The Problem
Most physicians use AI ad-hoc: open ChatGPT, type a question, get an answer, close the tab. This works, but it misses the real power of these tools: consistency.
A "workflow" is a repeatable process -- a prompt (or set of prompts) you save and reuse every time you do a specific task. In this tutorial, we build a Journal Club Assistant workflow.
What We Are Building
Take a PDF of any published paper and turn it into a structured one-page summary and a three-minute presentation script. Every time. Same quality. Two minutes of work.
Prerequisites
| What You Need | Why |
|---|---|
| Claude Pro or ChatGPT Plus account | File upload support for PDFs |
| A PDF of a medical paper | Your test input for the workflow |
| A note app (Apple Notes, Notion, etc.) | Where you will save the final prompt |
Step 1: Define the Output
Before writing the prompt, decide exactly what you want. For a Journal Club presentation, you typically need five things:
| Section | Purpose | Example |
|---|---|---|
| The Hook | Why was this study done? | Gap in current evidence for X |
| The PICO | Study design at a glance | Population, Intervention, Control, Outcome |
| The Result | Primary endpoint data with numbers | HR 0.75, 95% CI 0.60-0.93, p=0.03 |
| The Critique | Honest assessment of limitations | Small N, short follow-up, single-center |
| The Takeaway | Does this change practice? | Yes / No / Maybe, and why |
Be Specific About Format
The more precisely you define the output, the more consistent the AI's response will be. "Summarize this paper" gives you random results. A structured template gives you reliable ones.
Step 2: Write the System Prompt
This is the instruction manual for the AI. Save this text to a file so you can paste it every time.
Role: You are an expert academic physician preparing for Journal Club. You are critical, precise, and focused on Evidence-Based Medicine principles.
Input: I will provide the text of a medical journal article.
Task: Analyze the article and generate a structured summary.
Format Requirements:
Part 1: The One-Pager
- Title and Authors
- The "Why": 1-2 sentences on the gap in knowledge this study fills.
- Study Design (PICO):
- Population: (N number, key inclusion criteria)
- Intervention: (Specifics of treatment)
- Comparison: (Control arm)
- Outcomes: (Primary and key secondary endpoints)
- Results: Give the exact numbers (HR, p-values, CI). Do not say "significantly better" -- say "improved OS (HR 0.75, p=0.03)."
- Critique: List 3 major limitations (biases, small N, short follow-up).
- Conclusion: One sentence: Does this change practice? (Yes/No/Maybe).
Part 2: The Presentation Script Write a 3-minute spoken script for presenting this paper. Use a conversational but professional tone. Start with "Good morning everyone, today I'm presenting..."
Constraint: If the paper does not provide specific data (e.g., p-value), state "Not reported." Do not hallucinate a number.
The Hallucination Constraint
That last line matters. Without it, AI models will sometimes invent plausible-sounding statistics. Always include an explicit instruction to say "Not reported" instead of guessing.
Step 3: Run It
Open Claude.ai (or ChatGPT)
Go to your preferred AI platform. Claude is recommended for longer documents because of its larger context window.
Upload your PDF
Click the paperclip icon and attach the paper. The AI will extract and read the full text.
Paste the prompt
Copy the system prompt from Step 2 into the chat box, below the uploaded file.
Hit Enter
In about 30-60 seconds, you will have a structured summary and a presentation script.
Step 4: Refine and Save
Your first output will be close but not perfect. That is normal. Here is how to iterate:
| Problem | Fix |
|---|---|
| Missed the Hazard Ratio | Add to prompt: "Explicitly list the HR for the primary endpoint" |
| Script was too long | Add to prompt: "Keep the script under 300 words" |
| Too much jargon in the script | Add: "Write as if explaining to a PGY-1 on their first week" |
| Missing subgroup analysis | Add a section to the template for key subgroups |
Once you are happy with the result, save the prompt in a note app. This is your reusable tool now.
This Is Iterative Design
You are not writing a prompt once and praying. You are testing, finding gaps, and tightening the instructions. Each refinement makes the workflow more reliable. After 3-4 papers, your prompt will be dialed in.
Step 5: Make It Permanent
If you use Claude Projects or ChatGPT GPTs, you can skip the paste step entirely.
In Claude Projects:
- Create a Project called "Journal Club"
- In Custom Instructions, paste your prompt from Step 2
- Now every time you open this Project, just upload the PDF and type "Go"
In ChatGPT GPTs:
- Create a custom GPT with the prompt as its system instructions
- Share it with your co-residents if you want
What You Just Built
You built software. It is simple software, written in English, but it is a program that takes an input (PDF) and produces a reliable output (summary and script). You are now a developer.
Your Homework
Identify one other repetitive task you do and write a system prompt for it. Some ideas:
| Task | Input | Output |
|---|---|---|
| Letter of Medical Necessity | Diagnosis + treatment plan | Formatted insurance letter |
| Patient education handout | Condition name + reading level | Plain-language 1-pager |
| Clinic note template | H&P findings | Structured SOAP note draft |
| Email reply to referring MD | Consult question + your recommendation | Professional 3-paragraph email |