Dear Anze, I am working on the ensembl marts on the ensembl.org website so I am sorry I won't be able to let you know when the portal gets fixed. If you want to, you can use the latest version of the ensembl mart (release 70) at the following location: http://www.ensembl.org/biomart/martview/
Hope this helps, Regards, Thomas On 7 Feb 2013, at 16:59, Anze Zupanic wrote: > Dear Thomas, > > Dear Thomas, > > will try that later today or tomorrow, however the xml I got was generated by > Biomart Central Portal automatically from my GUI choices and as far as I can > tell I can’t change the xml in the Portal (I tried, but it just changes it > back to snptype each time). Thanks for your help and please let me know when > the Portal gets fixed. > > Best wishes > > Anze > > From: Thomas Maurel [mailto:[email protected]] > Sent: 07 February 2013 16:01 > To: Arek Kasprzyk > Cc: Anze Zupanic; [email protected] > Subject: Re: [BioMart Users] General query > > Dear Anze, > > In ensembl biomart release 69, we have renamed the "snptype_filters" internal > name to "so_parent_name" to allow us to use sequence ontology term as primary > terms to describe consequences of variations. > Could you please try to replace the following in your xml query: > <Filter name="snptype_filters" value="5_prime_UTR_variant"/> > with > <Filter name="so_parent_name" value="5_prime_UTR_variant"/> > > Hope this helps, > Regards, > Thomas > On 7 Feb 2013, at 15:24, Arek Kasprzyk wrote: > > Hi Anze, > it seems that "<Filter name="snptype_filters" value="5_prime_UTR_variant"/>" > is the problem here. > > Rhoda: - is that a known problem? > > a > > > > > On Thu, Feb 7, 2013 at 11:02 AM, Anze Zupanic <[email protected]> > wrote: > > Hi, > > All my queries that have variation as a filter return an error ("error has > occurred"). Here's a xml of the query that returns an error: > > <!DOCTYPE Query><Query client="true" processor="TSV" limit="-1" > header="1"><Dataset name="mmusculus_gene_ensembl" > config="gene_ensembl_config"><Filter name="biotype" > value="protein_coding"/><Filter name="status" value="KNOWN"/><Filter > name="transcript_status" value="KNOWN"/><Filter name="snptype_filters" > value="5_prime_UTR_variant"/><Attribute > name="ensembl_transcript_id"/></Dataset></Query> > > Any ideas? > > Thanks > > Anze > > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > www.biomart.org > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > > -- > Thomas Maurel > Bioinformatician - Ensembl Production Team > European Bioinformatics Institute (EMBL-EBI) > Wellcome Trust Genome Campus, Hinxton > Cambridge - CB10 1SD - UK -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK
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