pubmed-sdk

python SDK for searching PubMed

pubmed_sdk

Pubmed_SDK is a Python client library for searching PubMed using the NCBI E-Utilities.

• Examples
• About Pubmed_sdk
• Usage

About Pubmed_sdk

Pubmed_SDK is a Python SDK that facilitates searching PubMed and retrieving article details using the NCBI E-Utilities. It abstracts the process of making HTTP requests to the E-Utilities API and parsing the XML responses, making it easier to focus on the data itself.

Installation

pip install pubmed_sdk

Usage

Search PubMed

You can search PubMed by creating a PubMed object and calling the search method with your search term:

from pubmed_sdk import PubMed

pubmed = PubMed()
results = pubmed.search('COVID-19')

The search method supports the following parameters:

• term: The search term.
• db: The database to search (default is 'pubmed').
• retmax: The maximum number of results to return (default is 20).
• usehistory: Whether to use the NCBI history feature (default is 'y').

Fetch Article Details

After searching, you can fetch the details of the articles using the fetch_details method:

id_list = results['id_list']    # ['33725716', '33725717']
details = pubmed.fetch_details(id_list).get('PubmedArticle')

This method accepts a list of IDs and returns a list of dictionaries containing the details of each article.

Here's an example of how to iterate through the results and print some information about each article:

for detail in details:
    article = detail['MedlineCitation']['Article']
    print(article['ArticleTitle'])
    print(article['Abstract']['AbstractText'], '\n\n')