I am trying to obtain "mim_morbid_description" (among other attributes) from homo sapiens gene ensembl mart by using getBM function but I am getting this error:

> getBM(attributes=c("ensembl_gene_id","mim_morbid_description"), filters=c("hgnc_symbol"), values=c("brca2","lct"),mart=genemart, verbose=TRUE)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='0' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Attribute name = 'mim_morbid_description'/><Filter name = 'hgnc_symbol' value = 'brca2,lct' /></Dataset></Query>
#################
Results from server:
[1] "ENSG00000139618\t PANCREATIC CANCER, SUSCEPTIBILITY TO, 2\n;;PNCA2\n\nENSG00000139618\t GLIOMA SUSCEPTIBILITY 3; GLM3\n\nENSG00000139618\t BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2; BROVCA2\nBREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2, INCLUDED;;\nOVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2, INCLUDED\n\nENSG00000139618\t FANCONI ANEMIA, COMPLEMENTATION GROUP D1; FANCD1\n;;FAD1\n\nENSG00000139618\t FANCONI ANEMIA, COMPLEMENTATION GROUP A; FANCA\n;;FANCONI ANEMIA; FA\nFANCONI ANEMIA, ESTREN-DAMESHEK VARIANT, INCLUDED;;\nESTREN-DAMESHEK VARIANT OF FANCONI ANEMIA, INCLUDED;;\nESTREN-DAMESHEK VARIANT OF FANCONI PANCYTOPENIA, INCLUDED\n\nENSG00000139618\t BREAST CANCER\n;;BREAST CANCER, FAMILIAL\nBREAST CANCER, FAMILIAL MALE, INCLUDED\n\nLRG_293\t PANCREATIC CANCER, SUSCEPTIBILITY TO, 2\n;;PNCA2\n\nLRG_293\t GLIOMA SUSCEPTIBILITY 3; GLM3\n\nLRG_293\t BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2; BROVCA2\nBREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2, INCLUDED;;\nOVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2, INCLUDED\n\nLRG_293\t FANCONI ANEMIA, COMPLEMENTATION GROUP D1; FANCD1\n;;FAD1\n\nLRG_293\t FANCONI ANEMIA, COMPLEMENTATION GROUP A; FANCA\n;;FANCONI ANEMIA; FA\nFANCONI ANEMIA, ESTREN-DAMESHEK VARIANT, INCLUDED;;\nESTREN-DAMESHEK VARIANT OF FANCONI ANEMIA, INCLUDED;;\nESTREN-DAMESHEK VARIANT OF FANCONI PANCYTOPENIA, INCLUDED\n\nLRG_293\t BREAST CANCER\n;;BREAST CANCER, FAMILIAL\nBREAST CANCER, FAMILIAL MALE, INCLUDED\n\nENSG00000115850\t LACTASE DEFICIENCY, CONGENITAL\n;;ALACTASIA, CONGENITAL;;\nDISACCHARIDE INTOLERANCE II\n\n"
attr(,"Content-Type")
             
"text/plain"
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 2 did not have 2 elements

I guess that problem causes newline characters in mim-morbid-description strings in results from server but I do not know how to resolve this problem.

The sessionInfo() output:

R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.16.1 biomaRt_2.22.0      

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1  bitops_1.0-6         DBI_0.3.1            GenomeInfoDb_1.2.4   IRanges_2.0.1        parallel_3.1.2       RCurl_1.95-4.5       RSQLite_1.0.0        S4Vectors_0.4.0      stats4_3.1.2        
[13] tools_3.1.2          XML_3.98-1.1   

You pinpointed the problem correctly, the newline characters make the import fail. This is because the data is returned from the server as a tab-separated file which then is passed on to `read.table`; however, this requires the data input to be table like. The newlines break that.

As a user, there is unfortunately not much you can do right now. Here some ideas:

Short-term solutions:

1) If your query is fairly simple as in the example, you can go the ensembl biomart site, construct your query interactively and save the data in a file. Then you can import that file in R manually, which should boil down to a version of `read.table`.

Longer-term solutions:

1) Contact the ensembl helpdesk and ask them to remove the newline characters. There seems no use in having them.

2) Contact the biomaRt maintainer and ask for a fix. Please note that this can be harder, since the input data from ensembl behaves strangely here, in my opinion.

Thank you for your advices. The short-term solution is not very suitable so I will try to contact the mentioned parties.