[ensembl-dev] New REST server is out!--Jason Rozick.
Jason Rozick
jrozick at yahoo.com
Sat Jun 28 02:36:32 BST 2014
Hi, to Michael H. for Migali, and to Andrew Y.
BRAF, called v-raf murine sarcoma viral oncogene homolog B.
7q34, ser/thr kinase.
EC Enzyme Convention nomenclature, EC (2.7.)11.1, (Transfer Phosphorous containing groups).
UniprotKB: P15056., 766aa., at sited region (253-255,KLL).
Molecular processing, at sited region 1,M aa removed.
Chain, and focus on part of the sited region 253-255, inside the Chain (2-766).
Zn Finger sited region, (234-280), while focus is on mutational work, as in A246P, and Q257R. (A. Sarkozy)., in CFC1, CARDIOfaciocutaneous syndrome 1., and related to VAR 026113 and VAR 026114 respectively for mut’s, also more too.
Prot, at 245-258=LAF[C]DF[C]R{KLL}FQG., note C aa Cysteine(Glycine parent-Rgroup-ThioylMethane?-IUPAC nomenclature).
mRNA length 2949, at sited region 817-825, (aagctgctt=KLL).
ALL prior to UCSC Project scope planning., many values here (as in vectoring & Clin appl sensing), to make focus on chr 7: 140,453,136. Sited for ensemble dev group.
Jason Rozick. I’ll look into it soon, as for the SNP rs# mentioned, and related issues.
--------------------------------------------
On Thu, 6/26/14, Andy Yates <ayates at ebi.ac.uk> wrote:
Subject: Re: [ensembl-dev] New REST server is out!
To: "Ensembl developers list" <dev at ensembl.org>
Date: Thursday, June 26, 2014, 12:45 PM
Hi Michael,
I think it's better to see beta as our first attempt at
writing a REST service and this new version is what happens
when we try to expand it's scope. Whilst the output of the
data has changed dramatically and is not 1:1 with the
remainder of the style of the rest service this is backed by
a stupendous increase in speed. We will take on your
comments though especially as now is the time to make
changes. We are also investigating URL versioning to ensure
that transitions can be handled gracefully without the need
for sudden abrupt changes. Since we are now moving into a
solid service these changes will happen with the upmost care
& attention and we will continue to learn from services
like GitHub about how to design good RESTful interfaces.
I hope that even though you are not happy with the manner of
the changes you will be happy with the results
Cheers,
Andy
------------
Andrew Yates - Ensembl Support Coordinator
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
http://www.ensembl.org/
On 26 Jun 2014, at 17:19, Michael Heuer <heuermh at gmail.com>
wrote:
> Will McLaren <wm2 at ebi.ac.uk>
wrote:
>
>> 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.
>
> The data returned by these endpoints look nothing like
the data
> returned by any of the other endpoints, I see that as a
major problem.
>
>
>> 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.
>
> Right, that is what beta typically means, things may
change.
> Shouldn't these rather significant changes have been
made there first
> for feedback?
>
> michael
>
>
>> 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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>>>
>>>
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>>
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