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<p class="MsoNormal"><span style="font-size:12.0pt">Thank you for the updates, Jorge and Leanne.
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Regeneron - Internal<br>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Dev <dev-bounces@ensembl.org>
<b>On Behalf Of </b>Leanne Haggerty<br>
<b>Sent:</b> Monday, July 7, 2025 3:43 AM<br>
<b>To:</b> Ensembl developers list <dev@ensembl.org><br>
<b>Subject:</b> [External] Re: [ensembl-dev] Mouse Genomes Project gene symbols missing in Ensembl release 114<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-line-height-alt:.75pt"><span style="font-size:1.0pt;color:white">Hi Eric, Just to add to Jorge’s response, in case it’s useful, you can find the genomes and Ensembl annotations for the latest Mouse Genome Project on the Ensembl
project page: https:</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">//projects.</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">ensembl.</span><span style="font-size:1.0pt;font-family:"Arial",sans-serif;color:white"> </span><span style="font-size:1.0pt;color:white">org/mouse_genomes/
From this page, you<o:p></o:p></span></p>
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<p>Hi Eric,<o:p></o:p></p>
<p style="font-size:-apple-system-body">Just to add to Jorge’s response, in case it’s useful, you can find the genomes and Ensembl annotations for the latest Mouse Genome Project on the Ensembl project page:<br>
<a href="https://urldefense.com/v3/__https:/projects.ensembl.org/mouse_genomes/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwTHE0Zpeg$" target="_new">https://projects.ensembl.org/mouse_genomes/</a><o:p></o:p></p>
<p style="font-size:-apple-system-body">From this page, you can download the GFF files. Gene symbols have been added using a machine learning approach that closely replicates traditional Ensembl assignment methods with high accuracy. You can read more about
this approach here:<br>
<a href="https://urldefense.com/v3/__https:/www.embl.org/news/science/a-machine-learning-approach-for-allocating-gene-function/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwQukWtXbA$">https://www.embl.org/news/science/a-machine-learning-approach-for-allocating-gene-function/</a>,
and more on Ensembl’s conventional gene naming methods here: <a href="https://urldefense.com/v3/__https:/www.ensembl.org/info/genome/genebuild/gene_names.html__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwRVMMrB2w$" target="_new">https://www.ensembl.org/info/genome/genebuild/gene_names.html</a><o:p></o:p></p>
<p>I hope this is helpful while we await the release of these genomes in the new website.<o:p></o:p></p>
<p>All the best<br>
Leanne<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">On 4 Jul 2025, at 16:47, Jorge Batista da Rocha <</span><a href="mailto:jrocha@ebi.ac.uk"><span style="font-size:12.0pt">jrocha@ebi.ac.uk</span></a><span style="font-size:12.0pt">> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Hi Eric, <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Hope you are well, and thank you for reaching out. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">I’m sorry to say that the gene symbols are missing due to an error in our external references pipeline. Our data teams are looking into it. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">It will not be fixed for the upcoming 115 release in the autumn. Any fixes would be incorporated into the subsequent 116 release.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">We expect the updated builds to become available in our new site, </span><a href="https://urldefense.com/v3/__http:/beta.ensembl.org/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwRSykVPRQ$"><span style="font-size:12.0pt">beta.ensembl.org</span></a><span style="font-size:12.0pt"> within
the next few months. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Thanks and best wishes<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Jorge <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Dr Jorge Batista da Rocha<br>
Ensembl Outreach Project Leader<br>
European Bioinformatics Institute (EMBL-EBI) <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">On 1 Jul 2025, at 14:58, Eric Engelhard <</span><a href="mailto:eric.engelhard@regeneron.com"><span style="font-size:12.0pt">eric.engelhard@regeneron.com</span></a><span style="font-size:12.0pt">> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Ensembl release 114 includes new genome builds and annotations for the non-canonical Mouse Genome Project strains (</span><a href="https://urldefense.com/v3/__https:/www.ensembl.info/2025/05/07/ensembl-114-has-been-released/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwQRPgyK0w$"><span style="font-size:12.0pt;color:#467886">https://www.ensembl.info/2025/05/07/ensembl-114-has-been-released/</span></a><span style="font-size:12.0pt">).
I recently noticed, however, that new gene annotations now lack gene symbols for both the web service and within the MySQL sources. Additionally, BioMart sources are no longer synchronized to the new gene identifiers, all of which have been replaced.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Are gene symbol annotations and a BioMart update planned for the next release?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Thank you,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt">Eric<o:p></o:p></span></p>
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