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Search UniProt Taxonomic Names

Source: R/uniprot_taxonomy.R
rba_uniprot_taxonomy_name.Rd

Using this function, you can search and retrieve taxonomic nodes using their names from UniProt Taxonomy database.

Usage

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

Arguments

name

a name to to be used as search query.

field

Specify the field that your supplied name should be searched. It should be one of : "scientific" (default), "common" or "mnemonic".

search_type

The logical relationship between your supplied search query and the taxonomic name field. It should be one of "equal_to" (default), "start_with", "end_with" or "contain".

node_only

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

page_size

(numeric) Your search results 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) Your search results may be very long, thus UniProt API will paginate the results, you may use this argument to control the pagination. maximum value is 200.

...

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

Value

a list containing taxonomic nodes that match your supplied inputs.

Corresponding API Resources

"GET https://ebi.ac.uk/proteins/api/name/{name}"
"GET https://ebi.ac.uk/proteins/api/name/{name}/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(), rba_uniprot_taxonomy_lca(), rba_uniprot_taxonomy_lineage(), rba_uniprot_taxonomy_path(), rba_uniprot_taxonomy_relationship()

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)
# }