https://github.com/jannisborn/pymed

PyMed is a Python library that provides access to PubMed. This is a user-maintained fork from the archived original.
https://github.com/jannisborn/pymed

Last synced: about 1 month ago
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PyMed is a Python library that provides access to PubMed. This is a user-maintained fork from the archived original.

• Host: GitHub
• URL: https://github.com/jannisborn/pymed
• Owner: jannisborn
• License: mit
• Created: 2024-10-13T16:42:32.000Z (3 months ago)
• Default Branch: main
• Last Pushed: 2024-11-05T22:59:47.000Z (2 months ago)
• Last Synced: 2024-12-07T12:30:03.537Z (about 1 month ago)
• Language: Python
• Size: 297 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Contributing: .github/CONTRIBUTING.md
  • Code of conduct: .github/CODE_OF_CONDUCT.md

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NOTE: This is a user-maintained extension of the [pymed](https://pypi.org/project/pymed/) project which was [archived in 2020](https://github.com/gijswobben/pymed). Some bugs in `pymed` are fixed here. This package can be installed via `pip install pymed-paperscraper` since I forked it to support [`paperscraper`](https://github.com/jannisborn/paperscraper).

[![License:

MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

[![PyPI version](https://badge.fury.io/py/pymed_paperscraper.svg)](https://badge.fury.io/py/pymed_paperscraper)

[![Downloads](https://static.pepy.tech/badge/pymed_paperscraper)](https://pepy.tech/project/pymed_paperscraper)

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# PyMed - PubMed Access through Python

PyMed is a Python library that provides access to PubMed through the PubMed API.

## Why this library?

The PubMed API is not very well documented and querying it in a performant way is too complicated and time consuming for researchers. This wrapper provides access to the API in a consistent, readable and performant way.

## Features

This library takes care of the following for you:

- Querying the PubMed database (with the standard PubMed query language)

- Batching of requests for better performance

- Parsing and cleaning of the retrieved articles

## Examples

For full (working) examples have a look at the `examples/` folder in this repository. In essence you only need to import the `PubMed` class, instantiate it, and use it to query:

```python

from pymed_paperscraper import PubMed

pubmed = PubMed(tool="MyTool", email="[email protected]")

results = pubmed.query("Some query", max_results=500)

```

## Notes on the API

The original documentation of the PubMed API can be found here: [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/tools/developers/). PubMed Central kindly requests you to:

> - Do not make concurrent requests, even at off-peak times; and

> - Include two parameters that help to identify your service or application to our servers

>   * _tool_ should be the name of the application, as a string value with no internal spaces, and

>   * _email_ should be the e-mail address of the maintainer of the tool, and should be a valid e-mail address.