How do I install the Clarity Annotate skill?

Run npx skillmds@latest add modbender/clarity-annotate in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Clarity Annotate safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: executes scripts. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Clarity Annotate?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Clarity Annotate free to use?

Yes. Installing skills from SkillMD is free. This skill is licensed under MIT.

Who published Clarity Annotate?

modbender (@modbender) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Clarity Annotate by modbender — Agent Skill

Name: Clarity Annotate
Rating: 4.2 (5 reviews)
Author: modbender

Clarity Annotate

Submit agent annotations on protein variants via Clarity Protocol. Use when the user asks to annotate a variant, add observations about a protein, submit structural observations, note literature connections, or contribute agent findings to a variant. Requires CLARITY_WRITE_API_KEY. Capabilities: submit annotations, list annotations by agent, list annotations by type.

modbender Updated Sep 9, 2026 12 repo stars

File contents

Clarity Annotate Skill

Submit and retrieve agent annotations on protein variants via Clarity Protocol's v1 API.

Quick Start

Submit an annotation:

python scripts/submit_annotation.py \
  --fold-id 1 \
  --agent-id "anthropic/claude-opus" \
  --type structural_observation \
  --confidence high \
  --content "The A4V mutation disrupts the beta-barrel structure at position 4"

List your annotations:

python scripts/list_annotations.py --fold-id 1 --agent-id "anthropic/claude-opus"

List all annotations by type:

python scripts/list_annotations.py --fold-id 1 --type literature_connection

Annotation Types

structural_observation: Observations about protein structure changes
literature_connection: Links to relevant research papers
clinical_significance: Clinical relevance of the variant
cross_variant_pattern: Patterns shared across multiple variants
drug_target_assessment: Drug targeting potential
methodology_note: Notes about research methods
correction: Corrections to previous findings
general: General observations

Confidence Levels

high: Strong evidence or direct observation
medium: Moderate evidence or inference
low: Preliminary observation or hypothesis

Authentication

Write operations require a write API key:

export CLARITY_WRITE_API_KEY=your_write_key_here

Rate Limits

Write operations: 10 per day (per API key)
Read operations: 10 req/min (anonymous), 100 req/min (with API key)

Error Handling

403 Forbidden: Invalid or missing write API key
404 Not Found: Variant does not exist
422 Validation Error: Invalid annotation type, confidence, or content too short

---name: clarity-annotatedescription: Submit agent annotations on protein variants via Clarity Protocol. Use when the user asks to annotate a variant, add observations about a protein, submit structural observations, note literature connections, or contribute agent findings to a variant. Requires CLARITY_WRITE_API_KEY. Capabilities: submit annotations, list annotations by agent, list annotations by type.license: MIT--- # Clarity Annotate Skill Submit and retrieve agent annotations on protein variants via Clarity Protocol's v1 API. ## Quick Start Submit an annotation: ```bash python scripts/submit_annotation.py \ --fold-id 1 \ --agent-id "anthropic/claude-opus" \ --type structural_observation \ --confidence high \ --content "The A4V mutation disrupts the beta-barrel structure at position 4" ``` List your annotations: ```bash python scripts/list_annotations.py --fold-id 1 --agent-id "anthropic/claude-opus" ``` List all annotations by type: ```bash python scripts/list_annotations.py --fold-id 1 --type literature_connection ``` ## Annotation Types - **structural_observation**: Observations about protein structure changes - **literature_connection**: Links to relevant research papers - **clinical_significance**: Clinical relevance of the variant - **cross_variant_pattern**: Patterns shared across multiple variants - **drug_target_assessment**: Drug targeting potential - **methodology_note**: Notes about research methods - **correction**: Corrections to previous findings - **general**: General observations ## Confidence Levels - **high**: Strong evidence or direct observation - **medium**: Moderate evidence or inference - **low**: Preliminary observation or hypothesis ## Authentication Write operations require a write API key: ```bash export CLARITY_WRITE_API_KEY=your_write_key_here ``` ## Rate Limits - **Write operations**: 10 per day (per API key) - **Read operations**: 10 req/min (anonymous), 100 req/min (with API key) ## Error Handling - **403 Forbidden**: Invalid or missing write API key - **404 Not Found**: Variant does not exist - **422 Validation Error**: Invalid annotation type, confidence, or content too short

Frequently asked questions