PubMed API Search
Search PubMed via NCBI E-utilities API (ESearch + EFetch). Results are cached in SQLite for offline re-query.
Usage
Python: python3 (fallback: ask user for path if not found)
# Basic search
python3 <skill_path>/scripts/pubmed_search.py --query "your search terms" --max 20
# With date range
python3 <skill_path>/scripts/pubmed_search.py --query "brain tumor" --mindate 2023/01/01 --max 30
# Recent papers only
python3 <skill_path>/scripts/pubmed_search.py --query "surgical robot" --recent 3
# Brief mode (id + title + date only, saves tokens for large batch screening)
python3 <skill_path>/scripts/pubmed_search.py --query "..." --brief
# Query local database (no API call)
python3 <skill_path>/scripts/pubmed_search.py --db-query "keyword"
# Markdown output
python3 <skill_path>/scripts/pubmed_search.py --query "..." --format markdown
# With API key (higher rate limit: 10 req/s vs 3 req/s)
python3 <skill_path>/scripts/pubmed_search.py --query "..." --api-key YOUR_KEY
Parameters
| Param | Description |
|---|---|
--query, -q | Search query (supports PubMed syntax, see below) |
--max, -m | Max results, default 20 |
--recent | Filter to last N years |
--mindate | Start date (YYYY/MM/DD or YYYY/MM or YYYY) |
--maxdate | End date |
--brief | Minimal output: pmid, title, pub_date only |
--format, -f | json (default, compact) or markdown |
--db-query, -d | Search local cache instead of API |
--api-key | NCBI API key (optional, get from https://www.ncbi.nlm.nih.gov/account/) |
Query Syntax
term1 AND term2 # both required
term1 OR term2 # either
term1 NOT term2 # exclude
"exact phrase"[tiab] # title + abstract
keyword[MeSH] # MeSH term
author_name[Author] # author
journal_name[Journal] # journal
review[pt] # publication type filter
Common field tags: [ti] title, [ab] abstract, [tiab] both, [au] author, [ta] journal, [mh] MeSH, [pt] pub type.
Publication types: review[pt], clinical trial[pt], randomized controlled trial[pt], case reports[pt], meta-analysis[pt].
Output Fields
Default: pmid, title, abstract, pub_date, journal
Brief mode: pmid, title, pub_date
Authors, DOI, keywords are stored in database but excluded from output to save tokens.
Notes
- Results sorted by publication date (newest first)
- Rate limit: 3 req/s without API key, 10 req/s with key. Script has built-in retry with backoff.
- Database:
<skill_path>/data/pubmed_cache.db