searchpubmed
A Python helper‑library for programmatic PubMed work:
- Search – build and run complex boolean queries (E‑Search)
- Link – map PMIDs ↔ PMCIDs (E‑Link)
- Fetch – pull rich article metadata (E‑Fetch / E‑Summary)
- Full‑text – download JATS XML + HTML from PMC
- Analyse – get tidy results as pandas DataFrames
Query‑builder
The package now ships with a lightweight query‑builder and five pre‑tuned strategies for common real‑world‑data searches.
from searchpubmed import build_query, STRATEGY3_OPTS
print(build_query(STRATEGY3_OPTS)[:120] + "…")
# => (("observational" 5 "ehr"[tiab] OR …) AND english[lang] AND ("2010"[dp] : "3000"[dp]))
Create your own QueryOptions:
from searchpubmed import QueryOptions, build_query
opts = QueryOptions(
data_sources=["ehr", "claims"], # synonym keys
design_terms=["observational", "secondary"],
proximity_within=None,
)
print(build_query(opts))
Core features
- Perform complex boolean searches (AND/OR/NOT, phrase, proximity N)
- Batch retrieval of PMIDs and conversion to PMCIDs
- Fetch detailed metadata (title, abstract, authors, journal, date)
- Configurable rate‑limiting to stay within NCBI usage caps
- Results returned as pandas DataFrames for instant analysis
Installation
pip install searchpubmed
License
Apache 2.0 – see the LICENSE file for details.
1 maintainer
Metadata
1 maintainer
Release files for searchpubmed 0.5.4
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Source distribution (sdist)
| File | Size | Uploaded | |
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| searchpubmed-0.5.4.tar.gz | 34.5 kB | Details |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| searchpubmed-0.5.4-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 61.9 kB
Release files / searchpubmed-0.5.4.tar.gz
| Download URL | searchpubmed-0.5.4.tar.gz |
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| Size | 34.5 kB |
| Tags | Source |
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| Tags | Python 3 |
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