Clarity Literature

Search research papers and get publication details from Clarity Protocol. Use when the user asks to search research papers, find publications, PubMed referen...

Security Scan

The skill's code and instructions match its stated purpose (searching Clarity Protocol literature); it only makes expected API calls to clarityprotocol.io and requests an optional CLARITY_API_KEY.

Purpose & Capability

Name/description, SKILL.md, and the three Python scripts consistently implement searching and retrieving papers from clarityprotocol.io. The API_BASE endpoint matches the documented homepage. No unrelated services, binaries, or credentials are requested.

Instruction Scope

Runtime instructions tell the agent to run the provided scripts. The scripts only perform HTTP GETs to the Clarity Protocol API, print results, and handle common HTTP errors/rate limits. They do not read unrelated files, access other environment variables, or transmit data to endpoints other than clarityprotocol.io.

Install Mechanism

This is instruction-only with bundled Python scripts (no install spec). The scripts use the Python requests library, but no dependency installation is declared—users must ensure requests is available in the runtime. No remote downloads or archive extraction occur.

Credentials

Only an optional CLARITY_API_KEY environment variable is mentioned for higher rate limits; the code reads that env var and uses it as an X-API-Key header. No other secrets or unrelated credentials are requested.

Persistence & Privilege

always is false and the skill does not attempt to modify other skills or system-wide configuration. The skill does not request permanent privileges or write unexpected files.

Assessment

This skill appears to do exactly what it says: call clarityprotocol.io to list and fetch paper details. Before installing, verify clarityprotocol.io is the legitimate service you expect, and only set CLARITY_API_KEY if you trust that site. Ensure the runtime has the Python 'requests' package available (the scripts rely on it but no installer is provided). Review the included scripts (they are small and readable) and, if you run them on shared systems, avoid embedding sensitive data in search queries since queries are sent to the external API.

Clarity Literature Skill

Search and retrieve research papers from Clarity Protocol's curated literature database, sourced from PubMed and enriched with citation metrics from Semantic Scholar.

Quick Start

List all papers in the database:

python scripts/search_papers.py

Get details for a specific paper by PMID:

python scripts/get_paper.py --pmid 12345678

Get paper details in readable format:

python scripts/get_paper.py --pmid 12345678 --format summary

Paper Fields

Each paper includes:

• pmid: PubMed identifier
• doi: Digital Object Identifier
• title: Paper title
• first_author: First author name
• publication_year: Year published
• journal: Journal name
• abstract: Paper abstract (when available)
• citation_count: Number of citations (from Semantic Scholar)
• influential_citations: Number of highly influential citations
• has_fulltext: Whether full text is available in PubMed Central

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:

export CLARITY_API_KEY=your_key_here
python scripts/search_papers.py

Get your API key at https://clarityprotocol.io

Error Handling

404 Not Found: The paper with the specified PMID does not exist in the database.

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.

Pagination

Paper lists are paginated. The API returns a next_cursor field if more results are available.

Use Cases

• Find research papers related to protein variants
• Get citation metrics for a specific paper
• Check if a paper has full text available
• Extract abstracts for literature reviews
• Build bibliographies for protein research