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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