PubmedTools (pubmedtools)

PubmedTools (pubmedtools) package provides functions for searching and retrieving articles from the PubMed database using Biopython and NCBI Entrez Direct. This is not an official NCBI library and has no direct affiliation with the organization.

Features

• pubmedtoos.search.biopython_search: Searches the PubMed database using a Biopython Entrez module (Bio.Entrez).
• pubmedtoos.search.edirect_search: Searches the PubMed database using the official Entrez Direct tool.
• pubmedtoos.prepenv.edirect_folder: Prepares the Entrez Direct folder for use with the edirect_search function.

Installation

You can install PubmedTools using pip:

pip install pubmedtools

Functions

search

pubmedtools.search.biopython_search

Searches the PubMed database using a given term and retrieves the abstract, title, publication date, authors, MeSH terms, and other terms related to each article. This function use the Bio.Entrez module from Biopython. The search is limited to 10,000 results.

Parameters

• term : str
  • The search term to be used in the query.
• email : str, optional
  • Email address to be used in case the Entrez server needs to contact you.
• api_key : str, optional
  • API key to access the Entrez server.
• batch_size : int, optional
  • Number of articles to be downloaded per iteration. Default is 1000.
• verbose : bool, optional
  • Whether to print progress messages. Default is True.

Returns

• pandas.DataFrame
  • A DataFrame with columns 'pmid', 'ti', 'ab', 'fau', 'dp', 'mh', and 'ot'.
  • Each row contains information related to a single article retrieved from the search term query.

Raises

Exception - If the search returns more than 10,000 results, which is the limit of this function. In this case, the user should use the pubmedtools.search.edirect_search function.

pubmedtools.search.edirect_search

Searches the PubMed database using a given term and retrieves the abstract, title, publication date, authors, MeSH terms, and other terms related to each article. This function use the official NCBI Entrez Direct tool.

Parameters

• query : str
  • The query to be searched in PubMed.
• api_key : str, optional
  • The NCBI API key. If not provided, the search will be performed without the API key.

Returns

• pandas.DataFrame
  • A pandas DataFrame containing the search results.

Notes

• This function works with Linux and Windows systems using WSL (Windows Subsystem for Linux).

Raises

• Exception
  • If the operating system is not recognized.

prepenv

pubmedtools.prepenv.edirect_folder

Function to prepare the edirect folder for pubmed_search_edirect. Checks in pubmedtools package path if the edirect folder exists and contains the necessary files. If not, it downloads and extracts the required files.