[ensembl-dev] [External] Re: Mouse Genomes Project gene symbols missing in Ensembl release 114

[Eric Engelhard]

Thank you for the updates, Jorge and Leanne.



Regeneron - Internal
From: Dev <dev-bounces at ensembl.org> On Behalf Of Leanne Haggerty
Sent: Monday, July 7, 2025 3:43 AM
To: Ensembl developers list <dev at ensembl.org>
Subject: [External] Re: [ensembl-dev] Mouse Genomes Project gene symbols missing in Ensembl release 114

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: //projects. ensembl. org/mouse_genomes/ From this page, you


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://projects.ensembl.org/mouse_genomes/<https://urldefense.com/v3/__https:/projects.ensembl.org/mouse_genomes/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwTHE0Zpeg$>

>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:
https://www.embl.org/news/science/a-machine-learning-approach-for-allocating-gene-function/<https://urldefense.com/v3/__https:/www.embl.org/news/science/a-machine-learning-approach-for-allocating-gene-function/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwQukWtXbA$>, and more on Ensembl’s conventional gene naming methods here: https://www.ensembl.org/info/genome/genebuild/gene_names.html<https://urldefense.com/v3/__https:/www.ensembl.org/info/genome/genebuild/gene_names.html__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwRVMMrB2w$>

I hope this is helpful while we await the release of these genomes in the new website.

All the best
Leanne


On 4 Jul 2025, at 16:47, Jorge Batista da Rocha <jrocha at ebi.ac.uk<mailto:jrocha at ebi.ac.uk>> wrote:

Hi Eric,

Hope you are well, and thank you for reaching out.

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.

It will not be fixed for the upcoming 115 release in the autumn. Any fixes would be incorporated into the subsequent 116 release.

We expect the updated builds to become available in our new site, beta.ensembl.org<https://urldefense.com/v3/__http:/beta.ensembl.org/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwRSykVPRQ$> within the next few months.

Thanks and best wishes
Jorge





Dr Jorge Batista da Rocha
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)


On 1 Jul 2025, at 14:58, Eric Engelhard <eric.engelhard at regeneron.com<mailto:eric.engelhard at regeneron.com>> wrote:

Ensembl release 114 includes new genome builds and annotations for the non-canonical Mouse Genome Project strains (https://www.ensembl.info/2025/05/07/ensembl-114-has-been-released/<https://urldefense.com/v3/__https:/www.ensembl.info/2025/05/07/ensembl-114-has-been-released/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwQRPgyK0w$>). 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.

Are gene symbol annotations and a BioMart update planned for the next release?

Thank you,
Eric



Regeneron - Internal
********************************************************************
This e-mail and any attachment hereto, is intended only for use by the addressee(s) named above and may contain legally privileged and/or confidential information. If you are not the intended recipient of this e-mail, any dissemination, distribution or copying of this email, or any attachment hereto, is strictly prohibited. If you receive this email in error please immediately notify me by return electronic mail and permanently delete this email and any attachment hereto, any copy of this e-mail and of any such attachment, and any printout thereof. Finally, please note that only authorized representatives of Regeneron Pharmaceuticals, Inc. have the power and authority to enter into business dealings with any third party.
********************************************************************
_______________________________________________
Dev mailing list    Dev at ensembl.org<mailto:Dev at ensembl.org>
Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org<https://urldefense.com/v3/__https:/lists.ensembl.org/mailman/listinfo/dev_ensembl.org__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwTc_dtzZw$>
Ensembl Blog: http://www.ensembl.info/<https://urldefense.com/v3/__http:/www.ensembl.info/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwTl67A1FQ$>

_______________________________________________
Dev mailing list    Dev at ensembl.org<mailto:Dev at ensembl.org>
Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org<https://urldefense.com/v3/__https:/lists.ensembl.org/mailman/listinfo/dev_ensembl.org__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwTc_dtzZw$>
Ensembl Blog: http://www.ensembl.info/<https://urldefense.com/v3/__http:/www.ensembl.info/__;!!ODpDvJZr5w!D2zS1OFY1EPRlgYrFUiweK4MLwirrk-K9cFqiASzTXiH5DdaYQ9hluPhrFYnfUbzVmUtNmekpfeZrwTl67A1FQ$>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20250707/f4e3a3e2/attachment-0001.html>