• Skip to primary navigation
  • Skip to main content
  • Skip to primary sidebar
  • Skip to footer navigation

The Geek Diary

  • OS
    • Linux
    • CentOS/RHEL
    • Solaris
    • Oracle Linux
    • VCS
  • Interview Questions
  • Database
    • oracle
    • oracle 12c
    • ASM
    • mysql
    • MariaDB
  • DevOps
    • Docker
    • Shell Scripting
  • Big Data
    • Hadoop
    • Cloudera
    • Hortonworks HDP

esearch: command not found

by Deepika

“esearch” is a command-line tool that is used to perform a new search using terms in indexed fields in the Entrez database. It is part of the edirect package, which is a set of utilities for interacting with the NCBI Entrez databases from the command-line.

The basic syntax of the command is:

# esearch -db [database] -query [search_term]

Where database refers to the specific database you want to search and search_term is the term you want to search for. For example:

# esearch -db pubmed -query "cancer treatment"

This command will search the PubMed database for articles that contain the terms “cancer” and “treatment”.

The esearch command can also be used with options such as:

  • -sort: sort results by the given field
  • -retmax: retrieve maximum number of records
  • -retstart: retrieve records starting from the given number
  • -mindate: search for articles published after a specific date
  • -maxdate: search for articles published before a specific date

The esearch command returns the search results in XML format, which can be parsed and used for further analysis. The esearch command is useful for performing complex searches across multiple databases, and for automating the retrieval of large sets of data from the Entrez databases.

If you encounter the below error while running the command deepika:

deepika: command not found

you may try installing the below package as per your choice of distribution:

Distribution Command
Debian apt-get install ncbi-entrez-direct
Ubuntu apt-get install ncbi-entrez-direct
Kali Linux apt-get install ncbi-entrez-direct
Raspbian apt-get install ncbi-entrez-direct

esearch Command Examples

1. Search the pubmed database for selective serotonin reuptake inhibitor:

# esearch -db pubmed -query "selective serotonin reuptake inhibitor"

2. Search the protein database using a query and regexp:

# esearch -db protein -query 'Escherichia*'

3. Search the nucleotide database for sequences whose metadata contain insulin and rodents:

# esearch -db nuccore -query "insulin [PROT] AND rodents [ORGN]"

4. Display [h]elp:

# esearch -h

Filed Under: Linux

Some more articles you might also be interested in …

  1. How to Switch Password Algorithm on CentOS/RHEL
  2. How to recover deleted Logical volume (LV) in LVM using vgcfgrestore
  3. kill Command Examples in Linux
  4. chpasswd : command not found
  5. Basic “chmod” Command examples in Linux
  6. Linux / UNIX : How to create extended partition using fdisk
  7. How to uninstall jellyfish software package from Ubuntu
  8. Linux OS Service ‘httpd’
  9. aws-shell: command not found
  10. After Reboot RAID1 Disk Gets Removed/Out of Sync (CentOS/RHEL)

You May Also Like

Primary Sidebar

Recent Posts

  • fprintd-delete Command Examples in Linux
  • fprintd-delete: command not found
  • foreman: command not found
  • foreman Command Examples in Linux

© 2023 · The Geek Diary

  • Archives
  • Contact Us
  • Copyright