Are others having trouble querying biomart through the R biomaRt api? I am able to normally run these queries without a problem, so I am unclear why they stopped working recently. I am able to connect to some of the biomart servers, but specifically not to the snp_mart.
Able to query ensembl gene database:
library(biomaRt)
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org")
getBM( attributes = c("ensembl_gene_id", "entrezgene", "hgnc_symbol"), filters = "hgnc_symbol", values = "CD74", mart = ensembl)
# returns
# ensembl_gene_id entrezgene hgnc_symbol
# 1 ENSG00000019582 972 CD74
Unable to query snp_mart:
snp_mart <- useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host = "www.ensembl.org")
getBM(attributes = c("refsnp_id", "chr_name", "chrom_start", "chrom_end"),
filters = "snp_filter",
values = "rs10208643",
mart = snp_mart)
# returns
# Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
Based on the error message, it's very possible the service is temporarily down, but I see no message about it their website to confirm. Crawling through the biomart dev email lists, I see that at least one person has had a similar problem (http://lists.ensembl.org/pipermail/dev/2017-October/012678.html) , but I don't see a response from a dev yet. Anybody know the best way to contact the people who maintain biomart?
sessionInfo()R version 3.3.3 (2017-03-06) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1
locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] bindrcpp_0.2 biomaRt_2.30.0 GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 IRanges_2.8.2
[6] S4Vectors_0.12.2 BiocGenerics_0.20.0 ggplot2_2.2.1 dplyr_0.7.1 purrr_0.2.2.2
[11] tidyr_0.6.3 plyr_1.8.4 RCurl_1.95-4.8 bitops_1.0-6 data.table_1.10.4
loaded via a namespace (and not attached): [1] Rcpp_0.12.11 bindr_0.1 XVector_0.14.1 tools_3.3.3 zlibbioc_1.20.0
[6] digest_0.6.12 bit_1.1-12 memoise_1.1.0 RSQLite_2.0 tibble_1.3.3
[11] gtable_0.2.0 pkgconfig_2.0.1 rlang_0.1.1 DBI_0.7 knitr_1.16
[16] bit64_0.9-7 grid_3.3.3 Biobase_2.34.0 glue_1.1.1 R6_2.2.2
[21] AnnotationDbi_1.36.2 XML_3.98-1.9 blob_1.1.0 magrittr_1.5 scales_0.4.1
[26] assertthat_0.2.0 colorspace_1.3-2 stringi_1.1.5 lazyeval_0.2.0 munsell_0.4.3
This was also reported on the Bioconductor support site (https://support.bioconductor.org/p/101631/), and I can confirm I'm encountering the same issues. I also run into the same problems when using the web interface, and when I try the Ensembl mirror sites, suggesting it's a problem with the backend database, rather than the web interface.
Thanks for confirming this @Mike Smith. I found a post in the user google group for biomart that had the same problem. A bioinformatician from EMBL-EBI posted this morning (https://groups.google.com/forum/?fromgroups#!topic/biomart-users/ckiglj9Og6A) saying that the problem should be fixed. From my end, the first few tests that I ran using snpmart seem to be now working (Mon October 16, 2017, @9:30 am EST). Hopefully it works for you too now.
Best, Karsten