citation-management

Citation and Reference Management

Hard rules

1. No fabricated citations. Every cited work must resolve to a verifiable
2. No claim without provenance. Every quantitative or factual claim
3. No silent failure. Every script invocation, API call, or tool use must declare its exit status and what to do on non-zero. A skill that silently swallows errors is a violation.

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.

Cross-references

Other skills in this category:

• literature-search
• paper-lookup
• scoping-review
• systematic-review