Create a Claude Skill for Medical Research

Keeping up with medical research means wading through dense scientific papers filled with jargon. A Claude Skill is like having a research assistant that reads hundreds of papers and explains them in plain English - instead of spending hours searching PubMed and decoding technical language, you ask a simple question and get a clear summary based on the latest science.

In this tutorial, you’ll create a Claude Skill that searches peer-reviewed medical literature. We first create a Python script to query PubMed. The best part? You can ask Claude to do all the work! It has a Skill that creates Skills!

Key Concepts

Claude Skill - A specialized tool that extends Claude Code’s capabilities with custom instructions, code, and documentation stored in .claude/skills/
PubMed - Free database of 35+ million biomedical research papers maintained by the US National Library of Medicine
Biopython - Python library that provides tools to query PubMed’s database programmatically
Auto-edit mode - Feature activated with Shift+Tab that lets Claude make multiple file changes without asking permission each time

What You’ll Need

Completed Claude Code in VS Code on Windows or Claude Code in VS Code on Mac
Internet connection for PubMed searches
15-20 minutes

Step 1: Navigate to Project Folder

If you completed the slash commands tutorial, the test_claude folder already exists. These commands work either way.

Windows (WSL):

Open Ubuntu from the Start menu

Type these commands:

cd /mnt/c/Users/YOUR_USERNAME/Documents
mkdir -p test_claude
cd test_claude

Replace YOUR_USERNAME with your Windows username

Mac:

Open Terminal (find it in Applications > Utilities)

Type these commands:

cd ~/Documents
mkdir -p test_claude
cd test_claude

The -p flag creates the folder if it doesn’t exist, or simply does nothing if it already exists.

Step 2: Start Claude Code

Type this command:

claude

Claude Code starts and displays a welcome message.

Step 3: Enable Auto-Edit Mode

Press Shift+Tab to enable auto-edit mode. You’ll see a confirmation message.

Auto-edit mode allows Claude to create and modify multiple files without asking for permission each time. This is essential for building skills which involve creating many files.

Step 4: Create the PubMed Search Script

Copy and paste this prompt:

Write a Python script called pubmed_search.py that:
- Takes a search query as command line argument
- Retrieves up to 10 recent papers
- Returns PMID, title, authors, journal, year, abstract preview, and URL

Claude creates the script. It installs the required Biopython package, which includes a entrez module for interacting with PubMed. Review the output to see the script structure.

Step 5: Test the Script

Ask Claude to test it:

Test the script with the query "immunotherapy breast cancer"

Claude runs the script and displays 10 recent papers about immunotherapy for breast cancer. You’ll see titles, authors, abstracts, and PubMed links.

Note: The search finds thousands of papers but retrieves only the 10 most recent for quick review.

Step 6: Create the Medical Research Skill

Now we’ll package everything into a reusable skill. Copy and paste:

Create a Claude Skill called "medical-research" that:
- Takes on a medical question
- Designs queries to retrieve PubMed abstracts
- Creates plain-language summaries accessible to non-scientists
- Includes the pubmed_search.py script inside the skill folder

Claude creates the complete skill structure:

.claude/skills/medical-research/pubmed_search.py - The search script
.claude/skills/medical-research/SKILL.md - Instructions for Claude on how to use the skill
.claude/skills/medical-research/README.md - User documentation
.claude/skills/medical-research/EXAMPLES.md - Example outputs

This takes 2-3 minutes as Claude writes comprehensive documentation.

Step 7: Test the Skill

Ask a research question in plain language:

Can I lose weight via keto diet?

Claude automatically:

Recognizes this as a medical research question
Activates the medical-research skill
Searches PubMed for relevant papers
Analyzes the findings
Explains the research in plain language covering effectiveness, mechanisms, and considerations

The response includes sections like “How It Works,” “Research Findings,” “Important Considerations,” and “The Bottom Line.”

Step 8: Test Another Question

Try another research topic:

Does vaccine cause autism?

The response explains the scientific consensus, the origin of the myth, and real-world consequences.

Step 9: Explore the Skill Files (Optional)

Open VS Code to see the skill structure:

Windows:

Open File Explorer, navigate to C:\Users\YOUR_USERNAME\Documents\test_claude
Right-click the folder and select Open with Code

Mac:

Open Finder, navigate to Documents/test_claude
Right-click the folder and select Open with Visual Studio Code
Or just type code . from Terminal

In VS Code:

Expand .claude/skills/medical-research/ in the file explorer
Open SKILL.md to see detailed instructions for Claude
Open README.md to see user documentation
Open pubmed_search.py to see the Python code

Note: The skill is completely self-contained - all code and documentation live in one folder.

Step 10: Installing Skills from Anthropic’s Repository

Anthropic maintains a repository of pre-built skills that you can install and use instantly.

To install a skill from the repository, simply ask Claude:
```
Install the document skill from Anthropic's repository
```

Try this skill:

Create a PowerPoint presentation on Claude Skills.

The document skill helps you read and write files in PDF, Word, PowerPoint, and Excel. Claude will clone the skill into your .claude/skills/ folder.

Other available skills from Anthropic’s repository:

Browse the full catalog at github.com/anthropics/claude-skills
Ask Claude “What skills are available in the Anthropic repository?” to see the current list

Next Steps

PDF: Copy a few PDF files in a subfolder in this project folder and ask for summaries.
Other public skills: Try skills available from Anthropic.
Share skills: Skills are just zipped folders!
Create other skills: Anything you are interested in. For example, you can put your own data files in a skill folder.

Troubleshooting

Biopython not installed: Claude will automatically install Biopython when it creates the script. If you see import errors when testing, ask Claude to install Biopython manually with pip install biopython
Script not found: Check that auto-edit mode was enabled (Shift+Tab) - Claude needs permission to create files
Skill doesn’t activate: The skill should work immediately after creation - try asking the question again or check that SKILL.md has the correct name: medical-research in the header

Workflow Overview

Claude Skills are more powerful than slash commands - they combine code, documentation, and custom instructions
Auto-edit mode (Shift+Tab) streamlines creation by avoiding repeated permission prompts
Self-contained packaging - Scripts live inside skill folders, making them portable and shareable
Automatic activation - Skills trigger based on question patterns (research questions activate medical-research)
Plain-language interface - Ask natural questions without knowing the technical details

Skills vs Slash Commands

Feature	Skills	Slash Commands
What it contains	Prompts, code, data, and documentation	Prompts only
Activation	Automatically loaded when relevant	Manually triggered with `/command`
Use case	Complex workflows requiring code execution	Quick prompt templates and workflows
File location	`.claude/skills/skill-name/`	`.claude/commands/`
Structure	Multiple files (SKILL.md, README.md, code files)	Single `.md` file per command

Key Takeaway: Slash Commands just injects prompts from the UI. It is useful, but limited.

Created by Steven Ge on December 13, 2025.