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paperclip

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Search and read full-text biomedical papers, FDA/PMDA/EMA regulatory documents, clinical trial registries, and UniProt/PDB/ChEMBL entries with the Paperclip CLI from GXL. Covers installing and authenticating the `paperclip` binary with a PAPERCLIP_API_KEY, the read-only virtual filesystem under /papers, /fda, /trials, /proteins and /clipboard, source-scoped semantic search, corpus-wide grep, metadata lookup and SQL, map/reduce reading across many papers, figure vision analysis, opt-in paper repositories with claim verification, and line-pinned citations. Use when asked to install paperclip, run paperclip search/grep/map/reduce/sql/repo, find or read biomedical literature, regulatory filings or clinical trials through paperclip, or produce citations with line numbers.

plugins/KalarisLabs/research-agent-skills/skills/paperclip/SKILL.md

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Nov 7, 2026
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Apache-2.0

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# Paperclip CLI

Paperclip exposes roughly 11M full-text papers, 217K+ regulatory documents, 110K+ clinical trial
protocols, and 574K+ protein entries as a **read-only virtual filesystem** navigated with Unix
commands, backed by server-side semantic search and LLM readers.

Every document is line-numbered, and that is the point of the tool: you cite `#L45` and a reader
jumps to the exact sentence. Read the lines you cite, do not paraphrase past what they say, and never
present a semantic-search snippet as if you had read the paper.

## Step 1 — preflight

Run this before anything else. It answers "is it installed" and "who am I" in one call.