- name
- clarity-literature
- description
- >
- Capabilities
- search papers, get paper details by PMID.
- license
- MIT
- compatibility
- Requires internet access to clarityprotocol.io. Optional CLARITY_API_KEY env var for 100 req/min (vs 10 req/min).
- metadata
- author
- clarity-protocol
- version
- 1.0.0
- homepage
- https://clarityprotocol.io
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.pyGet details for a specific paper by PMID:
python scripts/get_paper.py --pmid 12345678Get paper details in readable format:
python scripts/get_paper.py --pmid 12345678 --format summaryPaper Fields
Each paper includes:
pmid: PubMed identifierdoi: Digital Object Identifiertitle: Paper titlefirst_author: First author namepublication_year: Year publishedjournal: Journal nameabstract: Paper abstract (when available)citation_count: Number of citations (from Semantic Scholar)influential_citations: Number of highly influential citationshas_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.pyGet 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