Convert Refseq Protein IDs to UniProt IDs
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sgupt46 • 0
@sgupt46-13716
Last seen 14 days ago
Canada

I have few RefSeq protein IDs eg. NP_853513.2, NP_000517.2. Is there a to find corresponding UniProt IDs in Bioconductor?

AnnotationDbi • 250 views
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@james-w-macdonald-5106
Last seen 15 hours ago
United States

Sometimes you can do this using an OrgDb package.

> library(org.Hs.eg.db)
> select(org.Hs.eg.db, c("NP_853513.2", "NP_000517.2"), "UNIPROT", "REFSEQ")
Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'REFSEQ'. Please use the keys method to see a listing of valid arguments.

## Ugh. Let's strip off the tailing version numbers
> select(org.Hs.eg.db, gsub("\\[1-9]$", "", c("NP_853513.2", "NP_000517.2")), "UNIPROT", "REFSEQ")
Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'REFSEQ'. Please use the keys method to see a listing of valid arguments.

## still no joy but is that because I'm a dummy? You actually have to strip the period AND the number

> select(org.Hs.eg.db, gsub("\\.[1-9]$", "", c("NP_853513.2", "NP_000517.2")), "UNIPROT", "REFSEQ")
'select()' returned 1:1 mapping between keys and columns
     REFSEQ UNIPROT
1 NP_853513  Q7Z3Y7
2 NP_000517  P02533

So let's try UniProt.ws.

> library(UniProt.ws)
Loading required package: RSQLite
Loading required package: RCurl
Warning messages:
1: package 'UniProt.ws' was built under R version 4.0.3 
2: package 'RSQLite' was built under R version 4.0.3 
3: package 'RCurl' was built under R version 4.0.3 
> up <- UniProt.ws()
> select(up, c("NP_853513.2", "NP_000517.2"), "UNIPROTKB", "REFSEQ_PROTEIN")
Getting mapping data for NP_853513.2 ... and ACC
error while trying to retrieve data in chunk 1:
    no results after 5 attempts; please try again later
continuing to try
Error in `colnames<-`(`*tmp*`, value = `*vtmp*`) : 
  attempt to set 'colnames' on an object with less than two dimensions

## Huh. That's a drag

Let's try biomaRt

> library(biomaRt)
> mart <- useEnsembl("ensembl","hsapiens_gene_ensembl")
> getBM(c("uniprot_gn_id","uniprotswissprot","refseq_peptide"), "refseq_peptide", c("NP_853513.2", "NP_000517.2"), mart)
[1] uniprot_gn_id    uniprotswissprot refseq_peptide  
<0 rows> (or 0-length row.names)

## Huh. Super annoying. Maybe it's the version numbers? Let's strip those off
> getBM(c("uniprot_gn_id","uniprotswissprot","refseq_peptide"), "refseq_peptide", gsub("\\.[1-9]$", "", c("NP_853513.2", "NP_000517.2")), mart)
  uniprot_gn_id uniprotswissprot refseq_peptide
1        P02533           P02533      NP_000517
2        Q7Z3Y7           Q7Z3Y7      NP_853513

## BOOM! nailed it on the third try...
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See edits. Turns out for these two proteins the OrgDb and biomaRt work. Unfortunately it appears UniProt.ws is having problems...

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sgupt46 • 0
@sgupt46-13716
Last seen 14 days ago
Canada

Thanks James. org.Hs.eg.db works.

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