DOCX Processing Toolkit
telagod/code-abyss
Routes Word document tasks to the right tool: pandoc for text, raw OOXML for structure and comments, docx-js for new files, and a mandatory redlining flow for edits to others' documents.
EndNote reference formatting workflow — converts [PMID: xxxx] markers in Markdown manuscripts to Word (.docx) using EndNote CWYW-recognized {Author, Year, Title} placeholders, while generating .ris…
Install Format References Endnote
$ npx skills add aipoch/medical-research-skills --skill format-references-endnote -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills format-references-endnote --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ 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-endnote' .claude/skills/format-references-endnote && rm -rf skills-srcUse ~/.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/
Install the "format-references-endnote" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Academic%20Writing/format-references-endnote into .claude/skills/format-references-endnote/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "format-references-endnote", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Academic%20Writing/format-references-endnoteType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add aipoch/medical-research-skills --skill format-references-endnote -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills format-references-endnote --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/'scientific-skills/Academic Writing/format-references-endnote' .agents/skills/format-references-endnote && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "format-references-endnote" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Academic%20Writing/format-references-endnote into .agents/skills/format-references-endnote/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "format-references-endnote", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aipoch/medical-research-skills --skill format-references-endnote -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills format-references-endnote --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/'scientific-skills/Academic Writing/format-references-endnote' .cursor/skills/format-references-endnote && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "format-references-endnote" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Academic%20Writing/format-references-endnote into .cursor/skills/format-references-endnote/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "format-references-endnote", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/aipoch/medical-research-skills.git --path 'scientific-skills/Academic Writing/format-references-endnote'--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add aipoch/medical-research-skills --skill format-references-endnote -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills format-references-endnote --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/'scientific-skills/Academic Writing/format-references-endnote' .gemini/skills/format-references-endnote && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "format-references-endnote" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Academic%20Writing/format-references-endnote into .gemini/skills/format-references-endnote/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "format-references-endnote", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install aipoch/medical-research-skills format-references-endnoteInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add aipoch/medical-research-skills --skill format-references-endnote -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/'scientific-skills/Academic Writing/format-references-endnote' .github/skills/format-references-endnote && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "format-references-endnote" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Academic%20Writing/format-references-endnote into .github/skills/format-references-endnote/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "format-references-endnote", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add aipoch/medical-research-skills --skill format-references-endnote -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aipoch/medical-research-skills format-references-endnote --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/'scientific-skills/Academic Writing/format-references-endnote' .opencode/skills/format-references-endnote && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "format-references-endnote" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Academic%20Writing/format-references-endnote into .opencode/skills/format-references-endnote/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "format-references-endnote", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
format-references-endnote- GitHub stars
- 2k
- Token cost
- ~1.5k tokens
- SKILL.md length
- 718 words
- Files
- 5 (incl. scripts)
- Skills in repo
- 567
- Repo updated
- First seen
- Licence
- MIT
At a glance
EndNote reference formatting workflow — converts [PMID: xxxx] markers in Markdown manuscripts to Word (.docx) using EndNote CWYW-recognized {Author, Year, Title} placeholders, while generating .ris…
- Works in 5 steps: Check environment (first time or on error) → Confirm the target file → Run the bundled processing script → …
- Tasks that involve Word documents
- SKILL.md covers When you're invoked, Workflow, Output files and Why this approach works, plus 4 more sections
- Runs Python scripts from its folder; calls python
What it does
Format References Endnote is an agent skill from aipoch/medical-research-skills. EndNote reference formatting workflow — converts [PMID: xxxx] markers in Markdown manuscripts to Word (.docx) using EndNote CWYW-recognized {Author, Year, Title} placeholders, while generating .ris files for automatic import into the local EndNote library. Users click "Update ...
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts (for example `POLISH_CHANGELOG.md`, `eval_report_format-references-endnote_result.json` and `scripts/check_env.py`).
It sits in Documents & Office, covering Word documents. It works with Microsoft Word, Python, PubMed and Pandoc. 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 Word documents
Example prompts
- “/format-references-endnote”
Requirements
- Python 3
Workflow steps
5 steps, taken from the step headings in SKILL.md.
