Agent skill

Pubmed

Search PubMed for scientific literature and retrieve abstracts

Apache-2.0Auto-check passedResearch & Science

Install Pubmed

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill pubmed -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw pubmed --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/pubmed .claude/skills/pubmed && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "pubmed" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/pubmed into .claude/skills/pubmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/lamm-mit/scienceclaw/tree/main/skills/pubmed

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill pubmed -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw pubmed --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/pubmed .agents/skills/pubmed && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "pubmed" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/pubmed into .agents/skills/pubmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill pubmed -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw pubmed --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/pubmed .cursor/skills/pubmed && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "pubmed" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/pubmed into .cursor/skills/pubmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/lamm-mit/scienceclaw.git --path skills/pubmed

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill pubmed -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw pubmed --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/pubmed .gemini/skills/pubmed && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "pubmed" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/pubmed into .gemini/skills/pubmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw pubmed

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill pubmed -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/pubmed .github/skills/pubmed && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "pubmed" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/pubmed into .github/skills/pubmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill pubmed -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw pubmed --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/pubmed .opencode/skills/pubmed && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "pubmed" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/pubmed into .opencode/skills/pubmed/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pubmed", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: pubmed
GitHub stars: 244
Token cost: ~817 tokens
SKILL.md length: 244 words
Files: 4 (incl. scripts, references)
Skills in repo: 85
Repo updated: Aug 21, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Search PubMed for scientific literature and retrieve abstracts

Tasks that involve Academic paper search
SKILL.md covers Overview, Usage, Parameters and Search Syntax, plus 3 more sections
Runs Python scripts from its folder; calls python3; needs NCBI_API_KEY
Tasks that involve Citation management

What it does

Pubmed is an agent skill from lamm-mit/scienceclaw. Search PubMed for scientific literature and retrieve abstracts

Its SKILL.md is about 820 tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts and reference files (for example `references/ncbi-api.md` and `scripts/pubmed_search.py`).

It sits in Research & Science, covering Academic paper search and Citation management. It works with PubMed, LaTeX and NCBI. The licence is Apache-2.0.

When your agent uses it

Tasks that involve Academic paper search
Tasks that involve Citation management

Example prompts

“/pubmed”

Requirements

Python 3
A credential in NCBI_API_KEY

What it can do on your machine

Read from SKILL.md and the folder at commit ab9aba1. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 2 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
- python3
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names these keys or tokens, usually read from environment variables:
- NCBI_API_KEY
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Pubmed loads about 817 tokens when it runs, and up to ~2.2k if it reads all its reference files. Until then it costs about 17 tokens; SKILL.md has 244 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~17
When it runs · the whole SKILL.md, loaded when a task matches: ~817
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~2.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from lamm-mit/scienceclaw at commit ab9aba1, republished under its Apache-2.0 licence (© lamm-mit). 244 words, ~817 tokens.

Download SKILL.mdSave it as .claude/skills/pubmed/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.

name: pubmed
description: Search PubMed for scientific literature and retrieve abstracts

PubMed Search

Search the PubMed database for scientific literature, retrieve abstracts, and format citations.

Overview

PubMed is a free database of biomedical literature from MEDLINE, life science journals, and online books. This skill uses NCBI's E-utilities API to search and fetch articles.

Usage

Basic search:

bash

python3 {baseDir}/scripts/pubmed_search.py --query "CRISPR gene editing"

Search with filters:

bash

python3 {baseDir}/scripts/pubmed_search.py --query "cancer immunotherapy" --year 2024 --max-results 20

Get full abstracts:

bash

python3 {baseDir}/scripts/pubmed_search.py --query "machine learning drug discovery" --format detailed

Export citations:

bash

python3 {baseDir}/scripts/pubmed_search.py --query "protein folding" --format bibtex

Fetch specific article by PMID:

bash

python3 {baseDir}/scripts/pubmed_search.py --pmid 35648464

Parameters

Parameter	Description	Default
`--query`	Search query (supports PubMed syntax)	Required*
`--pmid`	Specific PubMed ID to fetch	-
`--max-results`	Maximum number of results	10
`--year`	Filter by publication year	-
`--year-start`	Start year for date range	-
`--year-end`	End year for date range	-
`--author`	Filter by author name	-
`--journal`	Filter by journal name	-
`--format`	Output format: summary, detailed, bibtex, json	summary
`--sort`	Sort by: relevance, date, first_author	relevance

*Required unless --pmid is provided

Search Syntax

PubMed supports advanced search operators:

AND/OR/NOT: Combine terms (cancer AND therapy)
Phrases: Use quotes ("breast cancer")
Field tags: [Title], [Author], [Journal], [MeSH]
Wildcards: * for truncation (immun*)

Examples:

cancer[Title] AND therapy[Title]
"machine learning"[Title/Abstract]
Smith J[Author] AND 2024[Date - Publication]
Nature[Journal]
CRISPR[MeSH Terms]

Examples

Search recent papers on a topic:

bash

python3 {baseDir}/scripts/pubmed_search.py --query "AlphaFold protein structure" --year 2024 --max-results 15

Search by author:

bash

python3 {baseDir}/scripts/pubmed_search.py --query "CRISPR" --author "Doudna JA"

Get BibTeX for citations:

bash

python3 {baseDir}/scripts/pubmed_search.py --query "deep learning genomics" --format bibtex --max-results 5

Combine multiple filters:

bash

python3 {baseDir}/scripts/pubmed_search.py --query "COVID-19 vaccine" --year-start 2023 --year-end 2024 --sort date

Output Formats

Summary

Compact list with title, authors, journal, and year.

