[ensembl-dev] New REST server is out!--Jason Rozick continued follow up.

Sat Jun 28 11:23:49 BST 2014

BRAF, 7q34, and continued work.
RP11-837G3, 140,296,644-140,482,706, read in LR direction.
CTD 2382B2, start 140,469,394, covers ok to right.
G469R, and rs 121913357.
Noted heart issues, and NM 004333 polyA5.

V600Q, and rs 113488022, loc chr7: 140,453,136.
(V aa with R-group, isopropyl, and goes to Q aa, with R-group of proyl amide.  
Genbank, M21001, (140,434,397-140,481,493), S. Ikawa.
Affy core and extended probesets, 3076340-3076374. and 3076340-3076373 respectively.
3076374, GM12878 exon array signal rep ENCODE/UW.
Relevant ILMN 1652472 ().
Db SNP 138 ().

--------------------------------------------
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
 >>>> 
 >>>>
 _______________________________________________
 >>>> Dev mailing list    Dev at ensembl.org
 >>>> Posting guidelines and
 subscribe/unsubscribe info:
 >>>> http://lists.ensembl.org/mailman/listinfo/dev
 >>>> Ensembl Blog: http://www.ensembl.info/
 >>>> 
 >>> 
 >>>
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 >> 
 >> 
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