Agent skill · research science · k-dense-ai
paperclip
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.
Why this skill is useful
Provides specific commands and workflows for accessing and utilizing biomedical literature and regulatory documents that the AI wouldn't reliably generate on its own.
What it needs
Requires paperclip installed locally. Requires paperclip account access. About 12k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
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. Read the Auth: line — it decides everything that follows: Output Meaning Do this --- --- --- ✓ API key (env) The API key loaded. Correct state. Proceed, using the auth prefix below ✓ someone@example.com The key did not load — this is stored OAuth, a different identity If .env holds a key, you forgot the prefix. Fix it ✗ (run: paperclip login) No credential at all Ask the user to authenticate — see Installing paperclip NOT INSTALLED No binary See Installing Health: ✓ server reachable is an unauthenticated probe, and Auth: ✓ only means a credential is present, not valid. A junk key produces the same two lines. Prove the credential with a real query: Step 2 — operating rules These are the rules that make the difference between working and silently-wrong. They matter more than any individual command. 1. Put the auth prefix in every command Shell state does not survive between tool calls. Exporting the key in one call and running paperclip in the next means the key is gone — and Paperclip does not error, it silently falls back to stored OAuth, i.e. a different identity and possibly a different account. Prepend this to every invocation, in the directory holding .env: The [ -f .env ] guard is required, not decoration: a bare . ./.env on a missing file kills a POSIX shell, so an unguarded prefix silently discards the rest of your command. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/paperclip