GET xrefs/symbol/:species/:symbol

Looks up an external symbol and returns all objects linked to it. This can be a display name for a gene/transcript/translation, a synonym or an externally linked reference. If a gene's transcript is linked to the supplied symbol the service will return both gene and transcript (it supports transient links).

Parameters

Required

NameTypeDescriptionDefaultExample Values
species String Species name/alias - brugia_malayi_prjna10729
symbol String Symbol or display name of a gene - Bm994

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
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 core
external_db String Filter by external database - EntrezGene
object_type String Filter by feature type - gene
transcript

Example Requests

/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?';
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 = "https://parasite.wormbase.org"
ext = "/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?"

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

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

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

import requests, sys

server = "https://parasite.wormbase.org"
ext = "/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?"

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

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

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

require 'net/http'
require 'uri'

server='https://parasite.wormbase.org'
path = '/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?'

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 = "https://parasite.wormbase.org";
    String ext = "/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?";
    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 'https://parasite.wormbase.org/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?'  -O -

/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?external_db=EntrezGene;content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?external_db=EntrezGene';
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 = "https://parasite.wormbase.org"
ext = "/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?external_db=EntrezGene"

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

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

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

import requests, sys

server = "https://parasite.wormbase.org"
ext = "/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?external_db=EntrezGene"

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

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

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

require 'net/http'
require 'uri'

server='https://parasite.wormbase.org'
path = '/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?external_db=EntrezGene'

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 = "https://parasite.wormbase.org";
    String ext = "/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?external_db=EntrezGene";
    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 'https://parasite.wormbase.org/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?external_db=EntrezGene' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?external_db=EntrezGene'  -O -

/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?content-type=text/xml


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?';
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 = "https://parasite.wormbase.org"
ext = "/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?"

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

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


print r.text

import requests, sys

server = "https://parasite.wormbase.org"
ext = "/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?"

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

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


print(r.text)

require 'net/http'
require 'uri'

server='https://parasite.wormbase.org'
path = '/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?'

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 = "https://parasite.wormbase.org";
    String ext = "/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?";
    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 'https://parasite.wormbase.org/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?' -H 'Content-type:text/xml'

wget -q --header='Content-type:text/xml' 'https://parasite.wormbase.org/rest-19/xrefs/symbol/brugia_malayi_prjna10729/Bm994?'  -O -

Resource Information

MethodsGET
Response formatsjson
xml
jsonp