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On this page you find all important commands for the CLI tool esearch. If the command you are looking for is missing please ask our AI.

esearch

Esearch is a command line tool provided by the NCBI (National Center for Biotechnology Information) to search for biomedical literature using the Entrez search engine. It is a part of the Entrez Direct package, which is a collection of programs to help retrieve data from Entrez databases. Esearch allows users to search different databases such as PubMed, PubMed Central, Gene, and others, and retrieve information related to specific terms or keywords. It supports a range of search options, including simple text queries, Boolean operators, filters, and complex queries using field qualifiers. Users can also specify the number of results they want to retrieve and the format in which they want the results to be displayed. Esearch can be used interactively in a terminal or in scripts for automation and batch processing. The tool provides features like history tracking, which allows users to revisit previous searches and combine or modify them for new queries. Esearch also supports advanced search strategies, such as using the advanced search syntax supported by the Entrez system. It is a powerful tool for researchers, clinicians, and anyone involved in the biomedical field to explore and extract information from the vast collection of literature available in various NCBI databases. Overall, Esearch simplifies the process of searching and accessing biomedical literature, making it a valuable resource for information retrieval in the scientific community.

List of commands for esearch:

  • elink:tldr:5b001 elink: Search pubmed then find related sequences.
    $ esearch -db pubmed -query "${selective serotonin reuptake inhibitor}" | elink -target nuccore
    try on your machine
    explain this command
  • elink:tldr:90ff1 elink: Search nucleotide then find related biosamples.
    $ esearch -db nuccore -query "${insulin [PROT] AND rodents [ORGN]}" | elink -target biosample
    try on your machine
    explain this command
  • esearch:tldr:6dace esearch: Search the protein database using a query and regexp.
    $ esearch -db ${protein} -query ${'Escherichia*'}
    try on your machine
    explain this command
  • esearch:tldr:7eed9 esearch: Search the nucleotide database for sequences whose metadata contain insulin and rodents.
    $ esearch -db nuccore -query "${insulin [PROT] AND rodents [ORGN]}"
    try on your machine
    explain this command
  • esearch:tldr:d4347 esearch: Display [h]elp.
    $ esearch -h
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    explain this command
  • esearch:tldr:e2d77 esearch: Search the pubmed database for selective serotonin reuptake inhibitor.
    $ esearch -db pubmed -query "${selective serotonin reuptake inhibitor}"
    try on your machine
    explain this command
tool overview