Citation and Reference Management

Reference management is the scaffolding of reproducible research. A well-organized library saves hundreds of hours across a career, enables collaboration through group libraries, and ensures that citations are accurate in any document. This skill covers the full reference manager stack: from initial setup through export formats, citation styles, and PDF organization for modern research workflows.

When to use

• Starting a new research project and need to organize references systematically
• Collaborating with co-authors on a manuscript, grant, or systematic review
• Migrating from one reference manager to another (e.g., EndNote to Zotero)
• Setting up automated workflows: cite-while-you-write, version control integration
• Managing PDFs and annotations across hundreds or thousands of papers
• Generating bibliographies in specific citation styles (APA, Vancouver, Nature, etc.)
• Preparing data exports for systematic reviews, meta-analyses, or PRISMA diagrams
• Creating backup and version control of your reference library

When NOT to use

• Looking up a single paper by DOI — use ors-literature-research-paper-lookup instead
• Conducting a systematic review's screening process — use ors-literature-research-systematic-review instead
• Writing a manuscript in LaTeX/Word — this skill is about managing references, not the manuscript itself
• Managing code repositories — use Git, not a reference manager
• Cloud document management — use Dropbox, Google Drive, etc., not a reference manager

Prerequisites

• A working directory structure: library/ for the main Zotero library, pdfs/ for PDF storage
• Cloud storage account (optional but recommended): 5–10 GB free cloud storage (Google Drive, OneDrive, iCloud)
• Backup strategy: Zotero library is a SQLite database + files, needs regular backup
• Basic understanding of citation formats (APA, MLA, Chicago, Vancouver)
• LaTeX installation (optional, for BibTeX workflows)

Core workflow

1. Choose your reference manager

Three major options, each with strengths:

Recommendation: Zotero for academic research due to open-source nature, extensibility, and cost. Migrate from other managers if possible.

2. Set up Zotero

Download Zotero 6+ from zotero.org. Configure:

1. File → Preferences → General:

   • Set data directory to a location with backup
   • Enable automatic file renaming

2. Install recommended plugins:

   • Better BibTeX: Auto-generate citation keys, prevent duplicates
   • ZotFile or Zotero PDF Translate: PDF management, translation
   • Zotero PDF Reader: Built-in reader with OCR and annotations

3. Set up sync (optional but recommended):

   • Zotero cloud: 300 MB free, $20/year for 2 GB
   • Alternative: Sync via WebDAV (Nextcloud) or Git
   • Or: Manual backup of Zotero data directory

3. Import and organize references

Import references from:

• DOI: Drag a DOI into Zotero, or right-click → Add Item by Identifier
• PubMed: Use the magic wand icon in browser connector
• Web pages: Use browser connector to save web pages
• PDF files: Drag PDFs into Zotero — metadata auto-extracted
• Manual entry: Add Item button for book chapters, reports, etc.

Organize with Collections (folders):

Library/
├── by-project/
│   ├── systematic-review-diabetes/
│   ├── grant-application-2026/
│   └── manuscript-xyz/
├── by-topic/
│   ├── machine-learning/
│   ├── genomics/
│   └── clinical-trials/
├── by-status/
│   ├── to-read/
│   ├── reading/
│   ├── cited/
│   └── background/
└── shared/
    └── lab-group-library/

4. Manage PDFs and annotations

Configure PDF management:

1. Set up linked attachments (recommended for large libraries):"

   • Settings → Files and Folders → Custom "Linked Attachment Base Directory"
   • Store PDFs in pdfs/ folder, version controlled

2. Enable Zotero PDF Reader (Zotero 6+):

   • Built-in reader with highlighting, annotations, image extraction
   • OCR for scanned PDFs
   • Sync annotations across devices

3. Annotation workflows:

   • Highlight key findings, methodology, limitations
   • Tag annotations by type (methods, results, limitations)
   • Export annotations for literature review summaries

5. Configure citation styles

Zotero ships with 9,000+ citation styles. To use a specific style:

1. Install new style:

   • Settings → Cite → Styles → Get additional styles
   • Search by name (e.g., "American Psychological Association 7th")
   • Or paste CSL URL: https://citationstyles.org/

2. Common biomedical styles:

   • Vancouver: nlm-citation-style
   • APA 7: apa-7th-edition
   • Nature: nature
   • Cell: cell
   • Science: science
   • Chicago: chicago-author-date

3. Customize styles (advanced):

   • Edit CSL files directly (XML format)
   • Use Visual CSL Editor: https://editor.citationstyles.org/
   • Fork existing styles to create custom variants

