elink:tldr:5b001

The command you mentioned consists of two parts, separated by the pipe symbol "|".

1. esearch -db pubmed -query "${selective serotonin reuptake inhibitor}":

   • This part uses the "esearch" command-line tool.
   • It is used to perform a search in the PubMed database ("pubmed" is specified as the "-db" option).
   • The search query is "${selective serotonin reuptake inhibitor}". The phrase is wrapped in "${...}" to indicate that it is a variable name.
   • The specific query term is not provided in this command; it should be replaced with the desired term by the user. For example, if the desired term is "fluoxetine", the command will be "esearch -db pubmed -query "fluoxetine"".
   • The command will search for papers related to the specified query term in the PubMed database. It will provide a list of matching PubMed IDs (PMIDs) as output.

2. elink -target nuccore:

   • This part uses the "elink" command-line tool.
   • It is used to query related links in NCBI databases based on the provided list of PMIDs.
   • The "-target nuccore" option specifies that the desired target database is "nuccore", which contains nucleotide sequences.
   • The output from the "esearch" command (list of PMIDs) is passed as input to the "elink" command.
   • The "elink" command will retrieve the related nucleotide objects/sequences from the "nuccore" database, associated with the papers retrieved in the previous step.

In summary, the combined command allows you to search PubMed for papers related to a specific term (such as a selective serotonin reuptake inhibitor), and then retrieve the related nucleotide sequences from the "nuccore" database for those papers.