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:
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)
# 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)
# 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?