6. Cite-while-you-write integration

Word Integration

• Zotero toolbar in Word: Add/Edit Citation, Edit Bibliography, Refresh
• Add in-text citations: Type citation key or search by author/title
• Generate bibliography at end of document
• Update citations when library changes

LaTeX integration (with Better BibTeX)

• Generate unique citation keys automatically
• Export to .bib file
• Use \cite{key} in LaTeX

\documentclass{article}
\usepackage[backend=biber, style=nature]{biblatex}
\addbibresource{references.bib}

\begin{document}
Recent work by \cite{smith2023diabetes} shows...
\printbibliography
\end{document}

Quarto/Markdown integration

• Use bibliography: field in YAML header
• Zotero exports to .bib or .yaml (CSL-JSON) format

---
title: "My Analysis"
bibliography: references.bib
format: html
---

7. Export and sharing

Export formats

• BibTeX (.bib): LaTeX, R Markdown, Quarto
• CSL JSON (.json): Pandoc, academic tools
• RIS (.ris): Legacy format, some tools
• EndNote XML: EndNote compatibility
• CSV: Custom scripts, meta-analysis tools

Configure Better BibTeX auto-export:

1. Right-click collection → "Export Collection"
2. Format: "Better BibLaTeX" or "Better BibTeX"
3. Check "Export Notes" and "Export Files"
4. Set "On Change" to keep .bib file updated

Group libraries for collaboration

• Create group library (zotero.org/groups)
• Add co-authors with read/write permissions
• Share via link for read-only access
• Useful for lab groups, systematic reviews, manuscript co-authors

8. DOI and PMID management

Adding by DOI

Right-click → Add Item by Identifier → paste DOI

Programmatic DOI resolution

import requests
import re

def doi_to_metadata(doi):
    """Fetch metadata from Crossref API."""
    url = f"https://api.crossref.org/works/{doi}"
    response = requests.get(url, timeout=30)
    response.raise_for_status()
    data = response.json()["message"]
    
    return {
        "title": data.get("title", [""])[0],
        "authors": [f"{a.get('family', '')}, {a.get('given', '')}" 
                    for a in data.get("author", [])],
        "year": data.get("published", {}).get("date-parts", [[None]])[0][0],
        "journal": data.get("container-title", [""])[0],
        "doi": doi
    }

Importing from PubMed

• Install Zotero browser connector
• On PubMed search results, click Zotero connector icon
• Select references to import

Finding PDFs

• Right-click item → "Find Available PDF" (uses DOI, Unpaywall)
• Configure proxy for institutional access
• Manual: right-click → "Attach Linked File" or "Attach Stored Copy"

9. Backups and version control

Zotero library backup

• Library = SQLite database + files in data directory
• Back up entire data directory regularly
• Use Time Machine (macOS), File History (Windows), or rsync (Linux)
• Cloud sync (Zotero or WebDAV) is automatic backup

Version control for .bib files

• Export collection to .bib in Git-tracked directory
• Commit changes with descriptive messages
• Review diff to see added/removed/modified citations

git add references.bib
git commit -m "Add 15 new citations from systematic review search"

10. Migration between managers

From EndNote to Zotero

1. EndNote: File → Export → EndNote XML
2. Zotero: File → Import
3. Verify all references transferred correctly
4. Check for missing attachments

From Mendeley to Zotero

1. Mendeley: Tools → Options → Mendeley Web Importer
2. Zotero: File → Import → "Mendeley Database" or RIS
3. Use Zotero's Mendeley importer (built-in)

Preserving citation keys

• Better BibTeX maintains stable citation keys across sessions
• Export from old manager with keys, import to Zotero
• Verify keys match before deleting old library

Code patterns

Better BibTeX export configuration

// Better BibTeX settings (JSON config in Zotero)
{
  "citeKeyFormat": "auth+year",
  "citeKeyFormatAuthor": "LastName",
  "citeKeyFormatYear": "4-digit-year",
  "citeKeyTitle": 0,  // 0 = no title
  "citeKeyLowercase": "lower",
  "citeKeyReplace": "_",  // Replace spaces with underscores
  "citeKeyRemoveDiacritics": true,
  "autoPin": false  // Auto-pin citation keys
}

Programmatic import to Zotero via pyzotero

from pyzotero import zotero

# Connect to personal library
zot = zotero.Zotero(library_id, 'user', api_key)

# Add an item by DOI
zot.add_items([{
    "itemType": "journalArticle",
    "DOI": "10.1038/s41586-2020-1234",
    "url": "https://doi.org/10.1038/s41586-2020-1234"
}])

