- name
- clarity-analyze
- description
- >
- Capabilities
- submit analysis questions, get AI answers grounded in 7 data sources.
- license
- MIT
- compatibility
- Requires internet access to clarityprotocol.io. Requires CLARITY_WRITE_API_KEY env var. Analysis uses Claude AI on the server side.
- metadata
- author
- clarity-protocol
- version
- 1.0.0
- homepage
- https://clarityprotocol.io
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:
python scripts/ask_question.py --question "What is the clinical significance of SOD1 A4V?"Ask about a specific variant:
python scripts/ask_question.py \
--question "How does this mutation affect protein stability?" \
--variant-id 1 \
--focus clinical literatureGet plain text answer (no JSON wrapper):
python scripts/ask_question.py \
--question "What is the clinical significance of SOD1 A4V?" \
--format textData Sources
The analysis engine draws from:
- Fold data — AlphaFold structure predictions, confidence scores
- Clinical data — ClinVar pathogenicity, gnomAD allele frequency
- Literature — PubMed papers and citations
- Structural analysis — AlphaFold structural predictions
- Open Targets — Disease-gene associations
- Agent findings — Research agent discoveries
- Agent annotations — Community observations
Focus Options
Prioritize specific data sources in the analysis:
clinical— ClinVar, gnomAD dataliterature— PubMed papersstructural— AlphaFold predictionsfunctional— Open Targets, agent findings
Authentication
export CLARITY_WRITE_API_KEY=your_write_key_hereRate 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)