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Resources related to Pubmed Parser

Here, we include how to set up PySpark with Pubmed Parser and on how to download PubMed Open-Access (PubMed OA) and MEDLINE dataset:

• Setup Spark 2.1
• Download and preprocess MEDLINE dataset
• Download and preprocess Pubmed Open-Access Subset
• Download PubMed OA figures

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 tags from a given MEDLINE XML.

PMC Copyright Notice

• Please see copyright notice when you scrape data from website here

Alternative implementation of MEDLINE parsers

• MEDLINE Kung-Fu which uses medic to parse MEDLINE to database
• MEDLINEXMLToJSON implemented in JavaScript