PubMed Analyzer

EDirect Installation Instructions

• Open a terminal window and run one of the following commands to download and install the software:

  • sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"
  • sh -c "$(wget -q https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh -O -)"

This will prompt a number of script downloads that will be compiled into an "edirect" folder in the user's home directory

You may update the PATH environment variable in the user's configuration file:

• echo "export PATH=$HOME/edirect:$PATH" >> $HOME/.bash_profile

Answer "y" and press the Return key if you want to run the PATH update command

• If the PATH is already set or want to make editing changes manually, press Return
• Once installation is complete, run line below to set the PATH for the current terminal session
  • export PATH=${HOME}/edirect:${PATH}

PubMed Keyword PMID List

• Run the following command line below:
  • esearch -db pubmed -query "your keyword or search terms" | efetch -format uid

The command line will take the keyword or search terms and search the PubMed database to retrieve the records identified by the piped information and format the output into a simple list of unique identifiers

• In order to save the list of PMIDs to a file, utilize a redirection operator to the mentioned command line
  • esearch -db pubmed -query "your keyword or search terms" | efetch -format uid > file_name.txt

PubMed Keyword PMID, Authors, Affiliations, and Journal List

• Run the following command line below:
  • esearch -db pubmed -query "your search terms" |
    efetch -format xml |
    xtract -pattern PubmedArticle
    -element MedlineCitation/PMID ISOAbbreviation
    -block Author -sep " " -element LastName,Initials -sep ", " -block AffiliationInfo -element Affiliation \ > output.txt