[biomart-users] extra content at the end of document, biomaRt down?

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[biomart-users] extra content at the end of document, biomaRt down?

Anthony Colombo


Hi is biomaRt down?  the website www.ensembl.org and biomaRt.org seem to be okay,  however when I call getBM,  I get the error "extra content at the end of the document"  for my annotation routines.   is biomaRt down?
here is my script and yes I am using www.ensembl.org" as the host.


  speciesMart<-.findMart(commonNomen)
    speciesSymbol<-"hgnc_symbol"  #hugo nomenclature human only
         message("finding entrez IDs of top ensembl genes...")
         convertedEntrezID<-getBM(filters="ensembl_gene_id",
                    attributes=c("ensembl_gene_id","entrezgene",speciesSymbol,"description"),
                    values=resValues, #fitBundles ensembl Gene Ids
                    mart=speciesMart)


.findMart <- function(commonName=c("human","mouse"),host="www.ensembl.org"){#{{{

  dataset <- switch(match.arg(commonName),
                    human="hsapiens_gene_ensembl",
                    mouse="mmusculus_gene_ensembl")
  useMart("ENSEMBL_MART_ENSEMBL", dataset=dataset, host=host)


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Re: [biomart-users] extra content at the end of document, biomaRt down?

Thomas Maurel
Dear Anthony,

I am afraid that we had some BioMart server issues on Thursday. Could you please try your query again.
I’ve tried a similar query to yours and it ran fine:
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> convertedEntrezID<-getBM(filters="ensembl_gene_id",
+                          attributes=c("ensembl_gene_id","entrezgene",speciesSymbol,"description"),
+                          values="ENSG00000139618", #fitBundles ensembl Gene Ids
+                          mart=ensembl)
> convertedEntrezID
  ensembl_gene_id entrezgene hgnc_symbol                                        description
1 ENSG00000139618        675       BRCA2 breast cancer 2 [Source:HGNC Symbol;Acc:HGNC:1101]

Apologies for any inconvenience caused,
Best Regards,
Thomas
On 26 May 2016, at 23:49, Anthony Colombo <[hidden email]> wrote:



Hi is biomaRt down?  the website www.ensembl.org and biomaRt.org seem to be okay,  however when I call getBM,  I get the error "extra content at the end of the document"  for my annotation routines.   is biomaRt down?
here is my script and yes I am using www.ensembl.org" as the host.


  speciesMart<-.findMart(commonNomen)
    speciesSymbol<-"hgnc_symbol"  #hugo nomenclature human only
         message("finding entrez IDs of top ensembl genes...")
         convertedEntrezID<-getBM(filters="ensembl_gene_id",
                    attributes=c("ensembl_gene_id","entrezgene",speciesSymbol,"description"),
                    values=resValues, #fitBundles ensembl Gene Ids
                    mart=speciesMart)


.findMart <- function(commonName=c("human","mouse"),host="www.ensembl.org"){#{{{

  dataset <- switch(match.arg(commonName),
                    human="hsapiens_gene_ensembl",
                    mouse="mmusculus_gene_ensembl")
  useMart("ENSEMBL_MART_ENSEMBL", dataset=dataset, host=host)



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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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