rbioapi: rba_uniprot_proteins_search – R documentation

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rba_uniprot_proteins_search

Search UniProt entries

Description

Using this function, you can search and retrieve UniProt Knowledge-base (UniProtKB) protein entries using variety of options. You may also refine your search with modifiers such as sequence length, reviews status etc. refer to "Arguments" section" for more information.

Usage

rba_uniprot_proteins_search(
  accession = NA,
  reviewed = NA,
  isoform = NA,
  go_term = NA,
  keyword = NA,
  ec = NA,
  gene = NA,
  exact_gene = NA,
  protein = NA,
  organism = NA,
  taxid = NA,
  pubmed = NA,
  seq_length = NA,
  md5 = NA,
  ...
)

Arguments

`accession`	UniProtKB primary or secondary accession(s). You can provide up to 100 accession numbers.
`reviewed`	Logical: If TRUE, only return "UniProtKB/Swiss-Prot" (reviewed) entries; If FALSE, only return TrEMBL (un-reviewed) entries.
`isoform`	Numeric: you have three options: 0: Exclude isoforms. 1: Return isoforms only. 2: Return both. see: Alternative products
`go_term`	Limit the search to entries associated with your provided GO (Gene Ontology) term. You can provide Either GO ID or a character string -partially or fully- matching the term. e.g. "GO:0001776" or "leukocyte homeostasis". if You provide "leukocyte", any term containing that word will be included, e.g "leukocyte chemotaxis", "leukocyte activation".
`keyword`	Limit the search to entries that contain your provided keyword. see: UniProt Keywords
`ec`	EC (Enzyme Commission) number(s). You can provide up to 20 EC numbers.
`gene`	UniProt gene name(s). You can provide up to 20 gene names. e.g. if you provide "CD40", "CD40 ligand" will also be included.
`exact_gene`	UniProt exact gene name(s). You can provide up to 20 exact gene names. e.g. if you provide "CD40", "CD40 ligand" will not be included in the results.
`protein`	UniProt protein name
`organism`	Organism name.
`taxid`	NIH-NCBI Taxon ID. You can provide up to 20 taxon IDs.
`pubmed`	Entries which cite to the article with your provided PubMed ID.
`seq_length`	An exact sequence length (e.g. 150) or a range of sequence lengths (e.g. "130-158").
`md5`	Sequence md5 value.
`...`	rbioapi option(s). Refer to `rba_options`'s arguments documentation for more information on available options.

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.s
UniProt Entries are grouped in two sections:

Reviewed(Swiss-Prot): Manually annotated records with information extracted from literature and curator-evaluated computational analysis.
Unreviewed (TrEMBL): Computationally analyzed records that await full manual annotation.

Value

A List where each element corresponds to one UniProt entity returned by your search query. The element itself is a sub-list containing all information that UniProt has about that entity.

Corresponding API Resources

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

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_proteins_search(accession = "Q99616")


rba_uniprot_proteins_search(gene = "cd40")


rba_uniprot_proteins_search(gene = "cd40 ligand")


rba_uniprot_proteins_search(gene = "cd40",  reviewed = TRUE)


rba_uniprot_proteins_search(gene = "cd40",  reviewed = TRUE, isoform = 1)


rba_uniprot_proteins_search(keyword = "Inhibition of host chemokines by virus")


rba_uniprot_proteins_search(keyword = "chemokines")

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release