rnaCentralTextSearch: Searches the RNAcentral database with a text query

In ncRNAtools: An R toolkit for non-coding RNA

Description

Searches the RNAcentral database of non-coding RNA with a text query.

Usage

rnaCentralTextSearch(query)

Arguments

query

string to be used as the text query to search the RNAcentral database. The most basic usage involves providing a word or group of words to be matched against any of the fields of entries of the RNAcentral database. More refined searches can be done by using the field_name:"field value" syntax. Several search terms can be combined with logical operators (and, or, not). Asterisks ("*") can be added to signal any number of any characters. If not added to the query, only exact matches are produced. A detailed description of the syntax can be found at https://rnacentral.org/help/text-search. The entire query should be provided as a single string, and double quotes enclosing field values must be escaped with a backslash (“\“). It should also be noted that logical operators should be capitalized.

Value

A character vector where each element is the RNAcentral ID of an entry that matched the query. A maximum of 15 IDs will be returned.

References

https://rnacentral.org/about-us

https://rnacentral.org/help/text-search

Examples

# Find RNAcentral entries that correspond to the HOTAIR long noncoding RNA:

rnaCentralTextSearch("HOTAIR")

# Find RNAcentral entries that correspond to FMN riboswitches in Bacillus subtilis:

rnaCentralTextSearch("FMN AND species:\"Bacillus subtilis\"")

ncRNAtools documentation built on Nov. 8, 2020, 8:14 p.m.