lamm-mit/pubmed
skills/pubmed/SKILL.md
Search PubMed for scientific literature and retrieve abstracts
$ install --global
skillsauthnpx skillsauth add lamm-mit/scienceclaw pubmedInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- 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:
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_EMAILenvironment variable for better rate limits - Set
NCBI_API_KEYfor up to 10 requests/second (vs 3/second without) - Results are returned by relevance by default
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