Hi Arek, I have other users reporting the same issue, here is an example XML query that doesn't return a result:
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= "biomaRt"> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'hgnc_symbol'/><Attribute name = 'chromosome_name'/><Attribute name = 'start_position'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset><Dataset name = 'mmusculus_gene_ensembl' ><Attribute name = 'chromosome_name'/><Attribute name = 'start_position'/></Dataset></Query> Does this work for you? Cheers, Steffen On Tue, Nov 27, 2012 at 4:52 AM, Arek Kasprzyk <[email protected]>wrote: > Hi Katleen, > I am cc'ing Steffen Durinck who is an expert on the R interface and > hopefully will be able to help you with that > > > a > > > On Tue, Nov 27, 2012 at 12:32 PM, Katleen De Preter < > [email protected]> wrote: > >> Dear Arek,**** >> >> >> Thanks for your reply. However, it is still not working (via R): did >> something change in the structure of the database, so that the following R >> script doesn’t work anymore?**** >> >> ** ** >> >> library(biomaRt)**** >> >> human<-useMart("ensembl","hsapiens_gene_ensembl") #define human >> database, it works**** >> >> zebrafish<-useMart("ensembl","drerio_gene_ensembl") #define >> zebrafishdatabase, it works >> **** >> >> homolog.1<-getLDS(attributes=c("external_gene_id"),filters =" >> wikigene_name",values =my.list1,mart=human,**** >> >> attributesL=c("hgnc_symbol"),martL=zebrafish) # this >> last code line gives no results**** >> >> ** ** >> >> Or can you help me how to configure the online biomart request in order >> to get human gene symbols vs zebrafish gene symbols (and not only >> ensembl IDs).**** >> >> ** ** >> >> Kind regards,**** >> >> ** ** >> >> Katleen De Preter**** >> >> ** ** >> >> *From:* Arek Kasprzyk [mailto:[email protected]] >> *Sent:* dinsdag 27 november 2012 11:52 >> *To:* Katleen De Preter >> *Cc:* [email protected] >> *Subject:* Re: [BioMart Users] General query: ortholog searches**** >> >> ** ** >> >> Hi Katleen,**** >> >> We have recently updated the server to Ensembl 69, perhaps this was just >> a temporary glitch**** >> >> ** ** >> >> The following query : >> http://www.biomart.org/biomart/martview/1456454c60d2a4397ffb57525b5acbb3* >> *** >> >> ** ** >> >> produces the output:**** >> >> ** ** >> >> Ensembl Gene ID Ensembl Transcript ID Zebra Finch >> Ensembl Gene ID Mouse Ensembl Gene ID**** >> >> ENSG00000259662 ENST00000539570 ENSTGUG00000003187 >> ENSMUSG00000050503**** >> >> ENSG00000258865 ENST00000510508 ENSTGUG00000012784 >> ENSMUSG00000075707**** >> >> ENSG00000258664 ENST00000553856 ENSMUSG00000079252**** >> >> ENSG00000258518 ENST00000483851 ENSTGUG00000011221 >> ENSMUSG00000027833**** >> >> ENSG00000259741 ENST00000558098 ENSTGUG00000000764 >> ENSMUSG00000021156**** >> >> ENSG00000259741 ENST00000558098 ENSTGUG00000017137 >> ENSMUSG00000021156**** >> >> ENSG00000265969 ENST00000292095 ENSTGUG00000000184 >> ENSMUSG00000032086**** >> >> ENSG00000262355 ENST00000305831 ENSTGUG00000014163 >> ENSMUSG00000021838**** >> >> ENSG00000262355 ENST00000305831 ENSTGUG00000013086 >> ENSMUSG00000021838**** >> >> ENSG00000198888 ENST00000361390 ENSTGUG00000018737 >> ENSMUSG00000064341**** >> >> ** ** >> >> ** ** >> >> similarly the 08 server: **** >> >> ** ** >> >> >> http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+69+(WTSI%2C+UK)&step=4&attributes=homologs_ensembl_gene_id%2Cmouse_ensembl_gene%2Cinter_paralog_zebrafish_ensembl_gene&homolog_filters%5B%5D=with_mmusculus_homolog&homolog_filters%5B%5D=only&homolog_filters%5B%5D=Homolog+filters+Orthologous+Mouse+Genes<http://central.biomart.org/martwizard/#!/Genome?mart=Ensembl+Genes+69+(WTSI%2C+UK)&step=4&attributes=homologs_ensembl_gene_id%2Cmouse_ensembl_gene%2Cinter_paralog_zebrafish_ensembl_gene&homolog_filters%5B%5D=with_mmusculus_homolog&homolog_filters%5B%5D=only&homolog_filters%5B%5D=Homolog+filter> >> **** >> >> ** ** >> >> ** ** >> >> ** ** >> >> a.**** >> >> ** ** >> >> ** ** >> >> On Mon, Nov 26, 2012 at 9:40 AM, Katleen De Preter < >> [email protected]> wrote:**** >> >> Hi,**** >> >> **** >> >> I’m trying to perform cross-species ortholog searches >> (mice-human-zebrafish). However, it seems that this option is currently not >> working on biomart (website and via R). The same script that previously >> worked, is currently not successful. Do you know about this problem?**** >> >> **** >> >> Kind regards, >> >> Katleen De Preter**** >> >> **** >> >> **** >> >> -- >> >> dr. ir. Katleen De Preter >> Center for Medical Genetics Ghent (CMGG) >> Ghent University Hospital >> Medical Research Building (MRB), >> 2nd floor, room 120.038 >> De Pintelaan 185, >> B-9000 Ghent, Belgium >> +32 9 332 5533 (phone) | +32 9 332 6549 (fax) >> >> http://medgen.ugent.be >> [email protected] **** >> >> **** >> >> **** >> >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users**** >> >> ** ** >> ------------------------------ >> >> Geen virus gevonden in dit bericht. >> Gecontroleerd door AVG - www.avg.com >> Versie: 2012.0.2221 / Virusdatabase: 2629/5420 - datum van uitgifte: >> 11/26/12**** >> > >
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