[ensembl-dev] Dev Digest, Vol 48, Issue 21

Thu Jun 26 12:30:46 BST 2014

Heya Ensembl folk!

Is there any plans to allow access via HTTPS for the REST API? I've developing an (internal) web-based service which deals with patient data, and so I'd prefer to use SSL if at all possible, but most web browsers - sensibly - don't allow you to call resources over HTTP if you're using HTTPS.

Regards,
Algy :)

--
Algy Taylor MBCS
Web Developer
Bioinformatics Group
Genomic Diagnostics Laboratory
Manchester Centre for Genomic Medicine
Central Manchester University Hospitals NHS Foundation Trust
Saint Mary's Hospital
Oxford Road, Manchester.  M13 9WL
Tel: 0161 701 0443
Fax: 0161 276 6238

www.mangen.org.uk  MCGM includes: Clinical Genetics Service |
Genomic Diagnostics Laboratory | Willink Biochemical Genetics Unit | Bioinformatics Group |
University of Manchester Genetic Medicine | NIHR Genetics Clinical Trials Unit
MCGM Partners:  MAHSC Genomic Diagnostics and Innovation | NGRL | Nowgen |  
EMQN | ERNDIM 

www.cmft.nhs.uk  Central Manchester University Hospitals NHS Foundation Trust includes: Manchester Royal Infirmary, Manchester Royal Eye Hospital, Royal Manchester Children's Hospital, Saint Mary's Hospital, University Dental Hospital of Manchester, Trafford Hospitals and Community Services.

-----Original Message-----
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Sent: 26 June 2014 12:00
To: dev at ensembl.org
Subject: Dev Digest, Vol 48, Issue 21

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Today's Topics:

   1. New REST server is out! (mag)
   2. Re: Mouse genes discrepancies (Dan Sheppard)

----------------------------------------------------------------------

Message: 1
Date: Thu, 26 Jun 2014 11:34:32 +0100
From: mag <mr6 at ebi.ac.uk>
Subject: [ensembl-dev] New REST server is out!
To: Ensembl developers list <dev at ensembl.org>,
	ensembl-campus at ebi.ac.uk, 	announce at ensembl.org
Message-ID: <53ABF738.5090400 at ebi.ac.uk>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

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)<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)<https://github.com/Ensembl/ensembl-rest/wiki>
to get started.

Regards,
Magali
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Message: 2
Date: Thu, 26 Jun 2014 11:56:15 +0100
From: Dan Sheppard <dan at ebi.ac.uk>
Subject: Re: [ensembl-dev] Mouse genes discrepancies
To: dev at ensembl.org
Message-ID: <53ABFC4F.5080708 at ebi.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi,

Thanks for your queries, and sorry for the delay getting back to you.

Concerning your first query, -- on the name 'B930076A02' in e!75 mouse,
-- the synonym actually being matched is B930076A02Rik. Search considers this a plausible match to your query.

If you wish, you can use %-wildcards with fetch_all_by_external_name(), which instructs the API to return records by prefix. For example:

my $genes = $gene_adaptor->fetch_all_by_external_name('B930076A02%');

Concerning your second query, -- on LOC232400 and LOC241525, -- we do have some LOC% synonyms from a number of sources (EntrezGene, Uniprot, RFAM, RGD, ...). In this case the NCBI URLs are not overly informative, so it's hard to say whether they should be present or not, but most likely either we don't have the associated gene or the synonym is deprecated.

Hope this helps. Do let us know if you have any further queries about this.

All the best,
Dan.

On 19/06/14 12:58, Genomeo Dev wrote:
> Hi,
>
> I wanted to dig out some mouse genes from Ensembl using old symbols of 
> which I don't know the source. I am getting this discrepancy:
>
> 1) Between Ensembl website and API (75):
>
> B930076A02
>
> The website found this:
>
> http://www.ensembl.org/Multi/Search/Results?q=B930076A02;site=ensembl
>
>
> my $registry = 'Bio::EnsEMBL::Registry'; 
> $registry->load_registry_from_db( -host => 'ensembldb.ensembl.org 
> <http://ensembldb.ensembl.org>', -user => 'anonymous'
> );
>
> my $gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor( "mouse", 
> "core", "gene" ); my $genes = 
> $gene_adaptor->fetch_all_by_external_name('B930076A02');
>
> This code found nothing.
>
> 2) Ensmebl does not recognise these names while NCBI does:
>
> LOC232400
> LOC241525
>
> http://www.ncbi.nlm.nih.gov/gene/?term=LOC232400
> http://www.ncbi.nlm.nih.gov/gene/?term=LOC241525
>
> Thanks,
>
> --
> G.

------------------------------

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