Agent skill

Phenotype Introduction

by aipoch in aipoch/medical-research-skills

Expert system for generating comprehensive biomedical phenotype introductions with structured academic content.

Install Phenotype Introduction

skills CLI

$ npx skills add aipoch/medical-research-skills --skill phenotype-introduction -a claude-code

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

GitHub CLI

$ gh skill install aipoch/medical-research-skills phenotype-introduction --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/Evidence Insight/phenotype-introduction' .claude/skills/phenotype-introduction && 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/

Paste into Claude Code

Install the "phenotype-introduction" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/phenotype-introduction into .claude/skills/phenotype-introduction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-introduction", 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

$skill-installer install https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/phenotype-introduction

Type 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.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill phenotype-introduction -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills phenotype-introduction --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/'scientific-skills/Evidence Insight/phenotype-introduction' .agents/skills/phenotype-introduction && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "phenotype-introduction" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/phenotype-introduction into .agents/skills/phenotype-introduction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-introduction", 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.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill phenotype-introduction -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills phenotype-introduction --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/'scientific-skills/Evidence Insight/phenotype-introduction' .cursor/skills/phenotype-introduction && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "phenotype-introduction" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/phenotype-introduction into .cursor/skills/phenotype-introduction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-introduction", 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

$ gemini skills install https://github.com/aipoch/medical-research-skills.git --path 'scientific-skills/Evidence Insight/phenotype-introduction'

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill phenotype-introduction -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills phenotype-introduction --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/'scientific-skills/Evidence Insight/phenotype-introduction' .gemini/skills/phenotype-introduction && rm -rf skills-src

Use ~/.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/

Paste into Gemini CLI

Install the "phenotype-introduction" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/phenotype-introduction into .gemini/skills/phenotype-introduction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-introduction", 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.

GitHub CLI

$ gh skill install aipoch/medical-research-skills phenotype-introduction

Installs 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).

skills CLI

$ npx skills add aipoch/medical-research-skills --skill phenotype-introduction -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/'scientific-skills/Evidence Insight/phenotype-introduction' .github/skills/phenotype-introduction && rm -rf skills-src

Use ~/.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/

Paste into GitHub Copilot

Install the "phenotype-introduction" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/phenotype-introduction into .github/skills/phenotype-introduction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-introduction", 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.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill phenotype-introduction -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills phenotype-introduction --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/'scientific-skills/Evidence Insight/phenotype-introduction' .opencode/skills/phenotype-introduction && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "phenotype-introduction" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/phenotype-introduction into .opencode/skills/phenotype-introduction/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "phenotype-introduction", 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: phenotype-introduction
GitHub stars: 2k
Token cost: ~1.5k tokens
SKILL.md length: 596 words
Files: 7 (incl. scripts, references, assets)
Skills in repo: 567
Repo updated: Sep 17, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Expert system for generating comprehensive biomedical phenotype introductions with structured academic content.

Works in 4 steps: Concept Section (≥800 words) → Mechanism Section (≥800 words) → Regulation Section (≥800 words) → …
Users request detailed explanations of cellular phenotypes including concept
SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 6 more sections
Runs Python scripts from its folder; calls python

What it does

Phenotype Introduction is an agent skill from aipoch/medical-research-skills. Expert system for generating comprehensive biomedical phenotype introductions with structured academic content. Use when users request detailed explanations of cellular phenotypes including concept, mechanism, regulation, and detection methods in Chinese academic writing.

Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 9 other files, including scripts, reference files and assets (for example `phenotype-introduction_audit_result_v1.json`, `references/academic_writing_guide.md` and `references/api_reference.md`).

It sits in Research & Science, covering Scientific writing. 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

Users request detailed explanations of cellular phenotypes including concept
Detection methods in Chinese academic writing

Example prompts

“/phenotype-introduction”

Requirements

Python 3

Workflow steps

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

Concept Section (≥800 words)
Mechanism Section (≥800 words)
Regulation Section (≥800 words)
Marker Detection Section (≥500 words, ≥5 markers)

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
No URLs in SKILL.md.
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

Phenotype Introduction loads about 1.5k tokens when it runs, and up to ~2.6k if it reads all its reference files. Until then it costs about 74 tokens; SKILL.md has 596 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~74
When it runs · the whole SKILL.md, loaded when a task matches: ~1.5k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~2.6k

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). 596 words, ~1,476 tokens.

