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)

Search vs Retrieve

Most rbioapi UniProt function families have two variants: one retrieves data using a supported identifier, while the other (with a _search suffix) searches using one or more service-specific criteria. We first demonstrate this using an example, then provide a list of these function families in rbioapi.

Suppose we are interested in the human CD40 ligand protein and know that its UniProt accession is “P29965”. We can retrieve it directly:

## 1 Retrieve CD40 ligand by its UniProt accession
cd40 <- rba_uniprot_proteins(accession = "P29965")

## 2 Inspect the returned 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':    65 obs. of  9 variables:
#>  $ dbReferences    :'data.frame':    141 obs. of  4 variables:
#>  $ keywords        :'data.frame':    14 obs. of  1 variable:
#>  $ references      :'data.frame':    25 obs. of  3 variables:
#>  $ sequence        :List of 5

This returns the data represented by the UniProtKB entry for P29965. If we do not know the accession, or want to query by other criteria, we can use the function with the _search suffix:

## 1 Supply the criteria pertinent to the search
cd40_search <- rba_uniprot_proteins_search(
  protein = "CD40 ligand",
  organism = "human",
  reviewed = TRUE
)

## 2 Inspect the returned 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 65
#>   ..$ dbReferences    :List of 141
#>   ..$ keywords        :List of 14
#>   ..$ references      :List of 25
#>   ..$ sequence        :List of 5

This is analogous to an advanced search in the UniProt web portal. See the rba_uniprot_proteins_search manual for details. In *_search functions you do not need to fill every argument, but the Proteins API requires at least one of the primary search criteria documented for that function; refining modifiers do not constitute a search by themselves.

The applications of *_search variants are not limited to what the title ‘search’ implies. These functions also retrieve their search hits, so you can use them for bulk retrieval. Many arguments accept multiple values; see the functions’ manuals for the supported limits. 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")
)
## Inspect the returned object's structure
str(multi_prs1, 1)
#> List of 6
#>  $ P24941:List of 14
#>  $ P04637:List of 14
#>  $ P06493:List of 14
#>  $ P60953:List of 14
#>  $ Q02241:List of 14
#>  $ P38398:List of 14

## 2 Search by gene name, excluding isoforms and unreviewed 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
#>  $ Q9HCN2:List of 14
#>  $ P04637: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
#>  $ Q5VT25:List of 14
#>  $ Q00587:List of 14
#>  $ O14613:List of 14
#>  $ Q6DT37:List of 14
#>  $ Q9H3Q1:List of 14
#>  $ Q07960:List of 14
#>  $ Q9UKI2:List of 14
#>  $ Q6NZY7:List of 14
#>  $ Q9NRR8:List of 14
#>  $ Q9NRR3:List of 14
#>  $ P60953:List of 14
#>  $ Q9Y5S2:List of 14

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

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

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

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

Functions with *_search variant

The search variants are not limited to the examples above. The following function families have both retrieval and search variants. See their manuals for detailed guidance and examples.

1. rba_uniprot_proteins() and rba_uniprot_proteins_search()

2. rba_uniprot_features() and rba_uniprot_features_search()

3. rba_uniprot_variation() and rba_uniprot_variation_search()

4. rba_uniprot_antigens() and rba_uniprot_antigens_search()

5. rba_uniprot_epitope() and rba_uniprot_epitope_search()

6. rba_uniprot_rna_edit() and rba_uniprot_rna_edit_search()

7. rba_uniprot_proteomes() and rba_uniprot_proteomes_search()

8. rba_uniprot_mutagenesis() and rba_uniprot_mutagenesis_search()

9. rba_uniprot_proteomics_hpp() and rba_uniprot_proteomics_hpp_search()

10. rba_uniprot_proteomics_non_ptm() and rba_uniprot_proteomics_non_ptm_search()

11. rba_uniprot_proteomics_ptm() and rba_uniprot_proteomics_ptm_search()

12. rba_uniprot_genecentric() and rba_uniprot_genecentric_search()

13. rba_uniprot_uniparc() and rba_uniprot_uniparc_search()

UniProt functions categories

The Proteins API endpoints implemented by rbioapi are organized into six groups. Here are those categories and the corresponding rbioapi functions. See the functions’ manuals for more details.

How to Cite?

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

• The UniProt Consortium. (2025). UniProt: the Universal Protein Knowledgebase in 2025. Nucleic Acids Research, 53(D1), D609–D617. https://doi.org/10.1093/nar/gkae1010
• Nightingale, A., Antunes, R., Alpi, E., Bursteinas, B., Gonzales, L., Liu, W., Luo, J., Qi, G., Turner, E., & Martin, M. (2017). The Proteins API: Accessing key integrated protein and genome information. Nucleic Acids Research, 45(W1), 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

Links

• This article on the rbioapi documentation site

• Functions references in rbioapi documentation site

• rbioapi vignette index

Session info

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