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Titipat Achakulvisut edited this page Jan 16, 2020 · 18 revisions

Workflow of Pubmed Parser with PySpark

We include PySpark snippets on how to parse Pubmed Open-Access and MEDLINE dataset on the wiki page here

Links to download Pubmed and MEDLINE dataset

Here are links for downloading Pubmed OA and MEDLINE data

Pubmed Open-Access (OA) dataset is available at http://www.ncbi.nlm.nih.gov/pmc/tools/ftp/. Here is the FTP link for downloading the bulk of dataset.
the MEDLINE XMLs are available here ftp://ftp.nlm.nih.gov/nlmdata/.medleasebaseline/gz/
the MEDLINE XMLs weekly updates are available here ftp://ftp.nlm.nih.gov/nlmdata/.medlease/gz/
MEDLINE Document Type Definitions (DTDs) file is available at this link. We can use it to see available tag from MEDLINE xml.

PMC Copyright Notice

Please see copyright notice when you scrape data from website here

Alternative implementation of MEDLINE parsers

MEDLINE Kung-Fu, use medic to parse MEDLINE to database
MEDLINEXMLToJSON implemented in JavaScript