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2.G: UniProt & rbioapi

Moosa Rezwani

2024-03-30

0.1 Introduction

Directly quoting from UniProt:

The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc). The UniProt consortium and host institutions EMBL-EBI, SIB and PIR are committed to the long-term preservation of the UniProt databases.

(source: https://www.uniprot.org/help/about)

0.2 Search vs Retrieve

Most of rbioapi UniProt functions have two variants. one to retrieve data using a proper accession, and the second one (which have a _search suffix) is to search using any combination of arguments. We first demonstrate this using an example, then provide a list of such functions in rbioapi.

Suppose we are interested in Human CD40 ligand protein, and we know that it’s UniProt accession is “P29965”. We can simply do as the following:

## 1 We can retrieve CD40 protein's information by qurying it's UniProt accession:
cd40 <- rba_uniprot_proteins(accession = "P29965")

## 2 We use str() to inspect our object's structure
str(cd40, 1)
#> List of 13
#>  $ accession       : chr "P29965"
#>  $ id              : chr "CD40L_HUMAN"
#>  $ proteinExistence: chr "Evidence at protein level"
#>  $ info            :List of 4
#>  $ organism        :List of 3
#>  $ protein         :List of 4
#>  $ gene            :'data.frame':    1 obs. of  2 variables:
#>  $ comments        :'data.frame':    12 obs. of  10 variables:
#>  $ features        :'data.frame':    63 obs. of  9 variables:
#>  $ dbReferences    :'data.frame':    134 obs. of  4 variables:
#>  $ keywords        :'data.frame':    13 obs. of  1 variable:
#>  $ references      :'data.frame':    25 obs. of  3 variables:
#>  $ sequence        :List of 5

This is the equivalent of the page that UniProt have on this accession (UniProtKB - P29965). But what if we didn’t know the UniProt accession? Or simply want to perform a search using certain parameters? We can use the function with _search suffix:

## 1 From the available arguments, we fill only those which we think is pertinent
cd40_search <- rba_uniprot_proteins_search(protein = "CD40 ligand",
                                          organism = "human",
                                          reviewed = TRUE)
## 2 As always, we use str() to inspect our object's structure
str(cd40_search, 2)
#> List of 1
#>  $ P29965:List of 13
#>   ..$ accession       : chr "P29965"
#>   ..$ id              : chr "CD40L_HUMAN"
#>   ..$ proteinExistence: chr "Evidence at protein level"
#>   ..$ info            :List of 4
#>   ..$ organism        :List of 3
#>   ..$ protein         :List of 4
#>   ..$ gene            :List of 1
#>   ..$ comments        :List of 12
#>   ..$ features        :List of 63
#>   ..$ dbReferences    :List of 134
#>   ..$ keywords        :List of 13
#>   ..$ references      :List of 25
#>   ..$ sequence        :List of 5

This is the equivalent of ‘advanced search’ in UniProt web portal. See function rba_uniprot_proteins_search’s manual for more information. Remember that in *_search functions, you are not required to fill every argument, you can use any combination of arguments you see fit to build your search query.

The applications of *_search variants are not limited to what the title ‘search’ implies. These functions will also retrieve the search hits in their response; Thus you can use them for mass-retrieving. If you see the “argument” section in the functions’ manuals, you would see that many arguments accept a vector of values. consider the following examples:

## 1 As the simplest scenario, we can retrieve multiple proteins in one call
multi_prs1 <- rba_uniprot_proteins_search(accession = c("P04637",
                                                       "P38398",
                                                       "P24941",
                                                       "P60953",
                                                       "P06493",
                                                       "Q02241"))
## As always, we use str() to inspect our object's structure
str(multi_prs1, 1)
#> List of 6
#>  $ P60953:List of 14
#>  $ P24941:List of 14
#>  $ P04637:List of 14
#>  $ P06493:List of 14
#>  $ Q02241:List of 14
#>  $ P38398:List of 14