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 2 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
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 Endnote loads about 1.5k tokens when it runs. Until then it costs about 77 tokens; SKILL.md has 718 words of instructions outside code blocks.
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). 718 words, ~1,515 tokens.
Download SKILL.mdSave it as
.claude/skills/format-references-endnote/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.- name
- format-references-endnote
- description
- EndNote reference formatting workflow — converts [PMID: xxxx] markers in Markdown manuscripts to Word (.docx) using EndNote CWYW-recognized {Author, Year, Title} placeholders, while generating .ris files for automatic import into the local EndNote library. Users click "Update ...
- license
- MIT
- author
- AIPOCH
Medical Literature Reference Formatter
This skill automates the step of turning rough [PMID: xxxx] citation markers into professionally formatted Word documents that work with EndNote's one-click bibliography generation. No COM automation or macros — purely file-based, stable on any machine with Python + Pandoc.
When you're invoked
The user has a Markdown manuscript with inline [PMID: xxxx] markers and wants a .docx with citation placeholders that EndNote can resolve into a formatted bibliography.
Workflow
Step 0 — Check environment (first time or on error)
If this is the first run, or the user reports any unexpected error, run the bundled check script first:
python "<skill_dir>/scripts/check_env.py"It verifies: Python 3.7+, Pandoc, PubMed API connectivity, EndNote installation, and .ris file association.
If the output shows .ris not associated with EndNote, ask the user: "Would you like to set .ris files to open with EndNote by default? This will allow generated files to trigger automatic import." If they agree, run:
python "<skill_dir>/scripts/check_env.py" --fix-risStep 1 — Confirm the target file
If the user didn't specify a full path, ask. If they give a vague location like "on my Desktop", resolve it:
- Windows:
C:\Users\<username>\Desktop\<filename>.md - macOS:
/Users/<username>/Desktop/<filename>.md
Step 2 — Run the bundled processing script
The Python script is at scripts/process_references.py inside this skill's directory. Find the skill directory from the path this SKILL.md was loaded from, then run:
python "<skill_dir>/scripts/process_references.py" "<absolute_path_to_file.md>"The script handles the entire pipeline: PMID extraction → PubMed API fetch → placeholder substitution → Pandoc compile → RIS generation → auto-open both files.
Caching mechanism: After the first run, a <stem>_pubmed_cache.json file is generated. Subsequent runs automatically reuse the cache to avoid redundant PubMed fetches. When new PMIDs are added, only the new ones are fetched.
Force refresh: python process_references.py "<file>" --force-refresh clears the cache and re-fetches all records.
Step 3 — Handle failures gracefully
Pandoc not found: Tell the user to install it from https://pandoc.org/installing.html, then re-run.
PubMed API unreachable: The script fills failed PMIDs with {PMIDxxxxx, n.d., [fetch failed]} so the document is still generated. Offer to retry when network is available.
File path issues: Confirm the path exists and has the .md extension, then re-run.
EndNote not opening automatically: The .ris file association may not be configured. Tell the user to open EndNote manually and drag references_temp.ris into the library window.
Step 4 — Deliver the result
After the script exits successfully, say:
References have been automatically imported into EndNote and the document is open. Switch to the EndNote tab in Word and click "Update Citations and Bibliography" to complete formatting.
Also note the output files are saved in the same directory as the original .md file.
Show full SKILL.md (297 more words)Show less
Output files
| File | Purpose |
|---|---|
<stem>-endnote.docx | Word doc with {Author, Year, Title} unformatted citation placeholders |
<stem>.ris | All references in RIS format — opening this imports them into EndNote |
<stem>_pubmed_cache.json | PubMed metadata cache — avoids repeated network fetches |
Why this approach works
EndNote's CWYW (Cite While You Write) engine recognizes {Author, Year, Title} as an "unformatted citation". When the user clicks Update Citations, EndNote scans the document, matches placeholders against the library, and formats them according to the selected style. This is entirely text-based — no macros, no COM, no risk of security dialogs or permission prompts.