Detailed

Full abstract, author affiliations, MeSH terms, and DOI.

BibTeX

Citation format for LaTeX documents.

JSON

Machine-readable format with all metadata.

Notes

NCBI E-utilities have rate limits; heavy usage should use an API key
Set NCBI_EMAIL environment variable for better rate limits
Set NCBI_API_KEY for up to 10 requests/second (vs 3/second without)
Results are returned by relevance by default

Files

SKILL.md and 3 other files (scripts, references) in skills/pubmed of lamm-mit/scienceclaw.

SKILL.md
references/ncbi-api.md
scripts/__pycache__/pubmed_search.cpython-313.pyc
scripts/pubmed_search.py

Open the folder on GitHubat commit ab9aba1

Compare with similar skills

Pubmed next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Pubmed compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Pubmed this skilllamm-mit/scienceclaw	244	—	~817	Automated safety check: Pass	Apache-2.0	1 mo ago
Search LitAperivue/medsci-skills	329	—	~4.7k	Automated safety check: Pass	MIT	3 days ago
Citation Managementneflibata-feng/MyArxiv-Agent	126	20 repos	~8.1k	Automated safety check: Notes	MIT	yesterday
Nature Academic Searchjing1312/nature-figure-skill	167	—	~1.3k	Automated safety check: Notes	MIT	1 mo ago
Literature DownloaderLucaswangzcx/literature-downloader-skill	236	—	~1.4k	Automated safety check: Pass	MIT	5 mo ago
PubMed REST API Searchdavila7/claude-code-templates	32k	15 repos	~3.9k	Automated safety check: Pass	MIT	today

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Questions about Pubmed

What does Pubmed do?

Search PubMed for scientific literature and retrieve abstracts. Pubmed is an agent skill from lamm-mit/scienceclaw.

When should I use Pubmed?

Pubmed fits situations like: tasks that involve Academic paper search; tasks that involve Citation management.

How do I install Pubmed in Claude Code?

Run `npx skills add lamm-mit/scienceclaw --skill pubmed -a claude-code`. Or copy the skill folder (skills/pubmed in lamm-mit/scienceclaw) into .claude/skills/pubmed in your project. Claude Code loads it when a task matches its description.

How do I install Pubmed in Codex?

Run `npx skills add lamm-mit/scienceclaw --skill pubmed -a codex`. Or copy the skill folder (skills/pubmed in lamm-mit/scienceclaw) into .agents/skills/pubmed in your project. Codex loads it when a task matches its description.

Can I use Pubmed in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add lamm-mit/scienceclaw --skill pubmed -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pubmed, .gemini/skills/pubmed, .github/skills/pubmed and .opencode/skills/pubmed in your project.

What does Pubmed need to run?

Going by SKILL.md and its folder, Pubmed needs Python for the scripts in its folder, the command-line tools its instructions call (python3) and credentials named NCBI_API_KEY. Our summary lists: Python 3; A credential in NCBI_API_KEY.

Does Pubmed access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Pubmed safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Pubmed use?

Pubmed is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Pubmed use?

About 817 tokens (SKILL.md is roughly 3.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.4k tokens, read only when the agent opens those files.

What are the alternatives to Pubmed?

Skills that share tags, products or a category with Pubmed: Search Lit (Aperivue/medsci-skills, 329 stars), Citation Management (neflibata-feng/MyArxiv-Agent, 126 stars), Nature Academic Search (jing1312/nature-figure-skill, 167 stars) and Literature Downloader (Lucaswangzcx/literature-downloader-skill, 236 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Pubmed?

lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 244 GitHub stars. The repository holds 85 skills in this directory. The repository was last updated on August 21, 2026.

Source: lamm-mit/scienceclaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Pubmed

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

PubMed Search

Overview

Usage

Basic search:

Search with filters:

Get full abstracts:

Export citations:

Fetch specific article by PMID:

Parameters

Search Syntax

Examples:

Examples

Search recent papers on a topic:

Search by author:

Get BibTeX for citations:

Combine multiple filters:

Output Formats

Summary

Detailed

BibTeX

JSON

Notes

Files

Compare with similar skills

Similar skills

More from lamm-mit/scienceclaw

Related

Questions about Pubmed