paperclip

Search and read biomedical papers, regulatory documents, and clinical trials via the Paperclip CLI.

46.6k|4.2k|Updated Oct 19, 2025
One-click install
npx skills add https://github.com/K-Dense-AI/claude-scientific-skills --skill paperclip-k-dense-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: paperclip
Source: https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/skills/paperclip
Command: npx skills add https://github.com/K-Dense-AI/claude-scientific-skills --skill paperclip-k-dense-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve? Finding and citing specific evidence across millions of biomedical papers, FDA/PMDA/EMA regulatory filings, clinical trial registries, and protein databases normally requires juggling many separate tools and APIs. This Skill operates the Paperclip CLI from GXL, which exposes all of these corpora as one read-only virtual filesystem with line-numbered documents, so every claim can be cited to an exact line. ## Core Features & Use Cases - Source-scoped semantic search and corpus-wide grep: Search PMC, arXiv, bioRxiv, medRxiv, FDA, trial registries, and UniProt/PDB/ChEMBL with ranking modes, or run full-text regex across the entire corpus to find every paper mentioning a gene or term. - Map/reduce reading at scale: Run LLM readers over a result set to extract the same fields from many papers, then synthesize with reduce strategies like consensus or themes. - Line-pinned citations and claim verification: Every document is line-numbered for precise citation URLs, and opt-in paper repositories verify claims against full text on commit. - Use Case: A researcher asks for a comparison of lipid nanoparticle delivery efficiency across recent in vivo studies. The agent searches PMC, filters the result set, maps an extraction query over 10 papers, and produces an answer where every number links to the exact line it came from. ## Quick Start Ask the agent to use paperclip to search PMC for papers on your topic and summarize the top results with line-level citations.

Frequently Asked Questions about paperclip

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I search biomedical papers with the Paperclip CLI?▼

Run paperclip search with a mandatory source flag, for example paperclip search -s pmc "CRISPR base editing delivery" -n 5. Sources include pmc, arxiv, biorxiv, medrxiv, fda, trials, and proteins, and each search returns a result id you can feed to filter, map, or results.

How do I find every paper mentioning a specific gene or term?▼

Use corpus-wide grep, for example paperclip grep -l "SLC30A8" /papers/, which scans full document bodies rather than just abstracts. The scan is time-bounded, so re-run with --exhaustive before concluding a rare term is absent.

Does Paperclip work on Windows?▼

The native installer supports only macOS and Linux with a POSIX shell. On Windows, use the hosted MCP server at https://paperclip.gxl.ai/mcp configured in a client such as Claude Desktop, Cursor, or Codex.

How do I authenticate the Paperclip CLI?▼

Create an API key at https://paperclip.gxl.ai/keys and export it as PAPERCLIP_API_KEY, typically by sourcing a .env file in the same shell call as each command. Browser OAuth via paperclip login is an interactive fallback that a human must run.

Why does paperclip search output sometimes look like JSON and sometimes like rendered text?▼

The search command's output shape is nondeterministic in versions 0.7.14 and 0.7.15, and --json does not force JSON. Extract result ids with the regex s_[a-f0-9]{8}, and get structured rows from paperclip results <id> --save out.csv or meta.json instead.

Can I download figure images from papers through Paperclip?▼

No. Binary reads return corrupted UTF-8 replacement characters, and there is no working pull or copy route in versions 0.7.14-0.7.15. Analyze figures in place with ask-image, or give the user the publisher URL from meta.json.