Search UniProt Taxonomic Names

Search and retrieve taxonomic nodes by name from the UniProt Taxonomy database. Search results are paginated.

Usage

rba_uniprot_taxonomy_name(
  name,
  field = "scientific",
  search_type = "equal_to",
  node_only = TRUE,
  page_size = 200,
  page_number = 1,
  ...
)

Arguments

name: Character: Taxonomic name to search.
field: Character: (default = "scientific") Name field to search. One of "scientific", "common", or "mnemonic".
search_type: Character: (default = "equal_to") Relationship between the query and taxonomic name. One of "equal_to", "start_with", "end_with", or "contain".
node_only: Logical: (default = TRUE) If TRUE, return node information without links to parent, sibling, and child nodes.
page_size: Numeric: (default = 200) Number of results per page. The maximum is 200.
page_number: Numeric: (default = 1) Page to retrieve.
...: rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

A list containing matching taxonomic nodes and page information.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/taxonomy/name/{name}"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/name/{name}/node"

References

The UniProt Consortium. (2025). UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research, 53(D1), D609–D617. https://doi.org/10.1093/nar/gkae1010
Nightingale, A., Antunes, R., Alpi, E., Bursteinas, B., Gonzales, L., Liu, W., Luo, J., Qi, G., Turner, E., & Martin, M. (2017). The Proteins API: Accessing key integrated protein and genome information. Nucleic Acids Research, 45(W1), W539–W544. https://doi.org/10.1093/nar/gkx237
Proteins API Documentation
Citations note on UniProt website

Examples

# \donttest{
rba_uniprot_taxonomy_name(name = "homo", field = "scientific",
    search_type = "start_with")
# }
# \donttest{
rba_uniprot_taxonomy_name(name = "adenovirus", field = "scientific",
    search_type = "contain", page_size = 200, page_number = 2)
# }