Question

Problem with apostrophe in biomaRt query

1

Entering edit mode

analeonpalacio ▴ 10

@analeonpalacio-18199

Last seen 2.1 years ago

Spain

I am trying to get the snp associated to the phenotype Crohn's disease using biomaRt:

getBM(attributes = c('refsnp_id','allele','chrom_start','chrom_strand'),
filters = "phenotype_description",
values = "Crohn's disease',
mart = ensembl)

But I have this error:

Error in getBM(attributes = c("refsnp_id", "allele", "chrom_start", "chrom_strand"), :
Query ERROR: caught BioMart::Exception: non-BioMart die():
not well-formed (invalid token) at line 1, column 394, byte 394 at /nfs/services/ensweb-software/sharedsw/2018_08_22/linuxbrew/Cellar/perl/5.26.2_2/lib/perl5/site_perl/5.26.2/x86_64-linux-thread-multi/XML/Parser.pm line 187.
XML::Simple called at /nfs/public/release/ensweb/latest/live/mart/www_94/biomart-perl/lib/BioMart/Query.pm line 1935.

I thing it is a problem with the apostrophe because when I use "Crohn disease" it works. Any idea about how to fix it?

biomaRt • 890 views

ADD COMMENT • link updated 6.1 years ago by Mike Smith ★ 6.6k • written 6.1 years ago by analeonpalacio ▴ 10

score 2 · Accepted Answer · 2018-11-06

Thanks for reporting this. There's actually a couple of different things going on here.

First, you're absolutely right that the apostrophe is breaking the query. biomaRt uses apostrophes to separate the values when it submits the query, so sticking an extra one in leaves a mismatch and causes the error you see.

I've fixed this in the devel version of biomaRt (version 2.39.1), so it uses double quotes internally & your query will be submitted successfully.

However, if you look at the Ensembl BioMart web interface (https://www.ensembl.org/biomart) the phenotype filter isn't a free text search, but actually has a preset list of values, presumably populated by phenotype annotation that is actually used in the database.

You can view the list in an R session via with the code below, but be warned it returns a single huge string that significantly slows down my R session.

library(dplyr)
listFilters(mart = ensembl, what = c("name", "options")) %>%
    filter(name == "phenotype_description")

At the moment there's no elegant way to search the list of options, I'll have think about how to improve searchFilters() so you can find appropriate values more easily.

I think for now, the values you want for Crohn's disease are probably those below. I don't know how the annotation is assigned, but using this complete set will return a different set of SNPs compared to just using one.

values = c("Crohn disease",
           "Crohn's disease",
           "Crohn's disease (need for surgery)",
           "Crohn's disease (time to surgery)",
           "Crohn's disease and celiac disease",
           "Crohn's disease and psoriasis",
           "Crohn's disease and sarcoidosis (combined)",
           "Crohn's disease-related phenotypes")