format-references-zotero

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name: format-references-zotero description: Zotero reference formatting workflow. Converts [PMID: xxxx] markers in Markdown manuscripts to Word (.docx) with native Zotero field codes (ADDIN ZOTERO_ITEM / ADDIN ZOTERO_BIBL). Users click "Refresh" once in Word to complete formatting. Includes search_styles.py for searchin... license: MIT author: AIPOCH

Source: https://github.com/aipoch/medical-research-skills

Medical Literature Reference Formatter — Zotero Edition

Converts [PMID: xxxx] markers directly to native Word Zotero field codes, maintaining full editability: users can switch citation styles in Zotero at any time and Refresh once in Word to update the entire document.

Workflow

Step 0 — Check Environment (first run or on error)

python "<skill_dir>/scripts/check_env.py"

Checks: Python, python-docx, Pandoc, PubMed API, Zotero installation and running status.

If it reports .ris not associated with Zotero, ask the user if they want to fix it. If they agree, run:

python "<skill_dir>/scripts/check_env.py" --fix-ris

Step 1 — Confirm Target File

Ask when user has not provided a full path. Desktop path: C:\Users\<username>\Desktop\<filename>.md

Step 2 — Confirm Citation Style

Default is nature. If the user specifies another style (e.g., Vancouver, Elsevier, APA), first confirm it is installed:

python "<skill_dir>/scripts/search_styles.py" <keyword>          # search available styles
python "<skill_dir>/scripts/search_styles.py" --install <style-id>  # download and install

Styles are automatically installed to Zotero's local styles directory (located via prefs.js, cross-platform).

Step 3 — Run Processing Script

python "<skill_dir>/scripts/process_references.py" "<absolute_path>" [--style <style-id>]

Default style is nature; you can specify any installed style ID:

python "<skill_dir>/scripts/process_references.py" "paper.md" --style elsevier-harvard
python "<skill_dir>/scripts/process_references.py" "paper.md" --style vancouver

Script completes: PMID extraction → PubMed metadata → generate .docx with Zotero fields (including ZOTERO_PREF) → generate .ris → auto-open.

Step 3.5 — Change Style / Force Refresh Cache

python "<skill_dir>/scripts/process_references.py" "paper.md" --style vancouver
python "<skill_dir>/scripts/process_references.py" "paper.md" --force-refresh   # clear cache, re-fetch from PubMed

Cache file <stem>_pubmed_cache.json is auto-generated in the same directory as the .md file, avoiding redundant PubMed fetches. After adding new PMIDs, just run normally — existing references use cache, only new ones are fetched.

Step 4 — Integrity Check

After fetching from PubMed, the script automatically checks: if any PMID fetch failed, it lists the specific IDs and suggests retrying with --force-refresh.

Step 5 — Common Issues

Pandoc not installed: https://pandoc.org/installing.html

python-docx not installed: pip install python-docx

PubMed inaccessible: Network issue, retry later.

Zotero not running: Open Zotero desktop app — Word Refresh requires it to format citations.

Style not installed: Run search_styles.py --install <style-id> to auto-download and install.

Step 6 — Inform User

Document generated, .ris imported into Zotero library. Click "Refresh" in the Zotero tab in Word to complete formatting. To change styles later, run change_style.py with the new style, then Refresh once to update the entire document.

Output Files

File	Description
<stem>-zotero.docx	Word document with Zotero field codes
<stem>.ris	Reference data for Zotero library import (shared with EndNote edition)
<stem>_pubmed_cache.json	PubMed metadata cache to avoid redundant fetches

Citation Style Management (search_styles.py)

This skill includes search_styles.py for searching and installing CSL citation styles — no need to leave the command line or manually download .csl files.

Search Available Styles

python "<skill_dir>/scripts/search_styles.py" <keyword>

Keywords can be journal names or style names, for example:

python "<skill_dir>/scripts/search_styles.py" science       # search Science-related styles
python "<skill_dir>/scripts/search_styles.py" nature        # search Nature-related styles
python "<skill_dir>/scripts/search_styles.py" vancouver     # search Vancouver numbered styles
python "<skill_dir>/scripts/search_styles.py" elsevier      # search Elsevier journal styles
python "<skill_dir>/scripts/search_styles.py" chinese       # search Chinese journal styles

Install Style to Zotero

Find the desired style ID from search results, then install:

python "<skill_dir>/scripts/search_styles.py" --install <style-id>

Examples:

python "<skill_dir>/scripts/search_styles.py" --install science         # Science journal
python "<skill_dir>/scripts/search_styles.py" --install vancouver-nlm   # Vancouver numbered
python "<skill_dir>/scripts/search_styles.py" --install nature          # Nature
python "<skill_dir>/scripts/search_styles.py" --install elsevier-harvard # Elsevier Harvard

Styles are automatically downloaded to Zotero's local styles directory (~Zotero/styles/). After restarting Zotero, they become available in Word.

Generate Word Document with Installed Style

After installing a style, specify the installed style ID via --style in Step 3's process_references.py:

python "<skill_dir>/scripts/process_references.py" "paper.md" --style science
python "<skill_dir>/scripts/process_references.py" "paper.md" --style vancouver-nlm

Supported Style Sources

The script searches from the Zotero official style repository (https://www.zotero.org/styles), covering 9000+ journal and institution CSL styles, including but not limited to:

• Science / Nature / Cell / PNAS / JAMA / NEJM / Lancet / BMJ
• APA / MLA / Chicago / Vancouver / Harvard
• University thesis formats
• Chinese journals (Chinese Science Bulletin, Science China, etc.)
• Publisher-specific formats (Elsevier, Springer, Taylor & Francis, etc.)

Field Code Mechanism

The script replaces each [PMID: xxxx] with an ADDIN ZOTERO_ITEM CSL_CITATION field containing complete CSL JSON metadata, and inserts an ADDIN ZOTERO_BIBL field at the end. Zotero's Word plugin recognizes these fields and formats all citations and bibliography according to the current style on Refresh.

Process:

1. Pandoc compiles Markdown to intermediate .docx (with ZRCITE{pmid} markers)
2. python-docx opens .docx, replaces markers with Word field codes (w:fldChar / w:instrText)
3. Injects ZOTERO_PREF field to ensure style persistence after Refresh

Requirements

• Python 3.7+
• python-docx — pip install python-docx
• Pandoc — https://pandoc.org/installing.html
• Zotero desktop + Word plugin (Zotero must be running during Refresh)
• Network — access to PubMed API

Input Validation

This skill accepts requests that match the documented purpose of format-references-zotero and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

format-references-zotero only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.