Error accessing ensembl biomart via BiomaRt R package

Question

[lakhujanivijay]

Objective

I have a list of ~58K ensembl gene ids of h.sapiens for which I need to extract the gene names, descriptions and other annotations from biomart.

---

The online way is failing primarily because of the huge list I am uploading, hence, I though to give this a try with the BiomaRt R package. I am trying to access ensembl biomart using following commands

source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
library(biomaRt)
listEnsembl()

Error encountered

> listEnsembl()
Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:

From the error, it appears to be a problem with the URL - http://www.biomart.org, which I could infact access without any issue.

What I can see is a downtime notice here. Is it something related to this?

Can anybody suggest anything else?

[Mike Smith]

What version of R and biomaRt are you using? I suspect you might have an old version. While the www.biomart.org website still exists, it ceased to be the central reportistory for BioMart instances quite a while ago. All the defaults in the biomaRt package should now point to www.ensembl.org

You can check the version using the command sessionInfo(), here's mine along with the output i get when running listEnsembl()

> sessionInfo()   
R version 3.4.1 (2017-06-30)   
Platform: x86_64-pc-linux-gnu (64-bit)   
Running under: Linux Mint 18.1
Matrix products: default   BLAS:
/home/msmith/Applications/R/R-3.4.1/lib/libRblas.so LAPACK:
/home/msmith/Applications/R/R-3.4.1/lib/libRlapack.so

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

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

other attached packages:
[1] biomaRt_2.33.5

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12         AnnotationDbi_1.39.3 magrittr_1.5        
 [4] BiocGenerics_0.23.1  progress_1.1.2       IRanges_2.11.16     
 [7] bit_1.1-12           R6_2.2.2             rlang_0.1.2         
[10] stringr_1.2.0        blob_1.1.0           tools_3.4.1         
[13] parallel_3.4.1       Biobase_2.37.2       DBI_0.7             
[16] bit64_0.9-7          digest_0.6.12        assertthat_0.2.0    
[19] tibble_1.3.4         S4Vectors_0.15.8     bitops_1.0-6        
[22] RCurl_1.95-4.8       memoise_1.1.0        RSQLite_2.0         
[25] stringi_1.1.5        compiler_3.4.1       prettyunits_1.0.2   
[28] stats4_3.4.1         XML_3.98-1.9        

> listEnsembl()
             biomart               version
1            ensembl      Ensembl Genes 90
2 ENSEMBL_MART_MOUSE      Mouse strains 90
3                snp  Ensembl Variation 90
4         regulation Ensembl Regulation 90

[lakhujanivijay]

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

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

other attached packages:
[1] biomaRt_2.30.0       BiocInstaller_1.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9          IRanges_2.8.1        XML_3.98-1.5        
 [4] digest_0.6.12        bitops_1.0-6         DBI_0.5-1           
 [7] stats4_3.3.1         RSQLite_1.1-2        S4Vectors_0.12.1    
[10] tools_3.3.1          Biobase_2.34.0       RCurl_1.95-4.8      
[13] parallel_3.3.1       BiocGenerics_0.20.0  AnnotationDbi_1.36.1
[16] memoise_1.0.0

[Emily]

Working fine for me:

> library(biomaRt)
> listEnsembl()
             biomart               version
1            ensembl      Ensembl Genes 90
2 ENSEMBL_MART_MOUSE      Mouse strains 90
3                snp  Ensembl Variation 90
4         regulation Ensembl Regulation 90
>

[GenoMax]

Check to see if an overzealous intrusion prevention device (or a firewall admin) has disabled your access since it seems to be working for others.

Answer 1

[Mike Smith]

It looks like you're using a fairly old version of both R and biomaRt at the moment. I've made quite a few changes to the package over the past year, particularly regarding connectivity and error messages, so I'd suggest upgrading. You can keep the same version of R and install the latest biomaRt using the following command:

BiocInstaller::biocLite('grimbough/biomaRt')

I would then try re-running listEnsembl() with the verbose flag. This will print the actual URL it is trying to access, which you can then try in a web browser. It should be an XML file starting with <MartRegistry>.

listEnsembl(verbose = TRUE)

You can also try accessing one of the mirror sites, then report back here with any output, e.g.

listEnsembl(verbose = TRUE, mirror = "asia")