pubmed

name	pubmed
description	Search PubMed for scientific literature and retrieve abstracts
metadata	null

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