Ensembl Rest API - GET homology/symbol/:species/:symbol

Retrieves homology information (orthologs) by symbol

Parameters

Required

Name	Type	Description	Default	Example Values
species	`String`	Species name/alias	`-`	`homo_sapiens` `human`
symbol	`String`	Symbol or display name of a gene	`-`	`BRCA2`

Optional

Name	Type	Description	Default	Example Values
aligned	`Boolean`	Return the aligned string if true. Otherwise, return the original sequence (no insertions)	`1`	`-`
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`
cigar_line	`Boolean`	Return the aligned sequence encoded in CIGAR format	`1`	`-`
compara	`String`	Name of the compara database to use. Multiple comparas exist on a server for separate species divisions	`vertebrates`	`vertebrates`
external_db	`String`	Filter by external database	`-`	`HGNC`
format	`Enum(full,condensed)`	Layout of the response	`full`	`-`
sequence	`Enum(none, cdna, protein)`	The type of sequence to bring back. Setting it to none results in no sequence being returned	`protein`	`-`
target_species	`String`	Filter by species. Supports all species aliases	`-`	`homo_sapiens` `human`
target_taxon	`Integer`	Filter by taxon	`-`	`9606` `10090`
type	`Enum(orthologues, paralogues, projections, all)`	The type of homology to return from this call. Projections are orthology calls defined between alternative assemblies and the genes shared between them. Useful if you need only one type of homology back from the service	`all`	`-`

Example Requests

/homology/symbol/human/BRCA2?content-type=application/json

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://staging.rest.ensembl.org';
my $ext = '/homology/symbol/human/BRCA2?';
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://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?"

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://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?"

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://staging.rest.ensembl.org'
path = '/homology/symbol/human/BRCA2?'

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://staging.rest.ensembl.org";
    String ext = "/homology/symbol/human/BRCA2?";
    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);
  }
}

library(httr)
library(jsonlite)
library(xml2)

server <- "http://staging.rest.ensembl.org"
ext <- "/homology/symbol/human/BRCA2?"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))


curl 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?'  -O -

/homology/symbol/human/BRCA2?type=orthologues;format=condensed;content-type=application/json;target_taxon=10090;target_species=cow

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://staging.rest.ensembl.org';
my $ext = '/homology/symbol/human/BRCA2?type=orthologues;format=condensed;target_taxon=10090;target_species=cow';
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://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?type=orthologues;format=condensed;target_taxon=10090;target_species=cow"

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://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?type=orthologues;format=condensed;target_taxon=10090;target_species=cow"

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://staging.rest.ensembl.org'
path = '/homology/symbol/human/BRCA2?type=orthologues;format=condensed;target_taxon=10090;target_species=cow'

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://staging.rest.ensembl.org";
    String ext = "/homology/symbol/human/BRCA2?type=orthologues;format=condensed;target_taxon=10090;target_species=cow";
    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);
  }
}

library(httr)
library(jsonlite)
library(xml2)

server <- "http://staging.rest.ensembl.org"
ext <- "/homology/symbol/human/BRCA2?type=orthologues;format=condensed;target_taxon=10090;target_species=cow"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))


curl 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?type=orthologues;format=condensed;target_taxon=10090;target_species=cow' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?type=orthologues;format=condensed;target_taxon=10090;target_species=cow'  -O -

/homology/symbol/human/BRCA2?target_species=cow;content-type=application/json;target_taxon=10090;type=orthologues;sequence=cdna

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://staging.rest.ensembl.org';
my $ext = '/homology/symbol/human/BRCA2?target_taxon=10090;target_species=cow;type=orthologues;sequence=cdna';
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://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?target_taxon=10090;target_species=cow;type=orthologues;sequence=cdna"

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://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?target_taxon=10090;target_species=cow;type=orthologues;sequence=cdna"

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://staging.rest.ensembl.org'
path = '/homology/symbol/human/BRCA2?target_taxon=10090;target_species=cow;type=orthologues;sequence=cdna'

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://staging.rest.ensembl.org";
    String ext = "/homology/symbol/human/BRCA2?target_taxon=10090;target_species=cow;type=orthologues;sequence=cdna";
    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);
  }
}

library(httr)
library(jsonlite)
library(xml2)

server <- "http://staging.rest.ensembl.org"
ext <- "/homology/symbol/human/BRCA2?target_taxon=10090;target_species=cow;type=orthologues;sequence=cdna"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))


curl 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?target_taxon=10090;target_species=cow;type=orthologues;sequence=cdna' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?target_taxon=10090;target_species=cow;type=orthologues;sequence=cdna'  -O -

/homology/symbol/human/BRCA2?content-type=text/xml;format=condensed;type=orthologues

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://staging.rest.ensembl.org';
my $ext = '/homology/symbol/human/BRCA2?format=condensed;type=orthologues';
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://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?format=condensed;type=orthologues"

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://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?format=condensed;type=orthologues"

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://staging.rest.ensembl.org'
path = '/homology/symbol/human/BRCA2?format=condensed;type=orthologues'

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://staging.rest.ensembl.org";
    String ext = "/homology/symbol/human/BRCA2?format=condensed;type=orthologues";
    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);
  }
}

library(httr)
library(jsonlite)
library(xml2)

server <- "http://staging.rest.ensembl.org"
ext <- "/homology/symbol/human/BRCA2?format=condensed;type=orthologues"

r <- GET(paste(server, ext, sep = ""), content_type("text/xml"))

stop_for_status(r)


print(content(r))


curl 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?format=condensed;type=orthologues' -H 'Content-type:text/xml'

wget -q --header='Content-type:text/xml' 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?format=condensed;type=orthologues'  -O -

/homology/symbol/human/BRCA2?content-type=text/x-orthoxml%2Bxml

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://staging.rest.ensembl.org';
my $ext = '/homology/symbol/human/BRCA2?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-orthoxml+xml' }
});

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


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

import requests, sys

server = "http://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?"

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

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


print r.text

import requests, sys

server = "http://staging.rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?"

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

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


print(r.text)

require 'net/http'
require 'uri'

server='http://staging.rest.ensembl.org'
path = '/homology/symbol/human/BRCA2?'

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

request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-orthoxml+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://staging.rest.ensembl.org";
    String ext = "/homology/symbol/human/BRCA2?";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-orthoxml+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);
  }
}

library(httr)
library(jsonlite)
library(xml2)

server <- "http://staging.rest.ensembl.org"
ext <- "/homology/symbol/human/BRCA2?"

r <- GET(paste(server, ext, sep = ""), content_type("text/x-orthoxml+xml"))

stop_for_status(r)


print(content(r))


curl 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?' -H 'Content-type:text/x-orthoxml+xml'

wget -q --header='Content-type:text/x-orthoxml+xml' 'http://staging.rest.ensembl.org/homology/symbol/human/BRCA2?'  -O -

Resource Information

Methods	GET
Response formats	json xml orthoxml jsonp