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Hi Ed,<br>
<br>
Thank you for your feedback.<br>
<br>
We appreciate that you are interested in some specific genes and we
aim to provide high quality annotation.<br>
<br>
Doing so for over 60 species, we can not curate each gene
individually. For this, we rely on external resources like Uniprot.<br>
It would appear though that there is a definite loophole here since
Uniprot provides our own ensembl annotation along with existing
proteins.<br>
<br>
We have decided to exclude these annotations from our Uniprot import
and are hoping this will improve the naming for some of our species.<br>
<br>
Looking at specifics:<br>
For <span style="font-size: 11pt; font-family:
"Calibri","sans-serif";">ENSSSCG00000001427</span>,
we will not be using <span style="font-size: 11pt; font-family:
"Calibri","sans-serif";">F1RQW2 any more</span>,
so we will not be assigning C4 as a gene name.<br>
Unfortunately, we will not be able to use <span style="font-size:
11pt; font-family: "Calibri","sans-serif";">A5A8W8</span>
either, as its sequence is too different from our ensembl
translation.<br>
This could be due to sequencing errors in the assembly and is sadly
beyond our control.<br>
This gene has a one-to-one ortholog in human though,
ENSG00000224389.<br>
We will therefore be using the human name projected onto pig, C4A.<br>
<br>
We are aiming to update our name assignments for release 73.<br>
We hope this makes sense and will help reduce the confusion.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 26/06/13 04:21, Ed wrote:<br>
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<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks
Burt, I’m kind of a detailed guy who looks at specific
situations when I manage data. So while your explanation
sounds reasonable, lets look at the first of the two
examples I chose: C4A<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Vega:
Search Vega for C4, and you get nothing related to C4A.
Searches for C4A and C4B and you get useful information.
Specifically C4A OTTSUSG00000001346 .<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Uniprot:
Searching for C4: After leafing through pages of tobacco and
tomatoes, I found F1RQW2 (F1RQW2_PIG) that says “The
sequence shown here is derived from an Ensembl automatic
analysis pipeline and should be considered as preliminary
data.” Search for C4A, leads to the various C4As in mostly
mammals, and I find A5A8W8 (A5A8W8_PIG) with no Cautions
under the General annotation (Comments). So clearly Uniprot
has them both, one from a curated source and one from
ensembl’s preliminary predictions.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Search
for C4 in the Pig on Ensembl.org, you get 4 genes, one of
which is 4 Genes match your query ('C4') in Pig
ENSSSCG00000001427 that maps to C4A OTTSUSG00000001346 in
Vega.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Search
for C4A in ensemble.org, and you get <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Results
Summary - Your search of Pig with 'C4A' returned no results.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Taken
together, it would seem your predicted protein “C4” made it
to Uniprot and then somehow that allowed you to think
deleting the name C4A was in order.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Finally,
just look at ncbi for C4 and C4A: <a moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/gquery/?term=C4A">http://www.ncbi.nlm.nih.gov/gquery/?term=C4A</a>
vs <a moz-do-not-send="true"
href="http://www.ncbi.nlm.nih.gov/gquery/?term=C4">http://www.ncbi.nlm.nih.gov/gquery/?term=C4</a>
. Which is the correct name to use??<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">So
while I understand, appreciate and support your desire to
make sense of the big uncoordinated mess we all have called
gene annotations. However, in this case it seems that there
is something not entirely productive with your approach
since it seems to add more confusion.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Also
since C4A is a valid protein and apparently gene name in
Uniprot, I don’t think I can report a bug to them. Thank
you for your attention and assistance!<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ed<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a class="moz-txt-link-abbreviated" href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a class="moz-txt-link-freetext" href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>] <b>On
Behalf Of </b>Bert Overduin<br>
<b>Sent:</b> Monday, June 24, 2013 1:48 PM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] RE Lesser annotation names
in sscrofa in V72??<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Dear Ed,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">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 <span style="color:black"><a
moz-do-not-send="true" href="mailto:help@uniprot.org"><span
style="font-family:"Arial","sans-serif";text-decoration:none">help@uniprot.org</span></a>.
