[ensembl-dev] GRCH37 archive

[Wolf Beat]

One clarification to your answer Thomas.


I have a feeling you are refering to the

http://grch37.ensembl.org/index.html


Website when talking about the archive, where i'm talking about:

https://grch37-archive.ensembl.org/index.html


Notive the difference in the URL naming scheme to the current ensembl version archive from the same date:

http://jan2020.archive.ensembl.org/index.html


The current ensembl archive clearly indicates that it is the january 2020 archive. Which means, even in 5 years (if it is up that long), it is going to run with the ensembl 2020 release.


The grch37-archive version on the other hand, does at least from an URL naming scheme not give such assurances, making it to some degree not very useful, as it is not clear if it can be used as an actual archives, like the main ensembl archives.


Sorry for the second email, but i think this clarification was necessary


Kind regards


Beat Wolf






Dr Beat Wolf, PhD ▪ Lecturer & Researcher ▪ 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/> ▪ <http://humantech.institute/> https://icosys.ch/



________________________________
From: Dev <dev-bounces at ensembl.org> on behalf of Thomas Juettemann <juettemann at ebi.ac.uk>
Sent: Friday, June 5, 2020 9:42:54 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] GRCH37 archive

Hello Beat,

Thank you for using our resources. It looks like no one has gotten back to you yet, apologies for that.
I will try my best to answer your questions, to be save I cc’ed Andy, who is more knowledgable about the topic.

Please note that the best way to get any question about Ensembl answered is emailing
helpdesk at ensembl.org

As far as I am aware, the archive site will stay for the foreseeable future.
We created it when we updated the main website to use the current assembly, and have kept it stable since then.

We are doing occasional updates, see these links for more details:
http://www.ensembl.info/2015/03/31/first-update-of-the-ensembl-grch37-site/
http://www.ensembl.info/2015/10/08/second-update-of-the-ensembl-grch37-site/

A bigger change is the removal of all non-human data:
http://www.ensembl.info/2019/09/19/simplifying-our-grch37-services/

To answer your short question:
Yes, the version will change, but I am unsure how often the database is patched.  Andy can hopefully add more background here.

Best wishes,
Thomas

—
Thomas Juettemann
Ensembl Regulation

European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD
United Kingdom


On 28 May 2020, at 17:36, Wolf Beat <Beat.Wolf at hefr.ch> wrote:

Hi,


i have a question about the ensembl Grch37 archive:


https://grch37-archive.ensembl.org/index.html


My question is, is this a stable archive? For a very long time i have been looking for a stable archive that is more up to date than the february 2014 version, and i'm very happy to see that now there is one!

But what i'm worried is that this is not actually a stable archive, as there is no version name or date in the URL. Does this mean, that this archive will be updated periodically going forward?


I'm asking because i'm in the usecase where i need a stable endpoint of ensembl where i'm sure the API will not change. For the Grch38 version i can periodically update my code to support the latest versions, as there are fixed stable archive versions. Until now that was not possible will Grch37.


So in short:

Is  the https://grch37-archive.ensembl.org/index.html archive stable, or will the version (99) behind that URL change from time to time?


Kind regards


Beat Wolf






Dr Beat Wolf, PhD ▪ Lecturer & Researcher ▪ 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/> ▪ <http://humantech.institute/> https://icosys.ch/


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