Download SKILL.mdSave it as .claude/skills/phenotype-introduction/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.

name: phenotype-introduction
description: Expert system for generating comprehensive biomedical phenotype introductions with structured academic content. Use when users request detailed explanations of cellular phenotypes including concept, mechanism, regulation, and detection methods in Chinese academic writing.
license: MIT
author: AIPOCH

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

Phenotype Introduction

When to Use

Use this skill when you need "expert system for generating comprehensive biomedical phenotype introductions with structured academic content. use when users request detailed explanations of cellular phenotypes including concept, mechanism, regulation, and detection methods in chinese academic writing." in a reproducible workflow.
Use this skill when a evidence insight task needs a packaged method instead of ad-hoc freeform output.
Use this skill when the user expects a concrete deliverable, validation step, or file-based result.
Use this skill when scripts/example.py is the most direct path to complete the request.
Use this skill when you need the phenotype-introduction package behavior rather than a generic answer.

Key Features

Scope-focused workflow aligned to: "Expert system for generating comprehensive biomedical phenotype introductions with structured academic content. Use when users request detailed explanations of cellular phenotypes including concept, mechanism, regulation, and detection methods in Chinese academic writing.".
Packaged executable path(s): scripts/example.py plus 1 additional script(s).
Reference material available in references/ for task-specific guidance.
Reusable packaged asset(s), including assets/example_asset.txt.
Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

Python: 3.10+. Repository baseline for current packaged skills.
Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.

Example Usage

bash

cd "20260316/scientific-skills/Evidence Insight/phenotype-introduction"
python -m py_compile scripts/example.py
python scripts/example.py --help

Example run plan:

Confirm the user input, output path, and any required config values.
Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
Run python scripts/example.py with the validated inputs.
Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

See ## Overview above for related details.

Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
Primary implementation surface: scripts/example.py with additional helper scripts under scripts/.
Reference guidance: references/ contains supporting rules, prompts, or checklists.
Packaged assets: reusable files are available under assets/.
Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Show full SKILL.md (240 more words)Show less

Overview

This skill generates detailed academic introductions for biomedical phenotypes with strict content requirements and word count constraints. It produces structured academic content with four mandatory sections:

Concept
Mechanism and occurrence process
Regulation
Marker detection methods

Quick Start

When a user requests a phenotype introduction:

Parse the phenotype name from the user query.
Generate Concept section (≥800 words) including definition, biological characteristics, cellular functions, and historical background.
Generate Mechanism section (≥800 words) describing occurrence process, cellular impacts, and key molecular components.
Generate Regulation section (≥800 words) covering regulatory principles, molecular pathways, and phenotype crosstalk.
Generate Marker Detection section (≥500 words) listing ≥5 key markers with detection principles and methods.
Format output using strict academic structure.

Content Requirements

1. Concept Section (≥800 words)

Include:

Detailed phenotype definition
Biological characteristics
Cellular-level functions and roles
Historical development and background

2. Mechanism Section (≥800 words)

Include:

How the phenotype occurs
Cellular impacts and downstream effects
Key molecular components
Step-by-step occurrence description

3. Regulation Section (≥800 words)

Include:

Regulatory principles
Participating molecules and signaling pathways
Crosstalk with other phenotypes
Nested or hierarchical relationships

4. Marker Detection Section (≥500 words, ≥5 markers)

Include:

List of key marker molecules
Detection rationale for each marker
Common detection methods

Output Format

Strict academic structure:

1. Concept

[Content ≥800 words]

2. Mechanism and Occurrence Process

[Content ≥800 words]

3. Regulation

Regulation: [Regulatory content]

Phenotype Crosstalk: [Crosstalk content]

4. Markers and Detection Methods

Molecule: [Marker name]; Principle: [Detection principle]; Methods: [Detection method]

Molecule: [Marker name]; Principle: [Detection principle]; Methods: [Detection method]

[Repeat for ≥5 markers]

Quality Control

All outputs must pass validation for:

Word count per section
Minimum 5 marker molecules
Proper academic terminology
Complete section coverage
Logical scientific consistency

Files

SKILL.md and 6 other files (scripts, references, assets) in scientific-skills/Evidence Insight/phenotype-introduction of aipoch/medical-research-skills.

