ParsePubMed
A script that parses the pubmed xml release for use in python.
Install
pip install git+https://github.com/JSybrandt/ParsePubMed
Get PubMed Data
The following bash command creates a set of directories,
ftp.ncbi.nlm.gov/pubmed/baseline containing many .xml.gz files.
wget -r ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/
Run the Script
This package will convert each .xml.gz file into a pickle. Each pickle
contains a list of dictionaries, corresponding to cache pubmed record in the
corresponding xml file.
python3 -m parse_pubmed <path to .xml.gz directory> <path to output pickle dir>
Here's a real example:
wget -r ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline/
python3 -m parse_pubmed \
./ftp.ncbi.nlm.nih.gov/pubmed/baseline \
./parsed_pubmed_records