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]<mailto:[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]<mailto:[email protected]> https://lists.biomart.org/mailman/listinfo/users -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead www.biomart.org<http://www.biomart.org/> _______________________________________________ Users mailing list [email protected]<mailto:[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
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