Repository for scripts used for the abstract mining project for the Data Science 2016 Course at Poli USP
Bash script for downloading abstracts. The query term of interest should be placed in the "queryterm" placeholder. The output is a list with all relevant abstracts concatenated into a single file. In the script, the placeholder is "juvenile idiopathic arthritis", the query used in our project, for reproducibility.
esearch -db pubmed -query <queryterm> | efetch -format medline
Perl script for separating the result of download_abs.sh. The input is the abstracts file, and the output is a folder containing all separated abstracts.
perl get_abs.pl <abstractsfile>
R functions for interactive importing and analysis of the get_abs.pl script. The outputs are several PDF files containing the results of analyses