Request to BioMart web service failed. Tried multiple marts, can't seem to get it working

[Ian Pan]

Hi all,

I am using R. I have a dataframe that has 3 columns - chromosome number, chromosome start position, chromosome end position - for 483 genes of interest. 

I'm trying to use biomart to get all the rs numbers associated with each gene. Right now, my code looks like this:

require(biomaRt)

hg19.snpmart <- useMart(biomart="ENSEMBL_MART_SNP",  host="grch37.ensembl.org", path="/biomart/martservice", dataset="hsapiens_snp")

get.rs <- function(chr, start, end) {
    getBM(c("refsnp_id", "allele", "chrom_start", "chrom_strand"), filters=c("chr_name", "start", "end"),

               values=list(chr, start, end), mart=hg19.snpmart)

}

rsid <- with(dataframe, Map(get.rs, chr.name, chr_start, chr_end))

dataframe is the dataframe referred to in the beginning, chr.name, chr_start, chr_end are the columns.

The last line runs for a long time, then it says:

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.

I've tried using a different host (feb2014.archive.ensembl.org) as well as a different function: useEnsembl(biomart="snp", dataset="hsapiens_snp", GRCh=37). Both give the same result.

Does it have something to do with the fact that this function probably takes a long time to run so there's a web time out? Is there a way to circumvent this issue?

Thanks in advance.

[Thomas Maurel]

Dear Ian,

Do you remember when you had the error? We updated the GRCh37 website to e!83 yesterday early afternoon so that would explain the time out error as the website and marts had a short downtime.

If you still get the error, could you please try to use the Ensembl gene mart instead of the Variation mart since you are only interested in variant information associated with ensembl gene IDs. This will reduce the work that BioMart needs to do to retrieve the data that you are interested in.

For information, we have Variant and gene information available in the Ensembl gene and variation marts, the difference between the two is the following:

* Ensembl gene mart is gene centric and only contains variants linked to Ensembl Transcripts.

* Ensembl Variation mart is variant centric and contains all the variants available in Ensembl.

Your code will looks like the following for the Ensembl gene mart:

require(biomaRt)

hg19.genemart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",  host="grch37.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

get.rs <- function(chr, start, end) {

    getBM(c("variation_name", "allele", "chromosome_start", "snp_chromosome_strand"), filters=c("chromosome_name", "start", "end"),

               values=list(chromosome_name, start, end), mart=hg19.genemart)

}

rsid <- with(dataframe, Map(get.rs, chr.name, chr_start, chr_end))

Alternatively, please send me your dataframe so that I can have a look at the mart queries.

Hope this helps,

Regards,

Thomas

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Thomas Maurel
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European Bioinformatics Institute (EMBL-EBI)
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[Ian Pan]

This worked. Thanks!

[Ian Pan]

It turns out that using the gene mart misses some of the variants that I want. Previously, I had resolved the issue by querying only a subset of the 400 genes at one time. However, right now I'm only trying to query one gene and get all the variants between the start/end position of that gene and I'm getting the same error for some reason. I don't think the web service is down because I can carry out my query using the website online. However, I'm going to need to do this in R in order to repeat it for all of my gene start/end positions. Is the web service through R down for some reason?

[Thomas Maurel]

Dear Ian,

Do you still experience issues with the mart web service being down through R?

Could you please send me an example so that I can investigate further?

Thanks a lot,

Regards,

Thomas

[Justyna]

Hey guys,

I'm new in BioMart. Therefore, I'd appreciate your help.

I've encountered the Problem with connecting to BioMart. I tried to change the hosts

listMarts(host = "http://www.ensembl.org")

but still I have an error

equest 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: 

Any ideas what I can do to move forward?

Thanks a lot,

Justa