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

[Ed]

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-hum
an-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] 
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
<http://www.uniprot.org/uniprot/F1SF30?version=12&version=13> &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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