[ensembl-dev] RE Lesser annotation names in sscrofa in V72??

[Bert Overduin]

Dear Ed,

I am afraid this is not something that can be changed in Ensembl. As Magali
explained, Ensembl retrieves the gene names from UniProt and they have
removed the names in question. So, if you want to enquire whether these
gene names can be reinstated, you have to contact UniProt at
help at uniprot.org. Unless the removal is a bug, I assume they must have had
a valid reason to do this, though.

I appreciate that this possibly is not the answer you'd like to hear, but
these kind of things have to be fixed at the source, otherwise it would
become one big uncoordinated mess. I hope this makes sense.

With kind regards,
Bert


On Mon, Jun 24, 2013 at 6:35 PM, Ed <gray_ed at hotmail.com> wrote:

> ** **
>
> ** **
>
> *From:* Ed [mailto:gray_ed at hotmail.com]
> *Sent:* Monday, June 24, 2013 9:35 AM
> *To:* 'Magali'; 'dev at ensembl.org'
> *Subject:* RE: [ensembl-dev] Lesser annotation names in sscrofa in V72??**
> **
>
> ** **
>
> Dear Magali,****
>
> ** **
>
> Thank you so much for responding.  Your answer seems reasonable.****
>
> ** **
>
> I guess I was a little taken aback that a number of gene names removed
> were, I believe, the preferred HUGO name for the gene.****
>
> ** **
>
> Take for instance C4A.  By changing it to C4, it creates some confusion in
> the ensembl comparative genomics section on what is mapped.  C4B seems
> clearly mapped to C4B, while it looks like what is now C4 (used to be C4A)
> maps to both C4A and C4B.****
>
> ** **
>
> Another example is PDX-1, an important Gene for sure.  Recent news stories
> (
> http://www.telegraph.co.uk/science/science-news/8584443/Pigs-could-grow-human-organs-in-stem-cell-breakthrough.html) are based on work on the PDX-1 gene.  While Hugo has the gene listed as
> PDX1, PDX-1 is an approved synonym and many of the papers in academic
> journals use (and still use) PDX-1.****
>
> ** **
>
> Those two were notable only with 30 second review of the eliminated names
> from a single researcher.****
>
> ** **
>
> Thank you for your consideration and explanation, however, I’d suggest you
> may want to reconsider.****
>
> ** **
>
> Best wishes,****
>
> Ed****
>
> ** **
>
> ** **
>
> *From:* Magali [mailto:mr6 at ebi.ac.uk <mr6 at ebi.ac.uk>]
> *Sent:* Friday, June 21, 2013 4:57 AM
> *To:* Ensembl developers list
> *Cc:* Ed
> *Subject:* Re: [ensembl-dev] Lesser annotation names in sscrofa in V72??**
> **
>
> ** **
>
> Hi Ed,
>
> In release 72, we updated the external references for pig.
>
> This means we use the latest sets of data from external sources, like
> Uniprot for example.
> A number of gene names assigned in Uniprot have been removed in the latest
> set used in 72, causing the drop you notice.
>
> The number of assigned external references is still comparable or higher
> than in 71, but no trustworthy gene name was available for these
> annotations.
>
> See http://www.uniprot.org/uniprot/F1SF30?version=12&version=13 for
> example.
> Uniprot entry F1SF30 in pig has had its name remove between versions 12
> and 13.
> So we still assign that uniprot entry to ensembl gene ENSSSCG00000015625,
> but we cannot deduce a gene name from it.
>
>
> Hope that helps,
> Magali****
>
> On 20/06/13 19:27, Ed wrote:****
>
> Dear Ensembl developers,****
>
> ** **
>
> We extract ensembl annotations for sus scrofa 10.2 and load them into a****
>
> GBrowse database.  When we updated to ensembl V71, there were a few hundred****
>
> additional annotations, a generally expected result.****
>
> ** **
>
> A test load of ensembl 72 yielded an unexpected result, fewer annotations.****
>
> The 1241 'names' I believe were removed are listed below.****
>
> ** **
>
> I normally expect a few additional annotations and seeing so many removed****
>
> was a little unsettling.****
>
> ** **
>
> Any ideas or comments if this is a bug or a feature?****
>
> ** **
>
> Ed****
>
>
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-- 
Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert

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