Hi,

I'm trying to convert uniprot identifiers to KEGG identifiers using KEGGREST:keggConv but suddenly this has stopped working (I'm doing this routinely). I tried with many common genes and it returns an empty string (examples below). Does anyone know why this might be?

>  keggConv("hsa", "uniprot:Q06187")

character(0)

> 

>  keggConv("hsa", "uniprot:P04637")

character(0)

> 

>  keggConv("hsa", "uniprot:P31749")

character(0)

> 

> keggConv("hsa", "uniprot:P00533")

character(0)

> 

> keggConv("hsa", "uniprot:Q05397")

character(0)

> 

> keggConv("hsa", "uniprot:O14920")

character(0)

> 

> keggConv("hsa", "uniprot:P27361")

character(0)

> sessionInfo()

R version 3.2.2 (2015-08-14)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS Linux 7 (Core)

locale:

 [1] LC_CTYPE=C                 LC_NUMERIC=C              

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 

[8] methods   base     

other attached packages:

 [1] KEGGREST_1.10.1      org.Hs.eg.db_3.2.3   ReactomePA_1.14.4   

 [4] KEGG.db_3.2.2        GOstats_2.36.0       Category_2.36.0     

 [7] Matrix_1.2-3         topGO_2.22.0         SparseM_1.7         

[10] GO.db_3.2.2          AnnotationDbi_1.32.3 IRanges_2.4.6       

[13] S4Vectors_0.8.5      Biobase_2.30.0       graph_1.48.0        

[16] BiocGenerics_0.16.1  RSQLite_1.0.0        DBI_0.3.1           

loaded via a namespace (and not attached):

 [1] Rcpp_0.12.3            XVector_0.10.0         plyr_1.8.3            

 [4] zlibbioc_1.16.0        tools_3.2.2            annotate_1.48.0       

 [7] DOSE_2.8.2             gtable_0.1.2           lattice_0.20-33       

[10] png_0.1-7              igraph_1.0.1           curl_0.9.5            

[13] httr_1.1.0             genefilter_1.52.1      stringr_1.0.0         

[16] Biostrings_2.38.3      rappdirs_0.3           grid_3.2.2            

[19] qvalue_2.2.2           GSEABase_1.32.0        R6_2.1.2              

[22] XML_3.98-1.3           RBGL_1.46.0            survival_2.38-3       

[25] GOSemSim_1.28.2        reactome.db_1.54.1     ggplot2_2.0.0         

[28] reshape2_1.4.1         DO.db_2.9              magrittr_1.5          

[31] scales_0.3.0           splines_3.2.2          graphite_1.16.0       

[34] AnnotationForge_1.12.2 colorspace_1.2-6       xtable_1.8-0          

[37] stringi_1.0-1          munsell_0.4.2         

KEGGREST is just a thin layer on top of KEGG's REST API. If you type

options(KEGGREST_DEBUG=TRUE)

Then you can see each URL that is being hit on the KEGG server. Example:

> options(KEGGREST_DEBUG=TRUE)
> keggConv("hsa", "uniprot:Q06187")
url == http://rest.kegg.jp/conv/hsa/uniprot%3aQ06187
character(0)

If you then go to the displayed URL in a web browser, it returns nothing. Which seems to indicate the problem is on the KEGG side.

Even one of the "conv" examples on the KEGG API page (http://www.kegg.jp/kegg/rest/keggapi.html) is failing (though the others work): http://rest.kegg.jp/conv/genes/ncbi-geneid:3113320 also returns nothing.

I suggest you contact KEGG and provide them with the URLs you are trying to access and ask them why they are suddenly not working.

Please report back here what you learn so others can benefit.

Thanks.