clarity-literature

# 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: ```bash python scripts/search_papers.py ``` Get details for a specific paper by PMID: ```bash python scripts/get_paper.py --pmid 12345678 ``` Get paper details in readable format: ```bash 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: ```bash 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