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 >>>> 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**** >>>> >>> >>> >> > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > www.biomart.org >
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