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Get UniProt Taxonomy Nodes

Source: R/uniprot_taxonomy.R
rba_uniprot_taxonomy.Rd

Using this function, you can retrieve taxonomic nodes information by providing their NCBI taxonomic identifiers. also, you can explicitly retrieve other nodes in relation to your supplied node's hierarchy in UniProt Taxonomy database.

Usage

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

Arguments

ids

(numeric) a single or a numeric vector of NCBI taxonomic identifier(s)

hierarchy

Retrieve taxonomic nodes that have specific hierarchical relation to your supplied taxonomic node. should be one of: "children", "parent" or "siblings".

node_only

Retrieve only the node(s) information and exclude URL links to parents, siblings and children nodes.

page_size

(numeric) Only when hierarchy is supplied. hierarchy information may be very long, thus UniProt API will paginate the results, you may use this argument to control the pagination. maximum value is 200.

page_number

(numeric) Only when hierarchy is supplied. hierarchy information may be very long, thus UniProt API will paginate the results, you may use this argument to control the pagination.

...

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

Value

a list containing your supplied nodes or their related nodes taxonomic information.

Corresponding API Resources

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

References

  • The UniProt Consortium, UniProt: the universal protein knowledgebase in 2021, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100

  • Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin, The Proteins API: accessing key integrated protein and genome information, Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages 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")
# }