| name | hypothesis-generation |
| description | Structured hypothesis formulation for scientific research. Use when generating testable hypotheses from observations. |
Hypothesis Generation
When to Use
- After exploratory data analysis reveals interesting patterns
- When literature review suggests novel connections
- During target discovery or drug repositioning
- When designing experiments
Framework
1. Observation Phase
- What pattern or signal was observed?
- What is the data source and quality?
- Is it reproducible or a single observation?
2. Context Phase
- What does existing literature say?
- Are there known mechanisms that could explain the observation?
- What are related findings in adjacent fields?
3. Hypothesis Formulation
Use the IF-THEN-BECAUSE format:
- IF [specific intervention or condition]
- THEN [measurable outcome]
- BECAUSE [proposed mechanism]
4. Testability Assessment
- Is the hypothesis falsifiable?
- What experiment would test it?
- What controls are needed?
- What statistical test would evaluate results?
5. Impact Assessment
- If confirmed, what would change?
- Who benefits?
- What is the next step?
Tools to Support
differential_expression → discover gene-level signalsgene_set_enrichment → find pathway-level patternssearch_pubmed → validate against literaturesearch_clinical_trials → check if already being tested
