[ensembl-dev] Biomart Genomic Coding Start/End

Rhoda Kinsella rhoda at ebi.ac.uk
Fri May 25 13:47:58 BST 2012


Hi Simon and Beat,
The issues relating to the erroneous calculation of the UTR start and  
end coordinates and the Genomic coding start and end coordinates have  
now been fixed in the Ensembl gene mart and the new fixed version has  
been pushed to the live site, the ftp site, the public mysql database  
and the Ensembl mirrors. The issue was caused by a bug in Exon.pm in  
the API which has also been fixed. If you use the biomaRt package from  
Bioconductor you should set your host to www.ensembl.org to get the  
most up to date version. The BioMart Central Portal at www.biomart.org  
have been informed about the updated version and will push the new  
version live as soon as possible. Apologies for any inconvenience  
caused and thank you for reporting the issue. Please see our " Known  
Bugs" blog about this issue here: http://www.ensembl.info/contact-us/known-bugs/
Regards,
Rhoda



On 24 May 2012, at 17:18, Simon Chan wrote:

> Hi Rhoda,
>
> The first gene I noticed this issue was with BCORL1/ 
> ENSG00000085185.  Specifying Genomic Coding Start/End gives me UTR  
> coordinates as well.
>
> Thanks for looking into this.
> Simon.
>
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On  
> Behalf Of Rhoda Kinsella
> Sent: Thursday, May 24, 2012 1:00 AM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Biomart Genomic Coding Start/End
>
> Hi Simon
> Yes this is likely to be related to the issue below. Can you send me  
> a specific example so that I can check that this? We have rerun the  
> calculations and are in the process of testing to make sure all id  
> okay before copying the fixed mart to the live site. I will send an  
> email once the fix has been made live.
> Regards
> Rhoda
>
> On 23 May 2012, at 18:06, Simon Chan wrote:
>
>
> Hello,
>
> I'm using BioMart to fetch all protein coding portions of all exons  
> of all transcripts of my favourite gene (Ensembl Genes 67, Homo  
> sapiens genes GRCh37.p7).  In the past, 'Genomic coding start' and  
> 'Genomic coding end' would give me all exon coordinates minus UTRs.   
> However, now it seems to return the UTR coordinates as well.   
> Perhaps this is related to the UTR issue reported by Beat below?
>
> Thank you.
> Simon.
>
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On  
> Behalf Of Rhoda Kinsella
> Sent: Tuesday, May 22, 2012 3:38 AM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Ensembl release 67 is out!
>
> Hi Beat
> We are currently looking into why this has occurred but it is  
> certainly a bug in our mart databases. I will respond as soon as we  
> have a fix in place. Thank you for reporting this and apologies for  
> any inconvenience.
> Regards
> Rhoda
>
> On 19 May 2012, at 15:55, Beat Wolf wrote:
>
>
>
> Hi,
>
> i'm a computer scientist and not a biologist, so perhaps i missed  
> something about the DMD gene changing recently.
> I have an automated unit test for my application that uses biomart.  
> It happens to test the DMD-001 transcript of the DMD gene.
> In the 66 version of enembl, the UTR3 coordinates of the exon number  
> 79 where:
>
> 31137345
> to 31140035
> which was correct. Now with the version 67 of ensembl, the UTR3  
> region in the same exon is:
>
> 31137345 to
> 31137344
> Which can not be correct, because that means that UTR3 has a length  
> of 1. The other numbers don't match up either.
>
> Did the DMD gene change? Is the information stored differently in  
> ensembl? What values do i need to reconstruct the true UTR3 region?  
> Or is this a bug in the new ensembl version. If yes, how many other  
> genes are affected? Currently i will stay on the 66 version thanks  
> to the archives, but i have some connection issues with it, it seems  
> to be much less stable than the 67 version.
>
> Greetings
>
> Beat Wolf
>
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>
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
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> Ensembl Blog: http://www.ensembl.info/

Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

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