hypothesis-generation

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 signals
• gene_set_enrichment → find pathway-level patterns
• search_pubmed → validate against literature
• search_clinical_trials → check if already being tested