SKILL.md
assets/example_asset.txt
phenotype-introduction_audit_result_v1.json
references/academic_writing_guide.md
references/api_reference.md
scripts/example.py
scripts/validate_word_count.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Phenotype Introduction 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.

Phenotype Introduction compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Phenotype Introduction this skillaipoch/medical-research-skills	2k	—	~1.5k	Automated safety check: Pass	MIT	21 days ago
Citation Verification GuideGalaxy-Dawn/claude-scholar	5.7k	3 repos	~1.9k	Automated safety check: Pass	MIT	15 days ago
Nature-Style Scientific FiguresYuan1z0825/nature-skills	46k	—	~2.9k	Automated safety check: Pass	Apache-2.0	yesterday
Citation ManagementK-Dense-AI/claude-scientific-writer	2.4k	3 repos	~3.9k	Automated safety check: Notes	MIT	8 days ago
Academic Paper Composerlishix520/academic-paper-skills	1.4k	2 repos	~6.3k	Automated safety check: Pass	MIT	9 mo ago
Academic Paper Writing PipelineImbad0202/academic-research-skills	51k	—	~16k	Automated safety check: Pass	Custom licence	5 days ago

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Questions about Phenotype Introduction

What does Phenotype Introduction do?

Expert system for generating comprehensive biomedical phenotype introductions with structured academic content. Phenotype Introduction is an agent skill from aipoch/medical-research-skills. Expert system for generating comprehensive biomedical phenotype introductions with structured academic content.

When should I use Phenotype Introduction?

Phenotype Introduction fits situations like: users request detailed explanations of cellular phenotypes including concept; detection methods in Chinese academic writing.

How do I install Phenotype Introduction in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill phenotype-introduction -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/phenotype-introduction in aipoch/medical-research-skills) into .claude/skills/phenotype-introduction in your project. Claude Code loads it when a task matches its description.

How do I install Phenotype Introduction in Codex?

Run `npx skills add aipoch/medical-research-skills --skill phenotype-introduction -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/phenotype-introduction in aipoch/medical-research-skills) into .agents/skills/phenotype-introduction in your project. Codex loads it when a task matches its description.

Can I use Phenotype Introduction 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 phenotype-introduction -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/phenotype-introduction, .gemini/skills/phenotype-introduction, .github/skills/phenotype-introduction and .opencode/skills/phenotype-introduction in your project.

What does Phenotype Introduction need to run?

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

Does Phenotype Introduction access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Phenotype Introduction 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 Phenotype Introduction use?

Phenotype Introduction 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 Phenotype Introduction use?

About 1.5k tokens (SKILL.md is roughly 5.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.2k tokens, read only when the agent opens those files.

What are the alternatives to Phenotype Introduction?

Skills that share tags, products or a category with Phenotype Introduction: Citation Verification Guide (Galaxy-Dawn/claude-scholar, 5.7k stars), Nature-Style Scientific Figures (Yuan1z0825/nature-skills, 46k stars), Citation Management (K-Dense-AI/claude-scientific-writer, 2.4k stars) and Academic Paper Composer (lishix520/academic-paper-skills, 1.4k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Phenotype Introduction?

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.

Install Phenotype Introduction

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Phenotype Introduction

When to Use

Key Features

Dependencies

Example Usage

Implementation Details

Overview

Quick Start

Content Requirements

1. Concept Section (≥800 words)

2. Mechanism Section (≥800 words)

3. Regulation Section (≥800 words)

4. Marker Detection Section (≥500 words, ≥5 markers)

Output Format

Quality Control

Files

Compare with similar skills

Similar skills

More from aipoch/medical-research-skills

Related

Questions about Phenotype Introduction