GET lookup/symbol/:species/:symbol

Find the species and database for a symbol in a linked external database

Parameters

Required

NameTypeDescriptionDefaultExample Values
species String Species name/alias - arabidopsis_thaliana
Arabidopsis thaliana
symbol String A name or symbol from an annotation source has been linked to a genetic feature - PAD4

Optional

NameTypeDescriptionDefaultExample Values
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
expand Boolean(0,1) Expands the search to include any connected features. e.g. If the object is a gene, its transcripts, translations and exons will be returned as well. NULL -
format Enum(full,condensed) Specify the layout of the response full -

Example Requests

/lookup/symbol/arabidopsis_thaliana/PAD4?content-type=application/json;expand=1


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://test.rest.ensemblgenomes.org';
my $ext = '/lookup/symbol/arabidopsis_thaliana/PAD4?expand=1';
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://test.rest.ensemblgenomes.org"
ext = "/lookup/symbol/arabidopsis_thaliana/PAD4?expand=1"

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://test.rest.ensemblgenomes.org"
ext = "/lookup/symbol/arabidopsis_thaliana/PAD4?expand=1"

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://test.rest.ensemblgenomes.org'
path = '/lookup/symbol/arabidopsis_thaliana/PAD4?expand=1'

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://test.rest.ensemblgenomes.org";
    String ext = "/lookup/symbol/arabidopsis_thaliana/PAD4?expand=1";
    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://test.rest.ensemblgenomes.org/lookup/symbol/arabidopsis_thaliana/PAD4?expand=1' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://test.rest.ensemblgenomes.org/lookup/symbol/arabidopsis_thaliana/PAD4?expand=1'  -O -

/lookup/symbol/arabidopsis_thaliana/PAD4?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://test.rest.ensemblgenomes.org';
my $ext = '/lookup/symbol/arabidopsis_thaliana/PAD4?';
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://test.rest.ensemblgenomes.org"
ext = "/lookup/symbol/arabidopsis_thaliana/PAD4?"

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://test.rest.ensemblgenomes.org"
ext = "/lookup/symbol/arabidopsis_thaliana/PAD4?"

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://test.rest.ensemblgenomes.org'
path = '/lookup/symbol/arabidopsis_thaliana/PAD4?'

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://test.rest.ensemblgenomes.org";
    String ext = "/lookup/symbol/arabidopsis_thaliana/PAD4?";
    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://test.rest.ensemblgenomes.org/lookup/symbol/arabidopsis_thaliana/PAD4?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://test.rest.ensemblgenomes.org/lookup/symbol/arabidopsis_thaliana/PAD4?'  -O -

/lookup/symbol/arabidopsis_thaliana/PAD4?content-type=text/xml;format=condensed;db_type=core


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://test.rest.ensemblgenomes.org';
my $ext = '/lookup/symbol/arabidopsis_thaliana/PAD4?format=condensed;db_type=core';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/xml' }
});

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


print "$response->{status} $response->{reason}\n";

import requests, sys

server = "http://test.rest.ensemblgenomes.org"
ext = "/lookup/symbol/arabidopsis_thaliana/PAD4?format=condensed;db_type=core"

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

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


print r.text

import requests, sys

server = "http://test.rest.ensemblgenomes.org"
ext = "/lookup/symbol/arabidopsis_thaliana/PAD4?format=condensed;db_type=core"

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

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


print r.text

require 'net/http'
require 'uri'

server='http://test.rest.ensemblgenomes.org'
path = '/lookup/symbol/arabidopsis_thaliana/PAD4?format=condensed;db_type=core'

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

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

response = http.request(request)

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


puts response.body

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://test.rest.ensemblgenomes.org";
    String ext = "/lookup/symbol/arabidopsis_thaliana/PAD4?format=condensed;db_type=core";
    URL url = new URL(server + ext);

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

    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://test.rest.ensemblgenomes.org/lookup/symbol/arabidopsis_thaliana/PAD4?format=condensed;db_type=core' -H 'Content-type:text/xml'

wget -q --header='Content-type:text/xml' 'http://test.rest.ensemblgenomes.org/lookup/symbol/arabidopsis_thaliana/PAD4?format=condensed;db_type=core'  -O -

Resource Information

MethodsGET
Response formatsjson
xml
jsonp