“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