[ensembl-dev] Declaration of Intentions for Ensembl release 111 and Ensembl Genomes release 58

[Jose Gonzalez]

Hi Beat,


The GRCh37 GFF file does not contain any MANE_Select tag.


We need to consider whether it is worth adding a partial set of MANE 
Select tags or it might be confusing where users could be expecting the 
whole set.


Thanks,

Jose


On 24/09/2023 14:22, Wolf Beat wrote:
> Thank you for the answer.
> The question though is, does the GRCH37 GFF file contain the 
> MANE_SELECT tag for the transcripts that do match?
>
> Kind regards
>
> Beat Wolf
>
>
> 	
>
> 	
>
> *Dr Beat Wolf, PhD ▪ Assistant Professor ▪ Member of iCoSys Institute
> *University of Applied Sciences and Arts Western Switzerland ▪ 
> Pérolles 80 ▪ CH-1700 Fribourg
> Member of University of Applied Sciences of Western Switzerland
> https://www.heia-fr.ch <https://eia-fr.ch/>▪ https://icosys.ch/
>
>
> ------------------------------------------------------------------------
> *Von:* Jose Gonzalez <jmgonzalez at ebi.ac.uk>
> *Gesendet:* Donnerstag, 14. September 2023 11:02
> *An:* Ensembl developers list <dev at ensembl.org>; Wolf Beat 
> <Beat.Wolf at hefr.ch>
> *Betreff:* Re: [ensembl-dev] Declaration of Intentions for Ensembl 
> release 111 and Ensembl Genomes release 58
>
> 	
> Sie erhalten nicht oft eine E-Mail von jmgonzalez at ebi.ac.uk. Erfahren 
> Sie, warum dies wichtig ist 
> <https://aka.ms/LearnAboutSenderIdentification>
> 	
>
> Hi Beat,
>
>
> As far as I know, the only update is the RefSeq annotation in our 
> GRCh37 otherfeatures database, which has been imported using the file 
> below:
> https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz 
> <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz>
>
> The Ensembl GRCh37 annotation hasn't been updated, so only a fraction 
> of the RefSeq MANE v1.0 transcripts will be exactly matched by Ensembl 
> transcripts.
>
>
> Thanks,
> Jose
>
>
>
> On 13/09/2023 15:31, Wolf Beat wrote:
>> The mane 1.0 inclusion into grch37 sounds great. Related to this, 
>> will the gff file for grch37 also include this information? I know 
>> the grch38 does already do that.
>>
>> Kind regards
>>
>> Beat Wolf
>>
>>
>> 	
>>
>> 	
>>
>> *Dr Beat Wolf, PhD ▪ Assistant Professor ▪ Member of iCoSys Institute
>> *University of Applied Sciences and Arts Western Switzerland ▪ 
>> Pérolles 80 ▪ CH-1700 Fribourg
>> Member of University of Applied Sciences of Western Switzerland
>> https://www.heia-fr.ch <https://eia-fr.ch/>▪ https://icosys.ch/ 
>> <https://icosys.ch/>
>>
>>
>> ------------------------------------------------------------------------
>> *Von:* Dev <dev-bounces at ensembl.org> <mailto:dev-bounces at ensembl.org> 
>> im Auftrag von Benjamin Moore <bmoore at ebi.ac.uk> 
>> <mailto:bmoore at ebi.ac.uk>
>> *Gesendet:* Mittwoch, 13. September 2023 16:15
>> *An:* Ensembl developers list <dev at ensembl.org> <mailto:dev at ensembl.org>
>> *Betreff:* [ensembl-dev] Declaration of Intentions for Ensembl 
>> release 111 and Ensembl Genomes release 58
>> Dear all,
>> Ensembl release 111 and Ensembl Genomes release 58 are scheduled for 
>> November 2023.
>> Please find the summary of the declarations of intentions in our blog:
>> https://www.ensembl.info/2023/09/13/whats-coming-in-ensembl-111-ensembl-genomes-58/ 
>> <https://www.ensembl.info/2023/09/13/whats-coming-in-ensembl-111-ensembl-genomes-58/>
>> As with all releases, please note that these are intentions and are 
>> not guaranteed to make it into the releases.
>> Best wishes
>> Ben
>> On behalf of the Ensembl team
>> -- 
>> Dr. Ben Moore (he/him)
>> Ensembl Outreach Manager
>>
>> European Bioinformatics Institute (EMBL-EBI)
>> European Molecular Biology Laboratory
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge
>> CB10 1SD
>> UK
>>
>> bmoore at ebi.ac.uk  <mailto:bmoore at ebi.ac.uk>
>> +44 (0)1223 494265
>>
>> _______________________________________________
>> Dev mailing listDev at ensembl.org  <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info:https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org  <https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org>
>> Ensembl Blog:http://www.ensembl.info/  <http://www.ensembl.info/>
> -- 
> Dr Jose M. Gonzalez
> GENCODE Bioinformatician (Genome Interpretation Team)
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Genome Campus
> Hinxton, CB10 1SD, UK
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