Hi Steffen, yes, you are right, orthologue queries only offer a limited number of attributes
a On Wed, Nov 28, 2012 at 7:16 PM, Steffen Durinck <[email protected]> wrote: > 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 >> > > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead www.biomart.org
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