-only mode (no cloud account) Yes — first-class supported workflow Partial — limited without account Yes — desktop works standalone
Platforms macOS · Windows · Linux · iOS · Android macOS · Windows · Linux (legacy) · iOS · Android · Web macOS · Windows · iPad · Web
Word integration Yes — first-class Word + LibreOffice plugins, citation cluster updates as you write Yes — Mendeley Cite (newer; less mature than the legacy plugin) Best-in-class — Cite While You Write (CWYW) is the gold standard for heavy academic use
Browser capture Excellent — Zotero Connector (Chrome, Firefox, Safari, Edge); 600+ site translators Yes — Mendeley Web Importer Yes — EndNote Click (formerly Kopernio) for PDFs; Capture for metadata
PDF annotation Yes — built-in PDF reader with highlights + notes that sync Yes — built-in reader Yes — built-in reader
Citation styles 10,000+ CSL styles (community-maintained) ~10,000 CSL styles (uses Zotero's CSL repository) 7,000+ proprietary styles + CSL
Group libraries Unlimited public groups (free) · Private groups (paid) Yes — 5 free private groups, 25 members each Yes — up to 1,000 members per group
Notes & tagging Excellent — rich-text notes, hierarchical tags, related-item links, full-text search Yes — notes + tags Yes — notes + groups + custom fields
Local HTTP API Yes — localhost:23119 for read/write programmatic access (huge for scripting) No Limited — XML export only
Third-party / AI ecosystem Better BibTeX, ZotPilot (lab-built RAG), GPT4Bib, semantic-search plugins, hundreds of community add-ons Mendeley AI Assistant (Elsevier-internal); closed ecosystem Manuscript Matcher (Clarivate); closed ecosystem
Mobile iOS + Android (official native apps) iOS + Android (official); features narrower than desktop iPad only (no Android native; web works on phone)
Data portability (lock-in risk) Low — SQLite + attachments on disk; export to BibTeX/RIS/JSON anytime Medium — Elsevier cloud is mandatory; export via RIS
Best for Researchers wanting open source, scripting/automation, no lock-in, modern Mac/Linux workflow Existing Mendeley users; teams already on Elsevier platform Heavy academic use with institutional license; large legacy libraries; SR/MA workflows w/ deduplication

CSL = Citation Style Language, the open XML format both Zotero and Mendeley use for citation styles. EndNote also supports CSL alongside its proprietary format.

Why Zotero won as the lab default

Codified 2026-05-24 in .claude/rules/zotero-profiles.md. The deciding factors:

  1. Per-project profile architecture. Each manuscript gets its own isolated Zotero library (SQLite + attachments) co-located with the manuscript folder. Bulk-import dupes can't contaminate other projects. Manuscripts travel with their references — zip the folder and the citations come with it.
  2. Local-only by design. No Zotero cloud sync for the lab — eliminates a class of sync-drift bugs and removes the cloud dependency. References freeze at submission time as .bib + .ris + JSON snapshots committed alongside the manuscript.
  3. Scriptable via local HTTP API. Every RAG project in the lab (Pouchology, CORS RAG, SDH PubRAG, ZotPilot) talks to Zotero at localhost:23119 for programmatic library access. Mendeley and EndNote don't expose anything equivalent.
  4. Open source, AGPL. No vendor lock-in. The data format is documented, the SQLite schema is stable, and the entire codebase is on GitHub.
  5. Community ecosystem. Better BibTeX (per-project citation keys), ZotPilot (semantic RAG over the library), and a long tail of free plugins. Mendeley and EndNote have closed plugin systems.

EndNote's Cite While You Write is genuinely better than anything Zotero ships, and we still use EndNote read-only for some legacy CCF libraries — but the lock-in cost of making EndNote the default outweighed the CWYW polish.

Lab Zotero setup

Full architecture: awesome-zotero (curated plugin + workflow list) is a good starting point for further customization.

Migration cheats

EndNote → Zotero

  1. EndNote: File → Export → format RIS
  2. Zotero: File → Import → select the .ris
  3. PDFs: copy {EndNote-Library}.Data/PDF/ contents, then in Zotero Edit → Preferences → Advanced → Files and Folders → Linked Attachment Base Directory

Mendeley → Zotero

  1. Mendeley: File → Export → format BibTeX (or RIS)
  2. Zotero: File → Import → select the .bib/.ris
  3. PDFs: Mendeley stores in ~/Library/Application Support/Mendeley Desktop/ — import or use the official Zotero Mendeley Importer (docs)

Questions about setting up Zotero for a specific project?

webmaster@holubarlab.org