Question

ENSEMBL_MART_FUNCGEN not accessible through biomaRt?

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Sigve Nakken ▴ 50

@sigve-nakken-6575

Last seen 2.2 years ago

Norway

Hi,

I am trying to access the Ensembl Regulatory Build through the biomaRt package, using the following commands:

ensembl_mart <- biomaRt::useMart(“ENSEMBL_MART_FUNCGEN")

ensembl_mart <- biomaRt::useDataset(“hsapiens_regulatory_feature", mart = ensembl_mart)

queryAttributes <- c('regulatory_stable_id','feature_type_description','feature_type_name')

ensembl_reg <- biomaRt::getBM(attributes = queryAttributes, mart=ensembl_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.

I do not believe the availability of the web service is the underlying problem here. I have tried both GRCh38 and GRCh37, but neither was successful.

Does anyone know how/if Ensembl's regulatory data can be obtained through biomaRt?

regards,

Sigve Nakken

sessionInfo()

R version 3.3.0 (2016-05-03) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.5 (Yosemite)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached): [1] IRanges_2.6.0 rsconnect_0.4.3 parallel_3.3.0 DBI_0.4-1 tools_3.3.0 RCurl_1.95-4.8 Biobase_2.32.0 AnnotationDbi_1.34.3 biomaRt_2.28.0 RSQLite_1.0.0 [11] S4Vectors_0.10.1 BiocGenerics_0.18.0 stats4_3.3.0 bitops_1.0-6 XML_3.98-1.4

biomart regulatory ensemble mart ensembldb • 1.2k views

ADD COMMENT • link updated 8.5 years ago by Thomas Maurel ▴ 800 • written 8.5 years ago by Sigve Nakken ▴ 50

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I can confirm that I experience the same issue running your code. If i make the same query using the web interface it takes tens of minutes to return all the records.

I wonder if it is due to the volume of data you're requesting (every record in the regulatory features dataset) and it's timing out. The actual error returned by Rcurl is "error 18: transfer closed with outstanding read data remaining" indicating curl hasn't received everything it was expecting.

ADD REPLY • link 8.5 years ago Mike Smith ★ 6.6k

score 0 · Answer 1 · 2016-06-14

Dear Sigve,

I am afraid Mike is right, the issue is coming from the volume of data that you are requesting. I am afraid the BioMart software was not designed to handle genome wide queries. Could you please split your query in smaller chunks using a mart filter. For example you can use the chromosome name filter and query each chromosome one at a time.

Alternatively, if you are interested in all the regulatory features, we also provide data dumps on our FTP site: ftp://ftp.ensembl.org/pub/current_regulation

Hope this helps,

Best Regards,

Thomas