Title normalization
The script automatically normalizes titles to ensure EndNote CWYW can match citation placeholders against the RIS-imported library:
| Transformation | Example |
|---|---|
| Greek letters → Latin | α-synuclein → alpha-synuclein |
| Smart quotes → ASCII | ' " → ' " |
| Em/en dashes → hyphens | — → --, – → - |
| Brackets stripped | [Ca²⁺] → Ca²⁺ |
| Commas stripped | (field delimiter in {Author, Year, Title}) |
| Trailing period stripped | (some libraries omit it) |
Both the docx placeholder and the RIS file (TI field) use the identical normalized title.
Troubleshooting
"Update Citations" cannot find many references: Caused by title mismatch between docx and RIS. Re-run with --force-refresh to regenerate with normalized titles. Verify all records imported into EndNote.
EndNote crashes during Update: Split the work — select half the document, update, then the other half.
Requirements
- Python 3.7+ with standard library only (no pip installs needed)
- Pandoc for
.md → .docxconversion - Internet access for NCBI PubMed API calls
- EndNote installed, with
.risfile association configured
Input Validation
This skill accepts requests that match the documented purpose of format-references-endnote 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-endnoteonly 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 4 other files (scripts) in scientific-skills/Academic Writing/format-references-endnote of aipoch/medical-research-skills.
- SKILL.md
- POLISH_CHANGELOG.md
- eval_report_format-references-endnote_result.json
- scripts/check_env.py
- scripts/process_references.py
Open the folder on GitHubat commit 686e09d
Compare with similar skills
Format References Endnote 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Format References Endnote this skillaipoch/medical-research-skills | 2k | — | ~1.5k | Automated safety check: Pass | MIT | |
| DOCX Processing Toolkittelagod/code-abyss | 243 | — | ~668 | Automated safety check: Notes | MIT | |
| Word Document Reader and WriterHKUDS/DeepTutor | 41k | — | ~2.5k | Automated safety check: Pass | Apache-2.0 | |
| Pandoc DOCX TemplateAchuan-2/pandoc_docx_template | 1.1k | — | ~1k | Automated safety check: Pass | None | |
| Word Document Builderspinabot/brigade | 11k | — | ~2.1k | Automated safety check: Pass | MIT | |
| DOCX ToolkitXiaomiMiMo/MiMo-Code | 14k | — | ~2.4k | Automated safety check: Pass | Apache-2.0 |
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Questions about Format References Endnote
What does Format References Endnote do?
EndNote reference formatting workflow — converts [PMID: xxxx] markers in Markdown manuscripts to Word (.docx) using EndNote CWYW-recognized {Author, Year, Title} placeholders, while generating .ris…. Format References Endnote is an agent skill from aipoch/medical-research-skills.ris files for automatic import into the local EndNote library.
When should I use Format References Endnote?
Format References Endnote fits situations like: tasks that involve Word documents.
How do I install Format References Endnote in Claude Code?
Run `npx skills add aipoch/medical-research-skills --skill format-references-endnote -a claude-code`. Or copy the skill folder (scientific-skills/Academic Writing/format-references-endnote in aipoch/medical-research-skills) into .claude/skills/format-references-endnote in your project. Claude Code loads it when a task matches its description.
How do I install Format References Endnote in Codex?
Run `npx skills add aipoch/medical-research-skills --skill format-references-endnote -a codex`. Or copy the skill folder (scientific-skills/Academic Writing/format-references-endnote in aipoch/medical-research-skills) into .agents/skills/format-references-endnote in your project. Codex loads it when a task matches its description.
Can I use Format References Endnote 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-endnote -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-endnote, .gemini/skills/format-references-endnote, .github/skills/format-references-endnote and .opencode/skills/format-references-endnote in your project.
What does Format References Endnote need to run?
Going by SKILL.md and its folder, Format References Endnote needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Format References Endnote access the network?
SKILL.md names 1 domain. As links in the text: pandoc.org. This is read from the text; nothing was executed.
Is Format References Endnote 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 Endnote use?
Format References Endnote 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 Endnote use?
About 1.5k tokens (SKILL.md is roughly 6.1k 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 Endnote?
Skills that share tags, products or a category with Format References Endnote: DOCX Processing Toolkit (telagod/code-abyss, 243 stars), Word Document Reader and Writer (HKUDS/DeepTutor, 41k stars), Pandoc DOCX Template (Achuan-2/pandoc_docx_template, 1.1k stars) and Word Document Builder (spinabot/brigade, 11k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Format References Endnote?
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 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.