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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! Claude knows how to write Skills, too.

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 40+ million biomedical research papers maintained by the US National Library of Medicine
• Biopython - Python library that provides tools to query PubMed’s database programmatically
• Accept edits mode - A mode (switched 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
• Python installed (see Python Coding in VS Code). If you don’t have it, Claude will offer to help install it.
• 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 (PowerShell):

• Open PowerShell from the Start menu
• Type these commands:

  cd ~\Documents
  mkdir -Force test_claude
  cd test_claude
  

Mac:

• Open Terminal (find it in Applications > Utilities)
• Type these commands:

  cd ~/Documents
  mkdir -p test_claude
  cd test_claude
  

The -p (Mac) and -Force (Windows) flags create the folder if it doesn’t exist, or simply do nothing if it already exists.

Step 2: Start Claude Code

Type this command:

claude

Step 3: Let Claude Edit Files Without Asking

Look at the status line just below the Claude Code prompt:

• If it says auto mode on or accept edits on, you’re all set
• If it says manual mode on, press Shift+Tab until it says accept edits on

This 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 an 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 skill structure. The exact files can vary, for example:

• .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

First type /reload-skills so Claude Code loads the new Skill. Then ask a research question in plain language:

Can I lose weight on a 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:

Do vaccines 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 (on Windows 11, click Show more options first). If you don’t see it, open VS Code and use File > Open Folder instead

Mac:

• Open Finder, navigate to Documents/test_claude
• Right-click the folder and select Open With > Visual Studio Code
• Or, if you’ve set up VS Code’s code command, type code . in 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 (if Claude created one) 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 docx, pdf, pptx, and xlsx skills from github.com/anthropics/skills into my .claude/skills/ folder
  

• When Claude is done, type /reload-skills so Claude Code loads the new skills
• Try one of them:

  Create a PowerPoint presentation on Claude Skills.
  

These document skills help Claude read and write Word, PDF, PowerPoint, and Excel files. Claude copies them into your .claude/skills/ folder.

Other available skills from Anthropic’s repository:

• Browse the full catalog at github.com/anthropics/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 the status line shows accept edits on or auto mode on (press Shift+Tab to switch) - Claude needs permission to create files
• Skill doesn’t activate: Type /reload-skills (or restart Claude Code), then ask again. Also check that SKILL.md has name: medical-research in the header

Workflow Overview

• Claude Skills are more powerful than slash commands - they combine code, documentation, and custom instructions
• Accept edits 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

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

Created by Steven Ge on December 13, 2025.