Hi Arek, This is a known bug of ensembl mart 69 (http://www.ensembl.info/contact-us/known-bugs/), the Homologs attributes section is not working when using a second dataset. We had a request from the the bioconductor community to rename all the common names (internal names) from the homologs atribute section to latin names in order to make things more consistent throughout Ensembl BioMart. This renaming has created a bug when using a second dataset. This will be fixed for ensembl release 70 scheduled for January 2013.
Sorry for any inconvenience caused. Regards, Thomas On 28 Nov 2012, at 17:59, Arek Kasprzyk wrote: > Hi Steffen, > ok, that explains it. You are using explicit linking that it seems to be > broken at the moment. (I am waiting for Rhoda and/or Thomas comments) > > However, just to let you know that simple orthologue queries can be also > achieved (faster as well) through a single dataset as follows: > > > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE Query> > <Query virtualSchemaName = "default" formatter = "TSV" header = "0" > uniqueRows = "0" count = "" datasetConfigVersion = "0.6" > > > <Dataset name = "hsapiens_gene_ensembl" interface = "default" > > <Filter name = "with_homolog_mmus" excluded = "0"/> > <Attribute name = "ensembl_gene_id" /> > <Attribute name = "ensembl_transcript_id" /> > <Attribute name = "mmusculus_homolog_ensembl_gene" /> > <Attribute name = "drerio_homolog_ensembl_gene" /> > </Dataset> > </Query> > > > a > > > > > > On Wed, Nov 28, 2012 at 5:54 PM, Steffen Durinck <[email protected]> wrote: > Hi Arek, > > The R example Kathleen reported is similar though, it translates to: > > <?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 = 'external_gene_id'/><Filter name = > 'wikigene_name' value = 'TP53' /></Dataset><Dataset name = > 'drerio_gene_ensembl' ><Attribute name = 'hgnc_symbol'/></Dataset></Query> > > in XML > > Steffen > > > On Wed, Nov 28, 2012 at 9:16 AM, Arek Kasprzyk <[email protected]> > wrote: > Hi Steffen and Katleen, > > Indeed your example is not working, although the mechanism for those two > queries is rather different. > It appears that explicit linking with a mouse dataset produces no results > regardless of the query (The homologue queries in Katleen's examples are not > affected bc they are part of the human dataset). > > Rhoda, Thomas: could you help us here a bit? It appears that there maybe a > problem on Ensembl side? > > cheers, > a > > > > On Wed, Nov 28, 2012 at 3:56 PM, Steffen Durinck <[email protected]> wrote: > 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 zebrafish > database, 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 > > > > > > > > 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 > > > > > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > www.biomart.org > > > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > www.biomart.org -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK
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