How do I install the Pubmed skill?

Run npx skillmds@latest add lamm-mit/pubmed in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

What does the Pubmed skill do?

Search PubMed for scientific literature and retrieve abstracts It is listed under Research & Search on SkillMD.

Is Pubmed safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Pubmed?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Pubmed free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Pubmed?

lamm-mit (@lamm-mit) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Pubmed by lamm-mit — Agent Skill

Name: Pubmed
Author: lamm-mit

File contents

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:

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

Search with filters:

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

Get full abstracts:

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

Export citations:

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

Fetch specific article by PMID:

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:

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

Search by author:

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

Get BibTeX for citations:

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

Combine multiple filters:

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

---name: pubmeddescription: Search PubMed for scientific literature and retrieve abstracts---# PubMed SearchSearch the PubMed database for scientific literature, retrieve abstracts, and format citations.## OverviewPubMed 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:```bashpython3 {baseDir}/scripts/pubmed_search.py --query "CRISPR gene editing"```### Search with filters:```bashpython3 {baseDir}/scripts/pubmed_search.py --query "cancer immunotherapy" --year 2024 --max-results 20```### Get full abstracts:```bashpython3 {baseDir}/scripts/pubmed_search.py --query "machine learning drug discovery" --format detailed```### Export citations:```bashpython3 {baseDir}/scripts/pubmed_search.py --query "protein folding" --format bibtex```### Fetch specific article by PMID:```bashpython3 {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 SyntaxPubMed 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:```bashpython3 {baseDir}/scripts/pubmed_search.py --query "AlphaFold protein structure" --year 2024 --max-results 15```### Search by author:```bashpython3 {baseDir}/scripts/pubmed_search.py --query "CRISPR" --author "Doudna JA"```### Get BibTeX for citations:```bashpython3 {baseDir}/scripts/pubmed_search.py --query "deep learning genomics" --format bibtex --max-results 5```### Combine multiple filters:```bashpython3 {baseDir}/scripts/pubmed_search.py --query "COVID-19 vaccine" --year-start 2023 --year-end 2024 --sort date```## Output Formats### SummaryCompact list with title, authors, journal, and year.### DetailedFull abstract, author affiliations, MeSH terms, and DOI.### BibTeXCitation format for LaTeX documents.### JSONMachine-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

Frequently asked questions

Pubmed