GET overlap/id/:id

Retrieves features (e.g. genes, transcripts, variants and more) that overlap a region defined by the given identifier.

Parameters

Required

NameTypeDescriptionDefaultExample Values
feature Enum(gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation, structural_variation, somatic_structural_variation, constrained, regulatory, segmentation, motif, chipseq, array_probe) The type of feature to retrieve. Multiple values are accepted. none -
id String An Ensembl stable ID - AT3G52430

Optional

NameTypeDescriptionDefaultExample Values
biotype String The functional classification of the gene or transcript to fetch. Cannot be used in conjunction with logic_name when querying transcripts. - protein_coding
callback String Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. - randomlygeneratedname
db_type String Restrict the search to a database other than the default. Useful if you need to use a DB other than core - core
logic_name String Limit retrieval of genes, transcripts and exons by a given name of an analysis. - -
misc_set String Miscellaneous set which groups together feature entries. Consult the DB or returned data sets to discover what is available. - cloneset_30k
object_type String Filter by feature type - gene
so_term String Sequence Ontology term to narrow down the possible variants returned. - SO:0001650
species String Species name/alias. - arabidopsis_thaliana
species_set String Filter by species set for retrieving constrained elements. mammals -
variant_set String Short name of a set to restrict the variants found. (See list of short set names) - ClinVar

Example Requests

/overlap/id/AT3G52430?feature=gene;content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'http://rest.ensemblgenomes.org';
my $ext = '/overlap/id/AT3G52430?feature=gene';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'application/json' }
});

die "Failed!\n" unless $response->{success};


use JSON;
use Data::Dumper;
if(length $response->{content}) {
  my $hash = decode_json($response->{content});
  local $Data::Dumper::Terse = 1;
  local $Data::Dumper::Indent = 1;
  print Dumper $hash;
  print "\n";
}

import requests, sys

server = "http://rest.ensemblgenomes.org"
ext = "/overlap/id/AT3G52430?feature=gene"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print repr(decoded)

import requests, sys

server = "http://rest.ensemblgenomes.org"
ext = "/overlap/id/AT3G52430?feature=gene"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print(repr(decoded))

require 'net/http'
require 'uri'

server='http://rest.ensemblgenomes.org'
path = '/overlap/id/AT3G52430?feature=gene'

url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)

request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})

response = http.request(request)

if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end


require 'rubygems'
require 'json'
require 'yaml'

result = JSON.parse(response.body)
puts YAML::dump(result)

import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;


public class EnsemblRest {

  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensemblgenomes.org";
    String ext = "/overlap/id/AT3G52430?feature=gene";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "application/json");
    

    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();

    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }

    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }

    System.out.println(output);
  }
}


curl 'http://rest.ensemblgenomes.org/overlap/id/AT3G52430?feature=gene' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://rest.ensemblgenomes.org/overlap/id/AT3G52430?feature=gene'  -O -

Resource Information

MethodsGET
Response formatsjson
xml
gff3
bed
jsonp
Slice length5e6