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 type (recommend XML), utilize a redirection operator to the mentioned command line
  • esearch -db pubmed -query "your keyword or search terms" | efetch -format uid > file_name

This step was done to ensure that all PMIDs for the corresponding keyword appeared.

PubMed Keyword XML File

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

PubMed Keyword PMID, Authors, Affiliations, and Journal List

• Use the XML file created from the previous step to extract only the PMID, authors, affiliations, and journal list
  • xtract -input "file name" -pattern PubmedArticle -element MedlineCitation/PMID -block Author -pfx "\n" -element LastName,Initials,AffiliationInfo/Affiliation -sep "\n" > file_name