## 2 Or alternatively, search using Gene names, also we want to exclude isoforms and only retrieve swiss-prot entries
multi_prs2 <- rba_uniprot_proteins_search(gene = c("KIF23",
                                                  "BRCA1",
                                                  "TP53",
                                                  "CDC42"),
                                         reviewed = TRUE,
                                         taxid = 9606,
                                         isoform = 0)

str(multi_prs2, 1)
#> List of 29
#>  $ Q9ULZ0:List of 14
#>  $ Q02241:List of 14
#>  $ P38398:List of 14
#>  $ Q12888:List of 14
#>  $ P04637:List of 14
#>  $ Q9HCN2:List of 14
#>  $ A1A5B4:List of 14
#>  $ Q9Y2B4:List of 13
#>  $ Q8IXH6:List of 14
#>  $ Q53FA7:List of 14
#>  $ Q9NS56:List of 14
#>  $ Q96A56:List of 14
#>  $ O14683:List of 14
#>  $ Q96S44:List of 14
#>  $ Q8NBR0:List of 14
#>  $ Q13625:List of 14
#>  $ Q7L0Q8:List of 14
#>  $ Q9UKI2:List of 14
#>  $ Q6NZY7:List of 14
#>  $ Q5VT25:List of 14
#>  $ Q6DT37:List of 14
#>  $ Q00587:List of 14
#>  $ O14613:List of 14
#>  $ Q9H3Q1:List of 14
#>  $ Q07960:List of 14
#>  $ Q9NRR8:List of 14
#>  $ Q9NRR3:List of 14
#>  $ Q9Y5S2:List of 14
#>  $ P60953:List of 14

## 3 Search for every proteins with chemokines keyword
multi_prs3 <- rba_uniprot_proteins_search(keyword = "chemokines")

str(multi_prs3, 1)
#> List of 17
#>  $ P09703:List of 15
#>  $ P0DTM9:List of 14
#>  $ Q6SW98:List of 15
#>  $ P33854:List of 14
#>  $ P0DSV7:List of 15
#>  $ P19063:List of 14
#>  $ P16849:List of 15
#>  $ P69332:List of 15
#>  $ P24766:List of 15
#>  $ P34016:List of 14
#>  $ P21064:List of 14
#>  $ P0DSV8:List of 15
#>  $ F5HBX1:List of 14
#>  $ Q98314:List of 15
#>  $ P69333:List of 15
#>  $ P07562:List of 14
#>  $ F5HF62:List of 14

## 4 Search for every protein of "SARS-CoV-2" virus in Swiss-Prot
multi_prs4 <- rba_uniprot_proteins_search(organism = "SARS-CoV-2",
                                         reviewed = TRUE)

str(multi_prs4, 1)
#> List of 17
#>  $ P0DTD3    :List of 14
#>  $ P0DTC6    :List of 14
#>  $ P0DTG0    :List of 13
#>  $ P0DTC7    :List of 14
#>  $ P0DTC2    :List of 14
#>  $ P0DTC8    :List of 14
#>  $ P0DTC4    :List of 14
#>  $ A0A663DJA2:List of 14
#>  $ P0DTC9    :List of 14
#>  $ P0DTC5    :List of 14
#>  $ P0DTC3    :List of 14
#>  $ P0DTD8    :List of 14
#>  $ P0DTD2    :List of 14
#>  $ P0DTF1    :List of 13
#>  $ P0DTD1    :List of 14
#>  $ P0DTC1    :List of 13
#>  $ P0DTG1    :List of 13

0.3 Functions with `*_search` variant

The search variants are not limited to the above. Here is a list of the function that have both a retrieve and search variants. See their manuals for detailed guides and examples.

rba_uniprot_proteins() & rba_uniprot_proteins_search()
rba_uniprot_features() & rba_uniprot_features_search()
rba_uniprot_variation() & rba_uniprot_variation_search()
rba_uniprot_proteomics() & rba_uniprot_proteomics_search()
rba_uniprot_antigens() & rba_uniprot_antigens_search()
rba_uniprot_proteomes() & rba_uniprot_proteomes_search()
rba_uniprot_ptm() & rba_uniprot_ptm_search()
rba_uniprot_mutagenesis() & rba_uniprot_mutagenesis_search()
rba_uniprot_genecentric() & rba_uniprot_genecentric_search()
rba_uniprot_uniparc() & rba_uniprot_uniparc_search()

0.4 UniProt functions categories

The UniProt API endpoints are organized into 5 group. Here are those categories and rbioapi functions that correspond to each one. See the functions’ manuals for more details.

