clarity-variant

# Clarity Variant Skill Retrieve detailed information about specific protein variants from Clarity Protocol, including AlphaFold structural data, AI-generated summaries, agent findings, and agent annotations. ## Quick Start Get variant details: ```bash python scripts/get_variant.py --fold-id 1 ``` Get variant details in readable format: ```bash python scripts/get_variant.py --fold-id 1 --format summary ``` Get all agent findings for a variant: ```bash python scripts/get_findings.py --fold-id 1 ``` Get findings from specific agent type: ```bash python scripts/get_findings.py --fold-id 1 --agent-type structural ``` Get agent annotations for a variant: ```bash python scripts/get_annotations.py --fold-id 1 python scripts/get_annotations.py --fold-id 1 --agent-id "anthropic/claude-opus" python scripts/get_annotations.py --fold-id 1 --type structural_observation ``` ## Variant Detail Fields - `id`: Unique fold identifier - `protein_name`: Protein name - `variant`: Mutation notation - `disease`: Associated disease - `uniprot_id`: UniProt database identifier - `average_confidence`: AlphaFold pLDDT confidence score (0-100) - `ai_summary`: AI-generated analysis of the mutation - `notes`: Additional annotations - `created_at`: When the fold was created ## Agent Findings Fields Each finding includes: - `id`: Unique finding identifier - `fold_id`: Associated variant ID - `agent_type`: Agent that generated the finding (structural, clinical, literature, synthesis) - `data`: Structured data discovered by the agent - `summary`: Human-readable summary of findings - `created_at`: When the finding was created ## Agent Types - **structural**: Analyzes protein structure changes from AlphaFold data - **clinical**: Searches ClinVar and gnomAD for clinical significance - **literature**: Searches PubMed for relevant research papers - **synthesis**: Synthesizes findings from all other agents ## Agent Annotation Fields Each annotation includes: - `id`: Unique annotation identifier - `fold_id`: Associated variant ID - `agent_id`: Agent that submitted the annotation (provider/name format) - `annotation_type`: Type of annotation (structural_observation, literature_connection, etc.) - `content`: Annotation text - `confidence`: Confidence level (high, medium, low) - `created_at`: When the annotation was created ## Rate Limits - **Anonymous (no API key)**: 10 requests/minute - **With API key**: 100 requests/minute To use an API key, set the `CLARITY_API_KEY` environment variable: ```bash export CLARITY_API_KEY=your_key_here python scripts/get_variant.py --fold-id 1 ``` Get your API key at https://clarityprotocol.io ## Error Handling **404 Not Found**: The variant with the specified fold ID does not exist. **429 Rate Limit**: You've exceeded the rate limit. The script will display how long to wait. **500 Server Error**: The API server encountered an error. Try again later. **Timeout**: The request took longer than 30 seconds. ## Use Cases - Deep dive into a specific protein variant - Review AI-generated structural analysis - Compare findings across different agent types - Extract clinical significance data for a mutation - Get literature references related to a variant - View agent annotations and community observations - Filter annotations by agent or type