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Titipat Achakulvisut edited this page May 10, 2019 · 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

Alternative MEDLINE parsers

Alternative parser http://fnl.es/medline-kung-fu.html
Transform MEDLINE XML to json using node, https://github.com/ldbib/MEDLINEXMLToJSON

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/
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 DTD 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