[ensembl-dev] New REST server is out!

[Will McLaren]

Hi Michael,

Thanks for your feedback.

The new VEP REST endpoints now use the same backend code as the VEP script
and web interfaces. This has some big advantages, largely in performance
and in the ease with which we can develop and evolve all three methods of
VEP access.

There are downsides, one of which is the output generated by the VEP
endpoints is now a very basic JSON conversion of the data structure
returned by the VEP code. This data structure evolved primarily to feed the
VEP script, which uses these odd upper/lower cases in its field names - the
upper case ones generally are those found in the "Extra" field of the VEP
script's output format. You can find a list of the fields and their
definitions here:

http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#output

The beta.rest.ensembl.org server is still available if you wish to continue
using it for now.

Of course we will take any feedback on board and if we decide to make any
changes then the earlier the better in terms of reducing impact on our
users.

Thanks again

Will McLaren
Ensembl Variation


On 26 June 2014 16:41, Michael Heuer <heuermh at gmail.com> wrote:

> Hello Magali,
>
> The format of the data returned by the vep endpoints is completely
> different now, would have been nice to have some advanced notice.
>
> In fact, the conventions used to convert to JSON are completely
> different than used elsewhere and are in some cases invalid, e.g.
>
> {
>   "SYMBOL":"BRAF",
>   "SYMBOL_SOURCE":"HGNC"
>   "STRAND":-1
> ...
>
> Why ALLUPPERCASE for the field name?
>
>   "Uploaded_variation":"COSM476",
> ...
>
> Why Sentence_case for the field name?
>
>   "Existing_variation":"rs113488022,COSM18443,COSM476,COSM6137",
>   "CLIN_SIG":"other,pathogenic,untested"
>   "Consequence":"missense_variant,NMD_transcript_variant"
> ...
>
> Why is an array of string values shoved into a single value?
> Shouldn't these be array values?
>
>   "Location":"7:140453136"
>
> Location used to be a nested object:
>
>          "location" : {
>             "strand" : 1,
>             "name" : "7",
>             "coord_system" : "chromosome",
>             "start" : 140453136,
>             "end" : 140453136
>          },
>
>
> This looks to me like a step backwards for this particular endpoint.
>
>    michael
>
>
> On Thu, Jun 26, 2014 at 5:34 AM, mag <mr6 at ebi.ac.uk> wrote:
> > Dear all,
> >
> > We are pleased to announce the release of our new REST server,
> > http://rest.ensembl.org
> >
> > This new server comes with a higher rate limit, POST support and a huge
> > documentation rewrite.
> >
> > POST support is provided for the VEP and archive endpoints.
> > We have also added a new variation endpoint to retrieve information
> about a
> > variation id, including phenotypes, genotypes and population studies.
> > Full details of the new release can be found here:
> > https://github.com/Ensembl/ensembl-rest/wiki/Change-log
> >
> > The rate limit has been increased, allowing up to 15 requests per second.
> >
> > The current beta server, beta.rest.ensembl.org, will remain active until
> > release 76, scheduled for end of July.
> >
> > We encourage you to follow the guidelines on our wiki
> > (https://github.com/Ensembl/ensembl-rest/wiki/1.0-To-2.0-Migration) to
> > update your scripts to use the new version before beta is retired.
> >
> > If you are new to REST, please use our wiki
> > (https://github.com/Ensembl/ensembl-rest/wiki) to get started.
> >
> >
> > Regards,
> > Magali
> >
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