Finding the right articles for a systematic review or meta-analysis is the most challenging part. Janssens et. al has published a novel algorithm to expedite the process of finding eligible studies for meta-analysis based on the degree of co-citation. I have written a small shell script to implement the algorithm for PubMed using Entrez Direct.
- Get hold of a Linux box.
- Install Entrez Direct from NCBI by cutting and pasting the code below.
cd ~
perl -MNet::FTP -e \
'$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $ftp->login;
$ftp->binary; $ftp->get("/entrez/entrezdirect/edirect.zip");'
unzip -u -q edirect.zip
rm edirect.zip
export PATH=$PATH:$HOME/edirect
./edirect/setup.sh
- In the terminal window
sudo apt-get install xml-twig-tools - Download this script to a writable folder.
- Find the PMID of your key articles.
./ma.sh <PMID> <PMID> <PMID> - Example: ./ma.sh 18032878
- Grab a coffee and wait :)
- The results will be written to results.txt in the same folder
- Results include degree of co-citation along with corresponding PMID in each line.
- Enjoy!
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