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Traverse UniProt Taxonomic Tree Path

Source: R/uniprot_taxonomy.R
rba_uniprot_taxonomy_path.Rd

Using this function you can retrieve nodes that are located in the top or the bottom of your supplied node in UniProt Taxonomy database tree

Usage

rba_uniprot_taxonomy_path(id, direction, depth = 5, ...)

Arguments

id

(numeric) a NCBI taxonomic identifier

direction

direction of the taxonomic path, either "TOP" or "BOTTOM".

depth

(numeric) How many levels should be traversed on the taxonomic tree? (from 1 to 5, default = 5)

...

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

Value

a nested list containing the node which are in the path specified by your supplied argument in the UniProt taxonomic tree.

Corresponding API Resources

"GET https://ebi.ac.uk/proteins/api/path"

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(), rba_uniprot_taxonomy_lca(), rba_uniprot_taxonomy_lineage(), rba_uniprot_taxonomy_name(), rba_uniprot_taxonomy_relationship()

Examples

# \donttest{
rba_uniprot_taxonomy_path(id = 9606, direction = "TOP", depth = 3)
# }
# \donttest{
rba_uniprot_taxonomy_path(id = 207598, direction = "BOTTOM", depth = 3)
# }