biomaRt error while converting ensembl gene Id to uniprot ID

Question

[manaswwm]

Hello everyone,

I have been using biomaRt for some time now and it has been working nicely. However, today while trying to convert some ensembl gene ids to uniprotswissprot ids I have been facing some problems. The code and the error are as follows:

#importing the library
library(biomart)
#since I am working with thaliana - I create the mart object as follows
thaliana_mart = useMart(host="plants.ensembl.org", "plants_mart",
                      dataset = "athaliana_eg_gene")
#running a sample code where I want to retrieve a uniprotswissprot id
getBM(mart = thaliana_mart, attributes = "uniprotswissprot", values = "AT4G21050", filters = "ensembl_gene_id")

Here I expect to get the uniprotswissprot id - Q9SUA9 which is corresponding to AT4G21050, however, I get the following error.

Error in result_create(conn@ptr, statement) : no such table: metadata

Also, something that I should mention : I make requests in bulk. This piece of code is a part of a larger code which runs through 25 ids at a time and does a bunch of other functions. In order to not over-shoot the limit of 55000 requests per hour by ensembl's REST-API, I put the code to "sleep" after one batch of 25 ids for 1800 seconds (half hour).

Can anyone please help me?

Answer 1

[Elisabeth Gasteiger]

Have you tried the UniProt IDmapping service at https://www.uniprot.org/uploadlists ? It allows to map gene names from and to UniProtKB ACs, you can specifiy an optional organism name and use it programmatically too if necessary (https://www.uniprot.org/help/api%5Fidmapping).

Answer 2

[Kevin Blighe]

If you have many IDs to match, it may be more efficient to retrieve the entire table and then do post-filtering on that. For example:

library(biomaRt)
thaliana_mart = useMart(
  host = 'plants.ensembl.org',
  'plants_mart',
  dataset = 'athaliana_eg_gene')

annotTable <- getBM(mart = thaliana_mart,
  attributes = c('ensembl_gene_id', 'uniprotswissprot', 'description'))

head(annotTable)
  ensembl_gene_id uniprotswissprot
1       AT5G16970           Q39172
2       AT4G32100                 
3       AT2G43120                 
4       AT2G43120           Q9ZW82
5       AT1G30814                 
6       AT3G18710           Q9LSA6
                                                                                   description
1  NADPH-dependent oxidoreductase 2-alkenal reductase [Source:UniProtKB/Swiss-Prot;Acc:Q39172]
2 Beta-1,3-N-Acetylglucosaminyltransferase family protein [Source:UniProtKB/TrEMBL;Acc:F4JTI5]
3                             RmlC-like cupins superfamily protein [Source:TAIR;Acc:AT2G43120]
4                             RmlC-like cupins superfamily protein [Source:TAIR;Acc:AT2G43120]
5                                             unknown protein; Ha. [Source:TAIR;Acc:AT1G30814]
6                  RING-type E3 ubiquitin transferase [Source:UniProtKB/TrEMBL;Acc:A0A178VJJ8]

dim(annotTable)
[1] 33270     3

[manaswwm]

Hi Kevin, thanks for your answer. I agree this would be an efficient way of doing things instead of sending in requests one at a time, however, the point that I would like to make is that I am not able to send in any requests at the moment. For example, even when I run your code I still get the same error as I stated in the question, and I am not entirely sure what the error message means. Here I paste it again:

Error in result_create(conn@ptr, statement) : no such table: metadata

Edit : forgot to add that I have tried to uninstall and reinstall the biomaRt package, however this error still persists

[Kevin Blighe]

I see. That specific error is thrown from an SQL command. On which system and R version are you running biomaRt?

Also, what would be the output of biomartCacheInfo() if you ran it?

[manaswwm]

I am running this on a Debian system, to make things easier to understand, here is the sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS/LAPACK: /home/mjoshi/Desktop/work/miniconda3/envs/myTest/lib/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.42.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1           compiler_3.6.1       pillar_1.3.1         dbplyr_1.4.0         prettyunits_1.0.2    tools_3.6.1          progress_1.2.0      
 [8] digest_0.6.18        bit_1.1-14           RSQLite_2.1.1        memoise_1.1.0        BiocFileCache_1.10.0 tibble_2.1.1         pkgconfig_2.0.2     
[15] rlang_0.3.4          DBI_1.0.0            rstudioapi_0.10      yaml_2.2.0           curl_3.3             parallel_3.6.1       stringr_1.4.0       
[22] httr_1.4.0           dplyr_0.8.0.1        rappdirs_0.3.1       S4Vectors_0.24.0     askpass_1.0          IRanges_2.20.0       hms_0.4.2           
[29] tidyselect_0.2.5     stats4_3.6.1         bit64_0.9-7          glue_1.3.1           Biobase_2.46.0       R6_2.4.0             AnnotationDbi_1.48.0
[36] XML_3.98-1.19        purrr_0.3.2          blob_1.1.1           magrittr_1.5         BiocGenerics_0.32.0  assertthat_0.2.1     stringi_1.4.3       
[43] openssl_1.3          crayon_1.3.4

And if I run biomartCacheInfo(), I still get the same error:

Error in result_create(conn@ptr, statement) : no such table: metadata

Is there something that I did wrong? I also tried making a fresh install of my entire R environment but the error still persists.

Answer 3

[manaswwm]

Thanks for your suggestion, Elisabeth!

I realized I can also do this much later, what I ended up doing is using Uniprot's REST API service to convert my ensembl gene id to uniprot protein id - https://www.ebi.ac.uk/proteins/api/doc/#!/proteins/getByCrossReference (here I set dbtype - EnsemblPlants and reviewed - TRUE to get only UniprotSwissprot ids). So an example requestURL would look like - https://www.ebi.ac.uk/proteins/api/proteins/EnsemblPlants:AT4G21050?offset=0&size=100&reviewed=TRUE

[Elisabeth Gasteiger]

Yes, this is the EBI Proteins REST API. Other ways to access UniProt programmatically, including the website API, are listed here: https://www.uniprot.org/help/programmatic_access