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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