How do I install the Clarity Literature skill?

Run npx skillmds@latest add modbender/clarity-literature 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 Literature 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, makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Clarity Literature?

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 Literature free to use?

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

Who published Clarity Literature?

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

Clarity Literature by modbender — Agent Skill

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

Clarity Literature

Search research papers and get publication details from Clarity Protocol. Use when the user asks to search research papers, find publications, PubMed references, literature about protein, or citation details. Capabilities: search papers, get paper details by PMID.

modbender Updated Sep 9, 2026 12 repo stars

File contents

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

---name: clarity-literaturedescription: Search research papers and get publication details from Clarity Protocol. Use when the user asks to search research papers, find publications, PubMed references, literature about protein, or citation details. Capabilities: search papers, get paper details by PMID.license: MIT--- # 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

Frequently asked questions