pubmed-database

84 / 100 · Low risk

Fine to try. Some of what it can do is expected: a research skill usually looks things up on the internet.

By sharkrebel/everything-everywhere-for-antigravity (GitHub) · research · 89 stars · scanned at commit 71bf78c

Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs.

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

This is disclosed by the author in the skill's SKILL.md or README.

Found in 5 places.

skills/pubmed_database/SKILL.md, line 79uv run scripts/pubmed_api.py <output_file> <function_name> <required_args> [--flag value ...]
skills/pubmed_database/SKILL.md, line 93uv run scripts/pubmed_api.py ./search_results.json search_pubmed "BRCA1" --max_results 5
skills/pubmed_database/SKILL.md, line 104cat ./search_results.json | jq -r 'join(",")'

Show 2 more

skills/pubmed_database/SKILL.md, line 110cat ./abstracts.json | jq '[.[] | {pmid, title, snippet: (.abstract // "")[:500]}]'
skills/pubmed_database/SKILL.md, line 116cat ./abstracts.json | jq '[.[] | select((.title // "") | contains("Review"))]'

Connects to the internet

This is disclosed by the author in the skill's SKILL.md or README. Expected for a research skill.

Found in 1 place.

skills/pubmed_database/scripts/pubmed_api.py, line 129resp = get_eutils_client().fetch(url, method="POST", data=data_bytes)

Reads your saved credentials, such as SSH keys or .env files

This is disclosed by the author in the skill's SKILL.md or README.

Found in 1 place.

skills/pubmed_database/scripts/pubmed_api.py, line 636dotenv.load_dotenv(os.path.expanduser("~/.env"))

Other copies in this repository

sharkrebel/everything-everywhere-for-antigravity has 1 more folder with a skill named pubmed-database. This page shows the lowest-scoring copy.

plugins/science/skills/pubmed_database 84/100 · Low risk

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'pubmed-database' ] || [ -L ~/.agents/skills/'pubmed-database' ]; then echo 'A skill folder named pubmed-database already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/sharkrebel/everything-everywhere-for-antigravity' "$d" && git -C "$d" checkout --quiet '71bf78cfb929edcf8972b707085c40cc0cf23bae' -- 'skills/pubmed_database' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/pubmed_database' ~/.agents/skills/'pubmed-database' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'pubmed-database' ~/.claude/skills/'pubmed-database' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-11	`71bf78c`	84