pubmed

Research

Search PubMed for scientific literature and retrieve abstracts

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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