# Get all items in a collection
items = zot.collection_items("ABCD1234")
for item in items:
    print(item["data"]["title"])

CSL style snippet (APA 7th, simplified)

<style xmlns="http://purl.org/net/xbiblio/csl" 
       class="in-text" 
       version="1.0">
  <info>
    <title>American Psychological Association 7th edition</title>
    <id>http://www.zotero.org/styles/apa-7th-edition</id>
    <link href="http://www.zotero.org/styles/apa-7th-edition" 
          rel="self"/>
  </info>
  <citation>
    <layout prefix="(" suffix=")" delimiter="; ">
      <group delimiter=", ">
        <names variable="author">
          <name form="short" and="text" 
                initialize-with=". " 
                delimiter=", "/>
        </names>
        <date variable="issued">
          <date-part name="year"/>
        </date>
      </group>
    </layout>
  </citation>
  <bibliography>
    <layout suffix=".">
      <names variable="author" delimiter=", "/>
      <date variable="issued" prefix=" (" suffix=")">
        <date-part name="year"/>
      </date>
    </layout>
  </bibliography>
</style>

LaTeX BibTeX entry example

@article{smith2023diabetes,
  author  = {Smith, John A. and Doe, Jane B.},
  title   = {Effects of GLP-1 agonists on type 2 diabetes outcomes},
  journal = {Nature Medicine},
  year    = {2023},
  volume  = {29},
  number  = {5},
  pages   = {1234--1245},
  doi     = {10.1038/s41591-2023-0123-4},
  pmid    = {37212345}
}

R Markdown/Quarto bibliography setup

---
title: "My Analysis"
output: html_document
bibliography: references.bib
csl: nature.csl
---

Download CSL files from https://github.com/citation-style-language/styles.

Common pitfalls

• Not backing up regularly: Loss of library is catastrophic; set up automatic backups
• Mixing multiple citation managers: Creates duplicate citations and confusion
• Ignoring metadata quality: Missing fields lead to incomplete citations
• Not using collections: A flat library becomes unmanageable above 1000 references
• Cloud sync not configured: Limits device access and creates backup risk
• Citation keys changing unexpectedly: Use Better BibTeX's "pin" feature for stable keys
• PDF organization in wrong place: Don't let PDFs accumulate in Zotero storage if you need manual control
• Not removing duplicates: Duplicates from multiple imports cause citation errors
• Ignoring version control for exports: .bib files should be in Git for reproducibility
• Manual citation editing: Always use citation tools, never edit Word/LaTeX citations by hand
• PDF annotations lost on re-import: Sync annotations to avoid losing them

Validation

• Backup present: Regular backups of Zotero data directory
• Cloud sync working: Library accessible from multiple devices
• All references have DOIs/PMIDs: Easy to verify and re-find
• Citation style configured: Bibliography generates in target format
• Cite-while-you-write working: Citations insert in Word/LaTeX without errors
• Duplicate check passed: No duplicate references in library
• Group library permissions verified: Co-authors have appropriate access
• PDFs attached and accessible: No missing files or broken links
• Citation keys stable: Keys don't change unexpectedly (with Better BibTeX)
• Exports work correctly: .bib, RIS, CSL JSON files generate without errors

Open alternatives

References

Internal skills:

• ors-literature-research-literature-search — search strategies to feed into library
• ors-literature-research-paper-lookup — find specific papers to add to library
• ors-literature-research-systematic-review — uses exported library for screening
• ors-open-science-preprints — tracks preprints added to library
• ors-scientific-writing — uses Zotero for manuscript citations

External sources:

• Zotero documentation — zotero.org/support
• Better BibTeX documentation — retorque.re/zotero-better-bibtex
• Citation Style Language — citationstyles.org
• Crossref API — api.crossref.org
• pyzotero documentation — pyzotero.readthedocs.io
• DOI resolution — doi.org
• Unpaywall API — unpaywall.org
• APA Style — apastyle.apa.org
• Vancouver Style — nlm.nih.gov/bsd/uniform_requirements.html
• Nature citation style — nature.com/nature-portfolio/editorial-policies/citation-style

Changelog

• 1.0.0 (2026-06-10): Initial adaptation by Pradyumna Jayaram. Updated from Bioinfoskill reference-management with focus on Zotero as primary tool, modern PDF annotation workflows, Better BibTeX integration for version control, DOI/PMID management with programmatic examples, and CSL style customization.