Data extraction for systematic reviews and meta-analyses. Reads PDF and Word papers with pdfplumber and python-docx, keeps the page, section, and table cell of every value, and codes them against an Excel codebook in an interactive Shiny interface. Exports effect sizes for group, single-case, and correlation design studies. Companion to pubmlp, which handles screening.
Installation
pip install pubextractor
With optional dependencies:
pip install "pubextractor[semantic]" # sentence-transformers for passage search
From GitHub:
pip install git+https://github.com/mshin77/pubextractor.git
Load the pubextractor Package
import pubextractor
Alternatively, Launch and Browse the Shiny App
Launch and browse the app on the local computer:
from pubextractor import run_app
run_app()
Or in a terminal: pubextractor. The app opens at http://127.0.0.1:8000; use run_app(port=8001) if that port is in use.
Getting Started
See Quick Start and Using the App for tutorials.
Citation
- Shin, M. (2026). pubextractor: Data extraction for systematic reviews and meta-analyses (Python package version 0.1.0) [Computer software]. https://github.com/mshin77/pubextractor
1 maintainer
Metadata
1 maintainer
Release files for pubextractor 0.1.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| pubextractor-0.1.0.tar.gz | 270.5 kB | Without provenance | Details for pubextractor-0.1.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| pubextractor-0.1.0-py3-none-any.whl | Python 3 | none | any | Details for pubextractor-0.1.0-py3-none-any.whl |
Total release size: 466.2 kB
Release files / pubextractor-0.1.0.tar.gz
| Download URL | pubextractor-0.1.0.tar.gz |
|---|---|
| Size | 270.5 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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No |
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twine/7.0.0 CPython/3.14.6
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Release files / pubextractor-0.1.0-py3-none-any.whl
| Download URL | pubextractor-0.1.0-py3-none-any.whl |
|---|---|
| Size | 195.7 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.14.6
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Security for pubextractor 0.1.0
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