[ensembl-dev] BioMart 0.9 released

[Arek Kasprzyk]

Hi Paul,
Sorry, I should have been more clear in my message.

There is no need to migrate individual data providers (such as Ensembl) to
a new version of the web service.  In other words there is no need for you
guys to do anything at all. The system will work just fine.
In my email I was referring to third party programmers who are using
BioMart central portal as a hub for all BioMarts out there. They have an
option of migrating to 0.9 now to take advantage of some new features such
as Enrichment analysis. This will not affect you guys at all.


a





On 21 May 2014 20:29, Paul Flicek <flicek at ebi.ac.uk> wrote:

> Hi Arek,
>
> Congratulations on your recent release of BioMart and also on the new
> features. I am sure this is the start of a new beginning and we are looking
> forward to seeing further developments.
>
> To users of the Ensembl BioMarts, currently Ensembl does not plan to
> migrate our mart service away from the 0.7 release. We are aware of a
> number of pipelines dependent on the 0.7 web service interfaces and wish to
> be as un-disruptive as possible to those users. However we will continue to
> monitor your developments and will endeavour to review our current stance
> in the near future.
>
>
> Paul
>
>
> On 21 May 2014, at 10:25, Arek Kasprzyk <arek.kasprzyk at gmail.com> wrote:
>
> > Dear All,
> > It has been a while since I spammed this mailing list ;)
> >
> > Since BioMart remains a major interface to Ensembl data, I thought you
> may be interested in new developments there.
> >
> > a
> >
> > ---------- Forwarded message ----------
> > From: Arek Kasprzyk <arek.kasprzyk at gmail.com>
> > Date: 20 May 2014 16:22
> > Subject: BioMart 0.9 released
> > To: biomart-announce at googlegroups.com
> >
> >
> >
> >
> > We are pleased to announce the release of BioMart version 0.9.
> >
> >
> > The latest version of BioMart includes support for data analysis and
> visualisation tools. The first of the BioMart tools has already been
> implemented and is accessible from www.biomart.org. This tool enables
> enrichment analysis of genes in all Ensembl species and a broad range of
> gene identifiers for each species are also available. Furthermore, the tool
> supports cross-species analysis using Ensembl homology data. Finally, the
> enrichment tool facilitates analysis of BED files containing genomic
> features such as Copy Number Variations (CNVs) or Differentially Methylated
> Regions (DMRs).
> >
> >
> > The latest BioMart release comes with the new version of the REST and
> SOAP APIs. These APIs are available for testing at central.biomart.org.
> Third party developers who are currently using REST or SOAP version 0.7 are
> encouraged to start testing and transitioning to 0.9. The two servers
> providing access to BioMart data through REST and SOAP (version 0.7 and
> version 0.9) will be running in parallel to provide support for easy
> transition. The Enrichment tool is also accessible programmatically through
> 0.9 REST/SOAP interface.
> >
> >
> > Finally, the BioMart website has been completely redesigned to cater for
> a better user experience. The re-organised layout, incorporation of new
> functionality, such as the "quick tool access" and the use of subtle
> animation makes for clearer navigation and greater site interactivity.
> >
> >
> > Your feedback is welcome and appreciated.
> >
> >
> >
> >
> > On behalf of the BioMart developers
> >
> > Arek
> >
> >
> > --
> > Arek Kasprzyk, MD. MSc. Ph.D.
> >
> > Head of Data Management
> > Center for Translational Genomics and Bioinformatics
> > San Raffaele Scientific Institute
> > Via Olgettina 58
> > 20132 Milano
> > Italy
> >
> >
> >
> >
> >
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>
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-- 

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy
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