Unless the removal is a bug, I assume they must have had
a valid reason to do this, though.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">With kind regards,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Bert<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Mon, Jun 24, 2013 at 6:35 PM, Ed
<<a moz-do-not-send="true"
href="mailto:gray_ed@hotmail.com" target="_blank">gray_ed@hotmail.com</a>>
wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
Ed [mailto:<a moz-do-not-send="true"
href="mailto:gray_ed@hotmail.com"
target="_blank">gray_ed@hotmail.com</a>] <br>
<b>Sent:</b> Monday, June 24, 2013 9:35 AM<br>
<b>To:</b> 'Magali'; '<a
moz-do-not-send="true"
href="mailto:dev@ensembl.org"
target="_blank">dev@ensembl.org</a>'<br>
<b>Subject:</b> RE: [ensembl-dev] Lesser
annotation names in sscrofa in V72??</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear
Magali,</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thank
you so much for responding. Your answer seems
reasonable.</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Another
example is PDX-1, an important Gene for sure.
Recent news stories (<a moz-do-not-send="true"
href="http://www.telegraph.co.uk/science/science-news/8584443/Pigs-could-grow-human-organs-in-stem-cell-breakthrough.html"
target="_blank">http://www.telegraph.co.uk/science/science-news/8584443/Pigs-could-grow-human-organs-in-stem-cell-breakthrough.html</a>
) 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.</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Those
two were notable only with 30 second review of the
eliminated names from a single researcher.</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thank
you for your consideration and explanation,
however, I’d suggest you may want to reconsider.</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best
wishes,</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ed</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
Magali [<a moz-do-not-send="true"
href="mailto:mr6@ebi.ac.uk" target="_blank">mailto:mr6@ebi.ac.uk</a>]
<br>
<b>Sent:</b> Friday, June 21, 2013 4:57 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Cc:</b> Ed<br>
<b>Subject:</b> Re: [ensembl-dev] Lesser
annotation names in sscrofa in V72??</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;margin-bottom:12.0pt">Hi
Ed,<br>
<br>
In release 72, we updated the external references
for pig.<br>
<br>
This means we use the latest sets of data from
external sources, like Uniprot for example.<br>
A number of gene names assigned in Uniprot have been
removed in the latest set used in 72, causing the
drop you notice.<br>
<br>
The number of assigned external references is still
comparable or higher than in 71, but no trustworthy
gene name was available for these annotations.<br>
<br>
See <a moz-do-not-send="true"
href="http://www.uniprot.org/uniprot/F1SF30?version=12&version=13"
target="_blank">http://www.uniprot.org/uniprot/F1SF30?version=12&version=13</a>
for example.<br>
Uniprot entry F1SF30 in pig has had its name remove
between versions 12 and 13.<br>
So we still assign that uniprot entry to ensembl
gene ENSSSCG00000015625, but we cannot deduce a gene
name from it.<br>
<br>
<br>
Hope that helps,<br>
Magali<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On
20/06/13 19:27, Ed wrote:<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<pre>Dear Ensembl developers,<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>We extract ensembl annotations for sus scrofa 10.2 and load them into a<o:p></o:p></pre>
<pre>GBrowse database. When we updated to ensembl V71, there were a few hundred<o:p></o:p></pre>
<pre>additional annotations, a generally expected result.<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>A test load of ensembl 72 yielded an unexpected result, fewer annotations.<o:p></o:p></pre>
<pre>The 1241 'names' I believe were removed are listed below.<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>I normally expect a few additional annotations and seeing so many removed<o:p></o:p></pre>
<pre>was a little unsettling.<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Any ideas or comments if this is a bug or a feature?<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Ed<o:p></o:p></pre>
</blockquote>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
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<p class="MsoNormal"><br>
<br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <br>
Bert Overduin, Ph.D.<br>
Vertebrate Genomics Team<br>
<br>
EMBL - European Bioinformatics Institute<br>
Wellcome Trust Genome Campus<br>
Hinxton, Cambridge CB10 1SD<br>
United Kingdom<br>
<br>
<a moz-do-not-send="true"
href="http://www.ebi.ac.uk/%7Ebert" target="_blank">http://www.ebi.ac.uk/~bert</a><o:p></o:p></p>
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style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Ensembl
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<pre wrap="">_______________________________________________
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