Waypoint File Formats

---
name: clinical-trial-protocol-waypoint-file-formats
description: 'Sub-skill of clinical-trial-protocol: Waypoint File Formats (+2).'
version: 1.0.0
category: science
type: reference
scripts_exempt: true
---

# Waypoint File Formats (+2)

## Waypoint File Formats


**JSON Waypoints** (Steps 0, 1):
- Structured data for programmatic access
- Small file sizes (1-15KB)
- Easy to parse and reference

**Markdown Waypoints** (Steps 2, 3, 4):
- Step 2: `02_protocol_foundation.md` (Sections 1-6)
- Step 3: `03_protocol_intervention.md` (Sections 7-8)
- Step 4: `04_protocol_operations.md` (Sections 9-12)
- Step 4: `02_protocol_draft.md` (concatenated complete protocol)
- Human-readable protocol documents
- Can be directly edited by users
- Individual section files preserved for easier regeneration


## Data Minimization Strategy


Each step implements aggressive summarization:
- **Keep:** Top-N results (5-10 max)
- **Keep:** Key facts and IDs (NCT numbers, endpoint types)
- **Keep:** Concise rationale (2-3 sentences)
- **Discard:** Raw MCP query results (not needed after analysis)
- **Discard:** Full FDA guidance text (only excerpts/citations kept)
- **Discard:** Lower-ranked search results


## Step Independence


Each subskill is designed to:
- Read only from waypoint files (not conversation history)
- Produce complete output in single execution
- Not depend on conversation context from previous steps
- Be runnable standalone