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Get UniProt Taxonomy Nodes

Source: R/uniprot_taxonomy.R
rba_uniprot_taxonomy.Rd

Retrieve taxonomic-node information using NCBI taxonomic identifiers. You can also retrieve nodes related to one supplied node in UniProt Taxonomy database. Child and sibling results are paginated.

Usage

rba_uniprot_taxonomy(
  ids,
  hierarchy = NULL,
  node_only = TRUE,
  page_size = 200,
  page_number = 1,
  ...
)

Arguments

ids

Numeric: One or more NCBI taxonomic identifiers.

hierarchy

Character: (optional) Retrieve nodes related to one supplied node. One of "children", "parent", or "siblings".

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 child or sibling nodes per page. The maximum is 200.

page_number

Numeric: (default = 1) Page of child or sibling nodes to retrieve.

...

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

Value

A list containing taxonomy information for the requested nodes or their related nodes.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/taxonomy/id/{id}"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/ids/{ids}"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/ids/{ids}/node"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/id/{id}/node"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/id/{id}/children"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/id/{id}/children/node"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/id/{id}/parent"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/id/{id}/parent/node"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/id/{id}/siblings"
"GET https://www.ebi.ac.uk/proteins/api/taxonomy/id/{id}/siblings/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

See also

Other "UniProt - Taxonomy": rba_uniprot_taxonomy_lca(), rba_uniprot_taxonomy_lineage(), rba_uniprot_taxonomy_name(), rba_uniprot_taxonomy_path(), rba_uniprot_taxonomy_relationship()

Examples

# \donttest{
rba_uniprot_taxonomy(ids = c(9606, 10090))
# }
# \donttest{
rba_uniprot_taxonomy(ids = 9989, hierarchy = "children")
# }