• 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 Examples in Linux

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.

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. CentOS / RHEL 7 : How to enable telnet for a group of users
  2. RHEL 7 – RHCSA Notes – vi/vim editor
  3. Basic vi commands (cheat sheet)
  4. Which network ports are reserved by the Linux Operating System?
  5. uptime Command Examples in Linux
  6. How to disable lvmetad in CentOS/RHEL
  7. Command ‘df -i’ Shows ‘Inode=0’ on BTRFS File System
  8. parted: command not found
  9. Manual Changes Made To /etc/hosts Or /etc/sysconfig/network-scripts/ifcfg-* Are Lost
  10. Linux “rm” Command Examples

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