Pubmed Downloader

This code helps you to start a thematic collection of articles by automatically downloading them from PubMed.

It uses Pubmed official API, so there is no scraping involved and its completely in accordance with its usage policy.

Downloading

To start using it, follow the steps below.

from fetch import SearchAndCapture
S = SearchAndCapture('your@email.com', '((zika microcephaly) NOT zika[author])')
S.update_multiple_searches()
S.update_citations_concurrently()

That's all! You may want to run it once a day to include recently published articles. This will also update a separate collection with the citation network for all the PMIDs in the article collection

You need to have a local mongodb server running.

Export network data

You can export csv files with data structued for network analysis:

$ python3 network_analysis.py