rbioapi (version 0.8.1)

rba_uniprot_proteomes_search: Search Proteomes in UniProt

Description

UniProt collects and annotates proteomes (Protein sets expressed in an organism). Using this function you can search UniProt for available proteomes. see What are proteomes? for more information. You may also refine your search with modifiers such as keyword, taxon id etc. See "Arguments section" for more information.

Usage

rba_uniprot_proteomes_search(
  name = NULL,
  upid = NULL,
  taxid = NULL,
  keyword = NULL,
  xref = NULL,
  genome_acc = NULL,
  is_ref_proteome = NULL,
  is_redundant = NULL,
  ...
)

Value

A list where each element is a list that corresponds to a single proteome (search hit) and contains informations pertinent to that proteome.

Arguments

name

a keyword in proteome's name

upid

UniProt Proteome identifier (UPID). You can supply up to 100 UPIDs.

taxid

NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

keyword

Limit the search to entries that contain your supplied keyword. see: UniProt Keywords

xref

Proteome cross-references such as Genome assembly ID or Biosample ID. You can supply up to 20 cross-reference IDs.

genome_acc

Genome accession associated with the proteome's components.

is_ref_proteome

(logical) If TRUE, only return reference proteomes; If FALSE, only returns non-reference proteomes; If NULL (default), the results will not be filtered by this criteria see 'What are reference proteomes?' for more information.

is_redundant

(logical) If TRUE, only return redundant proteomes; If FALSE, only returns non-redundant proteomes; If NULL (default), the results will not be filtered by redundancy. see 'Reducing proteome redundancy' for more information.

...

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

Corresponding API Resources

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

Details

Note that this is a search function. Thus, you are not required to fill every argument; You may use whatever combinations of arguments you see fit for your query.

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 - Proteomes": rba_uniprot_genecentric(), rba_uniprot_genecentric_search(), rba_uniprot_proteomes()

Examples

# \donttest{
rba_uniprot_proteomes_search(name = "SARS-CoV")
# }
# \donttest{
rba_uniprot_proteomes_search(name = "SARS-CoV", is_ref_proteome = TRUE)
# }
# \donttest{
rba_uniprot_proteomes_search(name = "SARS-CoV", is_ref_proteome = TRUE)
# }
# \donttest{
rba_uniprot_proteomes_search(genome_acc = "AY274119")
# }