pymed-paperscraper 1.0.6

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.
• Titles and abstracts no longer get truncated when PubMed XML contains inline formatting tags such as italics.

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)