pymed-paperscraper 1.0.4

Python library for access to PubMed -- fork from archived PyMed

NOTE: This is a user-maintained extension of the pymed project which was archived in 2020. Some bugs in pymed are fixed here. This package can be installed via pip install pymed-paperscraper since I forked it to support paperscraper.

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:

from pymed_paperscraper import PubMed
pubmed = PubMed(tool="MyTool", email="[e-mail]")
results = pubmed.query("Some query", max_results=500)

Bugfixes compared to archived pymed:

• Article IDs are correctly extracted pymed#22
• Automatic retries if API is unresponsive/overloaded. Support for max_tries in PubMed class.

Notes on the API

The original documentation of the PubMed API can be found here: PubMed Central. 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.

Citation

If you use pymed_paperscraper in your work, please cite:

(Citation follows)