{"skill":{"slug":"clarity-submit","displayName":"Clarity Submit","summary":"Submit a protein variant hypothesis to Clarity Protocol for validation and folding. Use when the user asks to submit a hypothesis, propose a protein variant,...","description":"---\nname: clarity-submit\ndescription: >\n  Submit a protein variant hypothesis to Clarity Protocol for validation and folding.\n  Use when the user asks to submit a hypothesis, propose a protein variant, queue a fold,\n  or investigate a mutation. Requires CLARITY_WRITE_KEY env var.\n  Capabilities: submit hypothesis, check submission status.\nlicense: MIT\ncompatibility: Requires internet access to clarityprotocol.io. Requires CLARITY_WRITE_KEY env var for write access.\nmetadata:\n  author: clarity-protocol\n  version: \"1.0.0\"\n  homepage: https://clarityprotocol.io\n---\n\n# Clarity Submit Skill\n\nSubmit protein variant hypotheses to Clarity Protocol for automated validation and ColabFold structural prediction.\n\n## Quick Start\n\nSubmit a hypothesis:\n\n```bash\npython scripts/submit_hypothesis.py --protein SOD1 --variant A4V --rationale \"ALS-linked mutation with unknown structural impact\"\n```\n\nSubmit with optional fields:\n\n```bash\npython scripts/submit_hypothesis.py --protein MAPT --variant P301L --rationale \"Tau pathology in frontotemporal dementia\" --wallet \"YOUR_SOLANA_WALLET\"\n```\n\nCheck hypothesis status:\n\n```bash\npython scripts/check_status.py --id 42\n```\n\n## Setup\n\nSet your write API key:\n\n```bash\nexport CLARITY_WRITE_KEY=your_write_key_here\n```\n\nContact the Clarity Protocol team to request a write API key.\n\n## What Happens After Submission\n\n1. **Feasibility validation** runs automatically against UniProt, ClinVar, gnomAD, and PubMed\n2. If validated, the hypothesis is **auto-queued** for ColabFold structural prediction\n3. Four AI research agents continuously monitor the variant for new findings\n4. Results are available at the tracking URL returned after submission\n\n## Request Fields\n\n- `--protein` (required): Protein name (e.g., SOD1, MAPT, APP, SNCA)\n- `--variant` (required): Variant notation (e.g., A4V, P301L, G2019S)\n- `--rationale` (required): Why this variant is worth investigating (min 10 characters)\n- `--disease` (optional): Disease area (auto-detected from protein if omitted)\n- `--wallet` (optional): Solana wallet address for $FOLD reward eligibility\n\n## Response Fields\n\n- `id`: Unique hypothesis identifier\n- `protein_name`: Normalized protein name\n- `variant_notation`: Variant as submitted\n- `status`: Current status (submitted, validating, validated, queued, folding, complete, rejected)\n- `tracking_url`: URL to track progress on clarityprotocol.io\n\n## Rate Limits\n\n- **Write (POST)**: 10 submissions per day per key\n- **Read (GET)**: 100 requests per minute per key\n\n## Size Limits\n\nProteins up to 1,500 residues can be folded. Larger proteins (e.g., LRRK2 at 2,527 residues) exceed hardware capacity and will be rejected during validation.\n\n## Error Handling\n\n**403 Forbidden**: Invalid or missing write API key. Set CLARITY_WRITE_KEY env var.\n\n**422 Validation Error**: Invalid input (protein name empty, rationale too short, etc.).\n\n**429 Rate Limit**: You've exceeded 10 submissions/day. Wait until tomorrow.\n\n## Use Cases\n\n- Programmatically submit variants for investigation\n- Integrate Clarity Protocol into research pipelines\n- Batch submission of variants of interest\n- Agent-driven hypothesis generation and submission\n","tags":{"latest":"1.0.0"},"stats":{"comments":0,"downloads":621,"installsAllTime":0,"installsCurrent":0,"stars":0,"versions":1},"createdAt":1772055687724,"updatedAt":1778491644319},"latestVersion":{"version":"1.0.0","createdAt":1772055687724,"changelog":"Initial release of the Clarity Submit skill.\n\n- Submit protein variant hypotheses to Clarity Protocol for automated validation and structural prediction.\n- Supports checking submission status via unique ID.\n- Requires the CLARITY_WRITE_KEY environment variable for write access.\n- Enforces write/read rate limits and protein size limits.\n- Provides clear error codes for invalid input, authentication failure, and rate limiting.\n- Enables integration into research pipelines and supports programmatic or agent-driven submissions.","license":null},"metadata":null,"owner":{"handle":"clarityprotocol","userId":"s17dxnvxzf96xpcbsq9xq3thr1885n7v","displayName":"clarityprotocol","image":"https://avatars.githubusercontent.com/u/255743260?v=4"},"moderation":{"isSuspicious":false,"isMalwareBlocked":false,"verdict":"clean","reasonCodes":["review.llm_review"],"summary":"Review: review.llm_review","engineVersion":"v2.4.24","updatedAt":1779961075233}}