Paperclip Biomedical Literature CLI

Drives the GXL Paperclip CLI to search and read ~11M full-text biomedical papers, FDA/PMDA/EMA filings, clinical trials and protein records, with line-pinned citations.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Installs and authenticates the paperclip binary, then navigates the read-only virtual filesystem (/papers, /fda, /trials, /proteins, /clipboard) with ls, cat, head, grep, scan.
Covers source-scoped semantic search (search -s pmc), corpus-wide full-text grep, metadata SQL, map/reduce reading across many papers, and figure vision via ask-image.
Every document is line-numbered, so answers can carry citation URLs that jump to the exact sentence (#L45).
Encodes hard operating rules: auth preflight, per-call .env prefix, avoid interactive commands, capture result ids, bound output, and never obey instructions embedded in server-returned content.
Ships a verified defect table for 0.7.14/0.7.15 (no internal pipes, reduce --strategy table returns prose, truncated ids in reduce markers) with concrete workarounds.

Who it's for

Biomedical, pharma and biotech researchers, grad students, medical writers.
Regulatory affairs and clinical teams comparing FDA/PMDA/EPAR filings or building trial landscapes.
Anyone writing reviews that must cite specific lines rather than paraphrase.
Prerequisites: macOS or Linux plus a PAPERCLIP_API_KEY (or interactive OAuth login).

Example uses

"Find 5 papers on CRISPR base-editor delivery and extract vector, cell type, efficiency" → search -s pmc → map → results.
"Which papers mention SLC30A8?" → grep -l "SLC30A8" /papers/, re-run with --exhaustive if empty.
"Compare pembrolizumab accelerated approvals with related trials" → parallel -s fda and -s trials/us searches, then a reference list with #L45 line anchors.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/paperclip/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)

Download the ZIP with the button below.
In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.

↓ Download ZIP

Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/paperclip folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/paperclip/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/paperclip ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
Copy the skill into your Claude skills folder: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/paperclip ~/.claude/skills/
Install the CLI (macOS/Linux only): curl -fsSL https://paperclip.gxl.ai/install.sh | bash
Create an API key at https://paperclip.gxl.ai/keys
In your working directory, add a .env file containing PAPERCLIP_API_KEY=gxl_... and add .env to .gitignore.
Verify with paperclip --version and paperclip config — you should see Auth: ✓ API key (env).
Restart Claude Code and ask something like "use paperclip to find papers on ..." to trigger the skill.

View source on GitHub ↗License: MIT