Hi Arek, The ortholog queries within a single dataset seem limiting, one of the users query is for example:
<?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'/><Attribute name = 'mmusculus_homolog_chromosome'/><Attribute name = 'mmusculus_homolog_chrom_start'/><Filter name = 'hgnc_symbol' value = 'TP53' /></Dataset></Query> which does not work as the webservice returns the following error: Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed Cheers, Steffen On Wed, Nov 28, 2012 at 9:59 AM, Arek Kasprzyk <[email protected]>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<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 >>> >> >> > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > www.biomart.org >
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