rbioapi: rba_uniprot_taxonomy – R documentation

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rba_uniprot_taxonomy

Get UniProt Taxonomy Nodes

Description

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 provided node's hierarchy in UniProt Taxonomy database.

Usage

rba_uniprot_taxonomy(
  ids,
  hierarchy = NA,
  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 provided 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 provided. 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 provided. 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). Refer to `rba_options`'s arguments documentation for more information on available options.

Value

a list containing your provided 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

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

Examples

rba_uniprot_taxonomy(ids = c(9606, 10090))


rba_uniprot_taxonomy(ids = 9989, hierarchy = "children")

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release