Hi Junjun, This should be possible, I'll look into it.
Cheers, Steffen On Thu, Aug 4, 2011 at 12:21 PM, Junjun Zhang <[email protected]>wrote: > Hi Steffen, > > Yes, the error is thrown from the BioMart server side. But this is because > the original query XML the server received is not well-formed (as the error > message shows). > > It might be possible the original query XML looks like this: > > <Query> > <Dataset name = 'hsapiens_gene_ensembl'> > <Filter name = 'hgnc_symbol' value = '2'-PDE'/> > <Attribute name = 'ensembl_gene_id' /> > <Attribute name = 'hgnc_symbol' /> > </Dataset> > </Query> > > If that's the case, the solution is actually simple, we just need to escape > the apostrophe using the string "'" > > <Query> > <Dataset name = 'hsapiens_gene_ensembl'> > <Filter name = 'hgnc_symbol' value = '2'-PDE'/> > <Attribute name = 'ensembl_gene_id' /> > <Attribute name = 'hgnc_symbol' /> > </Dataset> > </Query> > > Do you think it's possible to escape special characters (eg, '<', '>', '&' > etc) in query XML in biomaRt before it sends to the BioMart server. > > Thanks, > > Junjun > > > From: Steffen Durinck <[email protected]> > Date: Fri, 15 Jul 2011 15:46:00 -0400 > To: Marie Wong-Erasmus <[email protected]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [BioMart Users] bug when gene ID contains an apostrophe > > The error is thrown on the BioMart side, I don't think it likes quotes in > gene symbols. > > In addition, if you want a mapping between all gene symbols and ensembl > gene ids you could do this in one query in R: > > library(biomaRt) > mart.ens <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") > map = getBM(attributes=c("ensembl_gene_id", "hgnc_symbol"), > filters="with_hgnc", values=TRUE, mart=mart.ens) > > head(map) > > ensembl_gene_id hgnc_symbol > 1 ENSG00000249567 MIMT1 > 2 ENSG00000246493 SNHG8 > 3 ENSG00000187667 WHAMML1 > 4 ENSG00000248334 WHAMML2 > 5 ENSG00000225273 UBE2Q2P2 > 6 ENSG00000186615 C14orf33 > > > Steffen > > > On Fri, Jul 15, 2011 at 10:45 AM, Marie Wong-Erasmus < > [email protected]> wrote: > >> hi Tim, >> >> You might want to post this to the bioconductor mailing list to get them >> to handle single quotes in the value field. >> >> Either way, aliases should just return an empty set. >> Only hgnc symbols that are not synonyms will have an associated ENSG id. >> So if you used IMP8 which is an alias for IPO8, you will get an empty set >> which is what should be returned if you used 2'-PDE >> >> Marie >> >> From: Timothée Flutre <[email protected]> >> Reply-To: "[email protected]" <[email protected]> >> Date: Fri, 15 Jul 2011 12:13:41 -0400 >> To: "[email protected]" <[email protected]> >> Subject: [BioMart Users] bug when gene ID contains an apostrophe >> >> Hello, >> >> I am using the R package "biomaRt" to find Ensembl IDs from a list of HGCN >> gene IDs: >> >> source("http://bioconductor.org/biocLite.R";) >> biocLite("biomaRt",lib="~/src/Rlibs/") >> library(biomaRt) >> mart.ens <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> getBM(attributes=c("ensembl_gene_id", "hgnc_symbol"), >> filters="hgnc_symbol", values="IPO8", mart=mart.ens) >> ensembl_gene_id hgnc_symbol >> 1 ENSG00000133704 IPO8 >> >> It's working pretty well until a HGCN ID contains an apostrophe (here >> "2'-PDE" is an alias for the gene "PDE12", see >> here<http://www.genenames.org/data/hgnc_data.php?hgnc_id=25386> >> ): >> >> getBM(attributes=c("ensembl_gene_id", "hgnc_symbol"), >> filters="hgnc_symbol", values="2'-PDE", mart=mart.ens) >> Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = >> "hgnc_symbol", : >> Query ERROR: caught BioMart::Exception: non-BioMart die(): >> not well-formed (invalid token) at line 1, column 322, byte 322 at >> /usr/lib/perl5/XML/Parser.pm line 187 >> >> I know how to work around this for my own case, but would it be possible >> to fix this for a future release? >> >> Best regards, >> Tim >> >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> >> >
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