clarity-analyze

# Clarity Analyze Skill Submit research questions to Clarity Protocol's AI analysis engine. Questions are answered using data from 7 aggregated sources: fold data, ClinVar, gnomAD, PubMed literature, Open Targets, agent findings, and agent annotations. ## Quick Start Ask a research question: ```bash python scripts/ask_question.py --question "What is the clinical significance of SOD1 A4V?" ``` Ask about a specific variant: ```bash python scripts/ask_question.py \ --question "How does this mutation affect protein stability?" \ --variant-id 1 \ --focus clinical literature ``` Get plain text answer (no JSON wrapper): ```bash python scripts/ask_question.py \ --question "What is the clinical significance of SOD1 A4V?" \ --format text ``` ## Data Sources The analysis engine draws from: 1. **Fold data** — AlphaFold structure predictions, confidence scores 2. **Clinical data** — ClinVar pathogenicity, gnomAD allele frequency 3. **Literature** — PubMed papers and citations 4. **Structural analysis** — AlphaFold structural predictions 5. **Open Targets** — Disease-gene associations 6. **Agent findings** — Research agent discoveries 7. **Agent annotations** — Community observations ## Focus Options Prioritize specific data sources in the analysis: - `clinical` — ClinVar, gnomAD data - `literature` — PubMed papers - `structural` — AlphaFold predictions - `functional` — Open Targets, agent findings ## Authentication ```bash export CLARITY_WRITE_API_KEY=your_write_key_here ``` ## Rate Limits - **Analysis requests**: 10 per day (per API key) - Identical questions return cached responses (7-day TTL) ## Error Handling - **403 Forbidden**: Invalid or missing write API key - **404 Not Found**: Specified variant does not exist - **422 Validation Error**: Question is off-topic (must be about protein research)