Dear all,

i having troubles since 2 weeks with the biomaRt function getBM or useMart. Before i did it like this and i get the info, please i want to know if it is server problem or im doing really something wrong.

Thank you.

I will explain my self to connect to biomart i've been using..

 Ensembl_Fun <- useMart(biomart = "ENSEMBL_MART_FUNCGEN",
                                 dataset="hsapiens_annotated_feature",   
                                 host = "sep2015.archive.ensembl.org")

and.... (i tried win other way too)

Ensembl_Fun <- useMart(biomart="ENSEMBL_MART_FUNCGEN"
                           host="grch37.ensembl.org",
                           path="/biomart/martservice",
                           dataset="hsapiens_gene_ensembl")

PD: i was asking for different "datasets", but i have troubles for all of them ("hsapiens_annotated_feature","hsapiens_motif_feature","hsapiens_regulatory_feature","hsapiens_mirna_target_feature","hsapiens_segmentation_feature","hsapiens_external_feature")

Them the attributes im asking for... (i know for each case is different but is an example)

Annotation_Ensembl_Fun <- getBM(attributes = c("chromosome_name",
                                                       "chromosome_start",
                                                       "chromosome_end",
                                                       "feature_type_name",
                                                       "feature_type_class",
                                                       "feature_type_description",
                                                       "cell_type_name",
                                                       "so_accession"),
                                        filters = "chromosomal_region",
                                        values = Chr_Region,
                                        mart = Ensembl_Fun)

And each time i run (it take like 20mins), i got:

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.

Here i put the SESSION INFO:

sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

locale:
[1] C

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

other attached packages:
[1] reshape_0.8.5  ggplot2_2.1.0  biomaRt_2.26.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5          IRanges_2.4.8        XML_3.98-1.4         bitops_1.0-6         grid_3.2.4          
 [6] plyr_1.8.3           gtable_0.2.0         DBI_0.4-1            stats4_3.2.4         RSQLite_1.0.0       
[11] scales_0.4.0         S4Vectors_0.8.11     labeling_0.3         tools_3.2.4          Biobase_2.30.0      
[16] munsell_0.4.3        RCurl_1.95-4.8       parallel_3.2.4       BiocGenerics_0.16.1  AnnotationDbi_1.32.3
[21] colorspace_1.2-6    

and the TRACE BACK....

traceback()
6: stop("Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.")
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch(postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery), 
       error = function(e) {
           stop("Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.")
       })
1: getBM(attributes = c("chromosome_name", "chromosome_start", "chromosome_end", 
       "feature_type_name", "feature_type_class", "feature_type_description", 
       "cell_type_name", "so_accession"), filters = "chromosomal_region", 
       values = Chr_Region, mart = Ensembl_Fun)

Thanks a lot, 

A follow up on this. I can confirm that the main BioMart at ensembl.org, including the web interface and martservice (which I believe biomaRt uses), works fine for the previous example. Chromosome 1 takes approximately 10 minutes to download due to the sheer volume of data, but the Y chromosome takes less than a second - I get similar results using biomaRt.

However, queries on individual regions (e.g. 1:100:100000) seem to be quite slow. I'll try and investigate why this is happening, though it would be very useful to know the volume and size of the regions you're using for queries.

Thanks,

Dan.

Hi Juan-Pablo,

I'd like to echo James's comments here - a self-contained example would be a great help in figuring out how to help you here. In particular, knowing what Chr_Region is set to would be very helpful. If we can also know what your use-case is, it would be very helpful to advise you on the best way to get the data you need. 

Having said that, can I ask a couple more questions? Firstly, is there any reason why you're using the September archive or the GRCh37 instance rather than ensembl.org? Secondly, if this was working before, can you confirm the rough runtime and the number of rows returned by your successful script.

However, I can confirm that the biomart instance at ensembl.org is behaving as expected and we're not seeing any unusual load on the mart server. If I use the biomart web interface to query hsapiens_annotated_feature with the filters and attributes in your example using chromosome 1, the full results are returned in a minute or two (though are over 500M and nearly 4 million rows). This is the URL if you can confirm this is a query you're having problems with:

http://www.ensembl.org/biomart/martview/f7bfbf194e6d312846ab46579f8bbe49?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_annotated_feature.default.annotated_feature.chromosome_name|hsapiens_annotated_feature.default.annotated_feature.chromosome_start|hsapiens_annotated_feature.default.annotated_feature.chromosome_end|hsapiens_annotated_feature.default.annotated_feature.feature_type_name|hsapiens_annotated_feature.default.annotated_feature.feature_type_class|hsapiens_annotated_feature.default.annotated_feature.so_accession|hsapiens_annotated_feature.default.annotated_feature.feature_type_description|hsapiens_annotated_feature.default.annotated_feature.cell_type_name|hsapiens_annotated_feature.default.annotated_feature.cell_type_description&FILTERS=hsapiens_annotated_feature.default.filters.chromosome_name."1"&VISIBLEPANEL=resultspanel

Thanks,

Dan.