I would like to use UniProt.ws to convert UniProt ids to SGD ids for Saccharomyces cerevisiae but my attempts so far have resulted in the error:

Error in .select(x, keys, columns, keytype) :
  No data is available for the keys provided.

Here is a minimal example, where I attempt to convert "I2HB52". The expected answer is "YBR056W-A" (see http://www.uniprot.org/uniprot/I2HB52 ).

library(UniProt.ws)
taxId(UniProt.ws) <- 4932
species(UniProt.ws)
res <- select(x=UniProt.ws, keys="I2HB52", columns="SGD", keytype="UNIPROTKB")

Is this particular conversion currently possible using UniProt.wd? Different choices for 'columns' also result in the same error.

Thanks in advance,

Joseph Barry

Session Info:

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] UniProt.ws_2.6.0 RCurl_1.95-4.5   bitops_1.0-6     RSQLite_1.0.0   
[5] DBI_0.3.1       

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1
[4] GenomeInfoDb_1.2.4   IRanges_2.0.1        parallel_3.1.2      
[7] S4Vectors_0.4.0      stats4_3.1.2         tools_3.1.2       

The link you have above is for a particular strain of yeast, but you are selecting the TaxonId for 'regular' yeast.

> library(UniProt.ws)
Loading required package: RSQLite
Loading required package: DBI
Loading required package: RCurl
Loading required package: bitops
> availableUniprotSpecies(pattern="cerevisiae")
   taxon ID                                                      Species name
1     11008                                Saccharomyces cerevisiae virus L-A
2     42478                               Saccharomyces cerevisiae virus L-BC
3     12450                          Saccharomyces cerevisiae killer virus M1
4    285006                         Saccharomyces cerevisiae (strain RM11-1a)
5    574961                          Saccharomyces cerevisiae (strain JAY291)
6    545124                        Saccharomyces cerevisiae (strain AWRI1631)
7    307796                          Saccharomyces cerevisiae (strain YJM789)
8    643680 Saccharomyces cerevisiae (strain Lalvin EC1118 / Prise de mousse)
9    764097                         Saccharomyces cerevisiae (strain AWRI796)
10   764102                        Saccharomyces cerevisiae (strain FostersB)
11   721032      Saccharomyces cerevisiae (strain Kyokai no. 7 / NBRC 101557)
12   764098                     Saccharomyces cerevisiae (strain Lalvin QA23)
13   764101                        Saccharomyces cerevisiae (strain FostersO)
14   559292             Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
15   764099                          Saccharomyces cerevisiae (strain VIN 13)
16     4932                                          Saccharomyces cerevisiae
17   764100                   Saccharomyces cerevisiae (strain Zymaflore VL3)
> taxId(UniProt.ws) <- 559292
> res <- select(x=UniProt.ws, keys="I2HB52", columns="SGD", keytype="UNIPROTKB")
Getting mapping data for I2HB52 ... and SGD_ID
> res
  UNIPROTKB        SGD
1    I2HB52 S000028736
> taxId(UniProt.ws) <- 4932
> res <- select(x=UniProt.ws, keys="I2HB52", columns="SGD", keytype="UNIPROTKB")
Error in .select(x, keys, columns, keytype) :
  No data is available for the keys provided.

Hi James,

Great, thanks a lot. Works like a charm now.

Best, Joseph

On a related note, I found somewhat strange NA behaviour. If one includes "ENSEMBL" in the "columns" vector, which returns NA, all other columns also switch to NA when returned. I guess this is not desirable behaviour for most users.

> taxId(UniProt.ws) <- 559292
> species(UniProt.ws)
[1] "Saccharomyces cerevisiae (strain ATCC 204508 / S288c)"
> res <- select(x=UniProt.ws, keys="I2HB52", columns=c("SGD", "SEQUENCE"), keytype="UNIPROTKB")
Getting mapping data for I2HB52 ... and SGD_ID
Getting extra data for I2HB52 NA NA etc
> print(res)
  UNIPROTKB        SGD
1    I2HB52 S000028736
                                                            SEQUENCE
1 MRHQYYQPQPMYYQPQPQPIYIQQGPPPPRNDCCCCCNCGDCCSAIANVLCCLCLIDLCCSCAGGM
> res <- select(x=UniProt.ws, keys="I2HB52", columns=c("SGD", "SEQUENCE", "ENSEMBL"), keytype="UNIPROTKB")
Getting mapping data for I2HB52 ... and ENSEMBL_ID
Getting mapping data for I2HB52 ... and SGD_ID
Getting extra data for I2HB52 NA NA etc
> print(res)
  UNIPROTKB  SGD SEQUENCE ENSEMBL
1    I2HB52 <NA>     <NA>    <NA>

That is indeed a safe looking change.

I have checked in the change proposed.  Thanks for the bug fix! 

You people are the best,

 Marc