1.0 To 3.0 Migration

Migrating your beta REST service client to work with release 3.0.0

The majority of functionality remains the same, but a few key changes have taken place to specific endpoints and general operation. Chiefly, our URL changes from beta.rest.ensembl.org to rest.ensembl.org. Read on:

URL Changes

VEP Endpoint

The VEP consequence URL has changed from:

http://beta.rest.ensembl.org/vep/human/9:22125503-22125502:1/C/consequences?content-type=application/json

To become:

http://rest.ensembl.org/vep/human/region/9:22125503-22125502:1/C?content-type=application/json

Feature Endpoint

The /feature endpoints have been renamed to /overlap.

http://beta.rest.ensembl.org/feature/region/human/7:140424943-140624564?feature=gene;content-type=application/json

Has now become:

http://rest.ensembl.org/overlap/region/human/7:140424943-140624564?feature=gene;content-type=application/json

Assembly Info

The /assembly/info endpoints were incorrectly namespaced in the API.

http://beta.rest.ensembl.org/assembly/info/homo_sapiens?content-type=application/json

Has become:

http://rest.ensembl.org/info/assembly/homo_sapiens?content-type=application/json

Ontology Descendants

The /ontology/descendents URL was mis-spelt.

http://beta.rest.ensembl.org/ontology/descendents/GO:0005667?content-type=application/json

Has become:

http://rest.ensembl.org/ontology/descendants/GO:0005667?content-type=application/json

Serialisation Formats

In the unlikely event that you chose to use Message Pack or Sereal for your output format, please switch to using JSON. JSON will be the primary supported input and output format for Ensembl REST, and there are good libraries in all common languages to transparently handle this data format.

Parameters

Retirement of phyloxml specific parameters

The two phyloxml parameters phyloxml_aligned and phyloxml_sequence have been retired from the GeneTree endpoints. Please use aligned and sequence instead.

Rate limiter increased

The basic rate limit has been increased to 15 requests per second. You can increase the client rate to match.

Output 'id' field

The output 'id'/'ID' field is now consistently returned in lowercase ('id') across all endpoints.

http://beta.rest.ensembl.org/archive/id/ENSG00000157764?content-type=application/json
{"ID":"ENSG00000157764","latest":"ENSG00000157764.8","version":"8","release":"75","peptide":null,"is_current":"1","type":"Gene","possible_replacement":[],"assembly":"GRCh37"}

Has changed to:

http://rest.ensembl.org/archive/id/ENSG00000157764?content-type=application/json
{"id":"ENSG00000157764","latest":"ENSG00000157764.8","version":"8","release":"75","peptide":null,"is_current":"1","type":"Gene","possible_replacement":[],"assembly":"GRCh37"}