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Search STRING Functional Terms

Source: R/stringdb.R
rba_string_functional_terms.Rd

STRING maps several functional annotation resources onto its proteins. This function searches for functional terms using an identifier or descriptive text and retrieves the matching terms and their annotated proteins.

Usage

rba_string_functional_terms(term_text, species, ...)

Arguments

term_text

Character: A functional term identifier or descriptive text used to match one or more functional terms.

species

Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A data frame in which every row is a matching functional term and the columns contain the term category, identifier, description, number of annotated proteins, preferred protein names, and STRING protein IDs. preferredNames and stringIds are returned as list-columns.

Details

This endpoint supports only one species per query. If multiple functional terms match term_text, STRING returns them in order of relevance, with the best match first.
The complete number of annotated proteins is reported in proteinCount.

Corresponding API Resources

"POST https://string-db.org/api/{output-format}/functional_terms?term_text= {your_term}&{optional_parameters}"

References

  • Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Katerina Nastou, Farrokh Mehryary, Radja Hachilif, Annika L Gable, Tao Fang, Nadezhda T Doncheva, Sampo Pyysalo, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D638–D646, https://doi.org/10.1093/nar/gkac1000

  • STRING API Documentation

  • Citations note on STRING website

See also

rba_string_annotations, rba_string_enrichment, rba_string_enrichment_image

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_image(), rba_string_enrichment_ppi(), rba_string_homology_inter(), rba_string_homology_intra(), rba_string_interaction_partners(), rba_string_interactions_network(), rba_string_map_ids(), rba_string_network_image(), rba_string_version()

Examples

# \donttest{
rba_string_functional_terms(
    term_text = "T cell receptor signaling pathway",
    species = 9606
)
# }