[ensembl-dev] Maintaining the Java API to Ensembl Datasources

[PATERSON Trevor]

It might be worth advertising here that we are still maintaining our Java Ensembl API.

JEnsembl can be used to load & access all releases of Ensembl and EnsemblGenomes (back to Ensembl release 50).

For the non-bacterial datasources full backwards compatibility is provided and multiple releases can be loaded and traversed by the API.

Because the Bacterial species list is now so large we have restricted  the API Registry  to working with a single bacterial release at a time .

The JEnsembl API can be found at http://jensembl.sourceforge.net/ .

ArkMAP, our demonstration Map drawing application (http://bioinformatics.roslin.ed.ac.uk/arkmap/),  can be used to pull down and draw chromosomes from any of the Ensembl datasources and  retrieve and align homology relationships between genomes.

We intend to keep the API and ArkMAP up-do-date with Ensembl releases - but are not *currently* implementing additional functionality.

(although we would consider interesting use cases, particularly those that have potential to turn into funded collaborations).


Trevor Paterson PhD
trevor.paterson at roslin.ed.ac.uk<mailto:trevor.paterson at roslin.ed.ac.uk>
Bioinformatics
The Roslin Institute
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Easter Bush
Midlothian
EH25 9RG
Scotland UK

phone +44 (0)131 651 9157

http://bioinformatics.roslin.ed.ac.uk/

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From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Beat Wolf
Sent: 24 February 2015 10:14
To: Ensembl developers list
Subject: Re: [ensembl-dev] Bacteria Biomart


Hi,



following the question about the biomart access to Ensembl bacteria/genomes i

got interested in the data myself. I quickly found that there is a REST API to access

the data, which is great. But sadly it does not seem to work correctly. Most of the

examples gives in the API description do not work and i got a lot of issues. Simple

requests like retrieving the list of supported species

(http://rest.ensemblgenomes.org/documentation/info/species[1<http://rest.ensemblgenomes.org/documentation/info/species%5b1>] ) give an error.



Is this known? Is there a plan in improving that rest interface and a timetable? Or is

the API documentation simply out of date and the REST interface actually works

but has different endpoints than described?



Thank you for your help



Kind regards



Beat Wolf





On Monday 23 February 2015 17.03:47 Dan Staines wrote:

> Hi Toni,

>

> We no longer provide a BioMart for Ensembl Bacteria following its

> expansion to over 20,000 genomes, which BioMart does not scale to. We're

> actively looking into alternative tools to replace mart - in the

> meantime, if you have specific needs, I'd be more than happy to help as

> far as I can.

>

> Regards,

>

> Dan.

--

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PhD Student Beat Wolf



University of Applied Sciences of Western Switzerland

&

University of Würzburg



PhD Website: http://beat.wolf.home.hefr.ch/

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