2.G: UniProt & rbioapi
Moosa Rezwani
2024-03-30
Source:vignettes/rbioapi_uniprot.Rmd
rbioapi_uniprot.RmdIntroduction
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)
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 5This 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 5This 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 13Functions 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_mutagenesis()&rba_uniprot_mutagenesis_search()rba_uniprot_genecentric()&rba_uniprot_genecentric_search()
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.
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
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