Clarity Analyze Skill

---

name: clarity-analyze

description: >

Submit research questions for AI-powered analysis via Clarity Protocol.

Use when the user asks to analyze a protein variant, ask a research question,

get AI analysis of a mutation, or query Clarity's aggregated data sources.

Requires CLARITY_WRITE_API_KEY.

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 literature

Get plain text answer (no JSON wrapper):

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:

Authentication

export CLARITY_WRITE_API_KEY=your_write_key_here

Rate Limits

Error Handling