EnsemblGenomes and Ensembl REST services merged

g_m_carstairs · 10 April 2019 16:45

This announcement from Ensembl

http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/

includes the merger of these REST service endpoints.

This states that rest.ensemblgenomes.org has been retired, although as of today it is still responding.

Before it is retired (i.e. now), Jalview users need to be advised to add this line to their .jalview_properties file in order to fetch ‘EnsemblGenomes’ accessions:

ENSEMBL_GENOMES_BASEURL=https://rest.ensembl.org

Jalview should then be ‘tidied up’ (code and documentation) to better reflect the merger of these services, however this is not urgent given the above workaround. Issue is JAL-3193.

Mungo

The University of Dundee is a registered Scottish Charity, No: SC015096

···

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017

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Today’s Topics:

Ensembl 96 and Ensembl Genomes 43 are out! (Astrid Gall)

Message: 1
Date: Tue, 09 Apr 2019 13:01:18 +0100
From: Astrid Gall agall@ebi.ac.uk
To: dev@ensembl.org, announce@ensembl.org,
ensembl-campus@ebi.ac.uk
Subject: [ensembl-announce] Ensembl 96 and Ensembl Genomes 43 are out!
Message-ID: 20190409120152.8134962BFE7_CAC89B0B@hh-mx3.ebi.ac.uk
Content-Type: text/plain; charset=“utf-8”

Dear all

We are pleased to announce that the latest Ensembl and Ensembl Genomes updates have been released:

http://www.ensembl.org/

http://ensemblgenomes.org

Highlights of this release include:
First-pass full annotation of the mouse genome (GENCODE M21 gene set)
Release of Ensembl-RefSeq MANE Select v0.5 transcripts
Update to GENCODE 30 for human
Joint REST server for Ensembl and Ensembl Genomes
Changes to FTP directory layout
New genomes: 19 birds, five reptiles and 12 mammals
New interface for configuration of regulation tracks

The release blog post with all news can be viewed here:

http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/

For the latest news from the Ensembl project visit our blog at:

http://www.ensembl.info

The release webinar is planned for Wednesday 17th April 2019 at 16:00 BST. Please register using the following URL:

https://attendee.gototraining.com/r/8260823671959775489

Registration is free.

Best regards,

Astrid

On behalf of the Ensembl team

–

Dr Astrid Gall