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Agent skill

Format References Zotero

by aipoch in aipoch/medical-research-skills

Zotero reference formatting workflow. An agent skill from aipoch/medical-research-skills.

MITAuto-check passedResearch & Science

Install Format References Zotero

skills CLI
$ npx skills add aipoch/medical-research-skills --skill format-references-zotero -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills format-references-zotero --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Academic Writing/format-references-zotero' .claude/skills/format-references-zotero && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
format-references-zotero
GitHub stars
1.9k
Token cost
~1.9k tokens
SKILL.md length
670 words
Files
6 (incl. scripts)
Skills in repo
578
Repo updated
First seen
Licence
MIT

At a glance

Zotero reference formatting workflow. An agent skill from aipoch/medical-research-skills.

  • Works in 8 steps: Check Environment (first run or on error) → Confirm Target File → Confirm Citation Style → …
  • Tasks that involve Citation management
  • SKILL.md covers Workflow, Output Files, Citation Style Management… and Field Code Mechanism, plus 2 more sections
  • Runs Python scripts from its folder; calls python and pip; reaches zotero.org

What it does

Format References Zotero is an agent skill from aipoch/medical-research-skills. Zotero reference formatting workflow. Converts [PMID: xxxx] markers in Markdown manuscripts to Word (.docx) with native Zotero field codes (ADDIN ZOTEROITEM / ADDIN ZOTEROBIBL). Users click "Refresh" once in Word to complete formatting. Includes searchstyles.py for searchin...

Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts (for example `POLISH_CHANGELOG.md`, `eval_report_format-references-zotero_result.json` and `scripts/check_env.py`).

It sits in Research & Science, covering Citation management and Word documents. It works with Zotero, Microsoft Word, PubMed and python-docx. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • Tasks that involve Citation management
  • Tasks that involve Word documents

Example prompts

  • “Refresh”
  • “/format-references-zotero”

Requirements

  • Python 3

Workflow steps

8 steps, taken from the step headings in SKILL.md.

  1. Check Environment (first run or on error)
  2. Confirm Target File
  3. Confirm Citation Style
  4. Run Processing Script
  5. 5 — Change Style / Force Refresh Cache
  6. Integrity Check
  7. Common Issues
  8. Inform User

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 3 files in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python
    • pip

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • zotero.org

    Also links to:

    • pandoc.org

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Format References Zotero loads about 1.9k tokens when it runs. Until then it costs about 76 tokens; SKILL.md has 670 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~76
When it runs · the whole SKILL.md, loaded when a task matches
~1.9k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 670 words, ~1,898 tokens.

Download SKILL.mdSave it as .claude/skills/format-references-zotero/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.
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)
bash
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:

bash
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:

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

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

bash
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
bash
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

FileDescription
<stem>-zotero.docxWord document with Zotero field codes
<stem>.risReference data for Zotero library import (shared with EndNote edition)
<stem>_pubmed_cache.jsonPubMed 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
bash
python "<skill_dir>/scripts/search_styles.py" <keyword>

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

bash
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
Show full SKILL.md (279 more words)Show less
Install Style to Zotero

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

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

Examples:

bash
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:

bash
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.

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 5 other files (scripts) in scientific-skills/Academic Writing/format-references-zotero of aipoch/medical-research-skills.

  • SKILL.md
  • POLISH_CHANGELOG.md
  • eval_report_format-references-zotero_result.json
  • scripts/check_env.py
  • scripts/process_references.py
  • scripts/search_styles.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Format References Zotero next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Format References Zotero compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Format References Zotero this skillaipoch/medical-research-skills1.9k—~1.9kAutomated safety check: PassMIT
ExportZimoLiao/scholaraio577—~1.6kAutomated safety check: PassMIT
Manage RefsAperivue/medsci-skills333—~4.1kAutomated safety check: PassMIT
Latex To Word Workflowhajimi-kun/latex-to-word-workflow128—~2.3kAutomated safety check: PassMIT
Systematic Review ScreenerImbad0202/academic-research-skills51k—~8.4kAutomated safety check: PassCustom licence
Docsagentdocsagent/docsagent625—~834Automated safety check: PassNone

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Works with

Categories

Questions about Format References Zotero

What does Format References Zotero do?

Zotero reference formatting workflow. An agent skill from aipoch/medical-research-skills. Format References Zotero is an agent skill from aipoch/medical-research-skills. Zotero reference formatting workflow.

When should I use Format References Zotero?

Format References Zotero fits situations like: tasks that involve Citation management; tasks that involve Word documents.

How do I install Format References Zotero in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill format-references-zotero -a claude-code`. Or copy the skill folder (scientific-skills/Academic Writing/format-references-zotero in aipoch/medical-research-skills) into .claude/skills/format-references-zotero in your project. Claude Code loads it when a task matches its description.

How do I install Format References Zotero in Codex?

Run `npx skills add aipoch/medical-research-skills --skill format-references-zotero -a codex`. Or copy the skill folder (scientific-skills/Academic Writing/format-references-zotero in aipoch/medical-research-skills) into .agents/skills/format-references-zotero in your project. Codex loads it when a task matches its description.

Can I use Format References Zotero in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill format-references-zotero -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/format-references-zotero, .gemini/skills/format-references-zotero, .github/skills/format-references-zotero and .opencode/skills/format-references-zotero in your project.

What does Format References Zotero need to run?

Going by SKILL.md and its folder, Format References Zotero needs Python for the scripts in its folder and the command-line tools its instructions call (python and pip). Our summary lists: Python 3.

Does Format References Zotero access the network?

SKILL.md names 2 domains. In commands or code: zotero.org; the agent is likely to contact it when it follows the instructions. As links in the text: pandoc.org. This is read from the text; nothing was executed.

Is Format References Zotero safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Format References Zotero use?

Format References Zotero is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Format References Zotero use?

About 1.9k tokens (SKILL.md is roughly 7.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Format References Zotero?

Skills that share tags, products or a category with Format References Zotero: Export (ZimoLiao/scholaraio, 577 stars), Manage Refs (Aperivue/medsci-skills, 333 stars), Latex To Word Workflow (hajimi-kun/latex-to-word-workflow, 128 stars) and Systematic Review Screener (Imbad0202/academic-research-skills, 51k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Format References Zotero?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,937 GitHub stars. The repository holds 578 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.