News: Welcome Ensembl REST with more endpoints!
9
gravatar for Denise - Open Targets
5.5 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.1k wrote:

REST stands for Representational State Transfer. It's an architectural style for web services offering a way for accessing resources remotely. The REST was originally described by Ron Fielding and inspired by the development of hypertext transfer protocol (HTTP).

Lots of bioinformatics resources are out there on web in a browser format, and Ensembl is no different. Browsers are pretty interactive and provide a graphical (and pretty) visualisation of genes, variants, alignments, regulatory information. However the utility of browsers can be compromised when/if users want to access a given resource systematically, or perhaps when/if they want to integrate those resources into a web portal or workbench application.

The Ensembl REST allows this systematic access to out database (and tools, such as VEP, lift over). You can query the database from a variety of programming languages such as Phyton, Ruby and JavaScript. It's an alternative to our Ensembl Perl APIs.

The Ensembl REST API has been available for over 2 years now and it was provided as a beta version, which has been recently retired. That's when Mag's blog post comes in: we welcome the new Ensembl REST, which is more robust than its beta version.

What can you do with the Ensembl REST API? You can:

1) get genomic (cDNA, CDS, protein) sequences

2) access the VEP (Variant Effect Predictor)

3) get homologies and gene trees

4) retrieve variation and regulation data 

just to mention a few endpoints...

This data can be retrieved in JSON, XML and a variety of bioinformatic formats such as FASTA.

How can you access the Ensembl REST API?

It can be accessed at http://rest.ensembl.org. There is one version for the previous human assembly too!

Happy RESTing!

Check Mag's blog post here

p.s let me know if you want more information and I can put you in touch with my colleagues in the Ensembl Core team! We can also come to your institution to teach about the Ensembl REST and Perl APIs.

rest-api news ensembl • 2.3k views
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Denise - Open Targets5.1k
1

This is a HUGE update for people like me. Thank you!

ADD REPLYlink written 5.5 years ago by Dan D7.0k

That's great to know! Give Ensembl REST a go and get in touch through here or at helpdesk@ensembl.org if you have got any questions/comments!

ADD REPLYlink written 5.5 years ago by Denise - Open Targets5.1k
Could you please provide a little bit info on what is REST in this post?
ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by mikhail.shugay3.4k
2

Thank you both for your feedback! I'm a newbie here and still learning how/what to post.

<rest of the content moved to main post>

ADD REPLYlink modified 5.5 years ago by Istvan Albert ♦♦ 83k • written 5.5 years ago by Denise - Open Targets5.1k

I agree. A post that is just a link to another blog post is not a good source of information.

A short summary or other type of additional information would be really helpful.

ADD REPLYlink written 5.5 years ago by Istvan Albert ♦♦ 83k

That's a great summary and resource thanks for the details.

PS. I moved the content from the comment into the main post so that new readers don't have to scroll all the way down - editing existing posts to change/improve them  is also acceptable use (even if it means that the comments become invalid - we can always delete the comments)

ADD REPLYlink written 5.5 years ago by Istvan Albert ♦♦ 83k

Glad to know! Thanks for moving the content into the main post!

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Denise - Open Targets5.1k
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