0.4.1 Proteins

0.4.1.1 Proteins:

rba_uniprot_proteins()
rba_uniprot_proteins_search()
rba_uniprot_proteins_crossref()

0.4.1.2 Features

rba_uniprot_features()
rba_uniprot_features_search()

0.4.1.3 Variation

rba_uniprot_variation()

rba_uniprot_variation_search()

0.4.1.4 Proteomics

rba_uniprot_proteomics()
rba_uniprot_proteomics_search()

0.4.2 Post-Translational Modification (PTM)

rba_uniprot_ptm()
rba_uniprot_ptm_search()

0.4.3 Antigens

rba_uniprot_antigens()
rba_uniprot_antigens_search()

0.4.4 Mutagenesis

rba_uniprot_mutagenesis()
rba_uniprot_mutagenesis_search()

0.4.5 Proteomes

rba_uniprot_proteomes()
rba_uniprot_proteomes_search()
rba_uniprot_genecentric()
rba_uniprot_genecentric_search()

0.4.6 Taxonomy

rba_uniprot_taxonomy()
rba_uniprot_taxonomy_lca()
rba_uniprot_taxonomy_lineage()
rba_uniprot_taxonomy_name()
rba_uniprot_taxonomy_path()
rba_uniprot_taxonomy_relationship()

0.4.7 Coordinates

rba_uniprot_coordinates()
rba_uniprot_coordinates_search()
rba_uniprot_coordinates_location()
rba_uniprot_coordinates_sequence()

0.4.8 UniParc

rba_uniprot_uniparc()
rba_uniprot_uniparc_search()
rba_uniprot_uniparc_bestguess()
rba_uniprot_uniparc_sequence()

0.5 How to Cite?

To cite UniProt (Please see https://www.uniprot.org/help/publications):

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

To cite rbioapi:

Moosa Rezwani, Ali Akbar Pourfathollah, Farshid Noorbakhsh, rbioapi: user-friendly R interface to biologic web services’ API, Bioinformatics, Volume 38, Issue 10, 15 May 2022, Pages 2952–2953, https://doi.org/10.1093/bioinformatics/btac172

1 Links

2 Session info

#> R version 4.3.3 (2024-02-29 ucrt)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 11 x64 (build 22631)
#> 
#> Matrix products: default
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#> [1] LC_COLLATE=C                          
#> [2] LC_CTYPE=English_United States.utf8   
#> [3] LC_MONETARY=English_United States.utf8
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.utf8    
#> 
#> time zone: Europe/Brussels
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] rbioapi_0.8.1
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.35     R6_2.5.1          fastmap_1.1.1     xfun_0.43        
#>  [5] magrittr_2.0.3    cachem_1.0.8      knitr_1.45        htmltools_0.5.8  
#>  [9] png_0.1-8         rmarkdown_2.26    lifecycle_1.0.4   DT_0.32          
#> [13] cli_3.6.2         grid_4.3.3        sass_0.4.9        jquerylib_0.1.4  
#> [17] compiler_4.3.3    highr_0.10        httr_1.4.7        rstudioapi_0.16.0
#> [21] tools_4.3.3       curl_5.2.1        evaluate_0.23     bslib_0.6.2      
#> [25] yaml_2.3.8        htmlwidgets_1.6.4 rlang_1.1.3       jsonlite_1.8.8   
#> [29] crosstalk_1.2.1

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.