Retrieves homology information (orthologs) by symbol
| Name | Type | Description | Default | Example Values |
|---|---|---|---|---|
| species | String | Species name/alias | - |
homo_sapiens human |
| symbol | String | Symbol or display name of a gene | - |
BRCA2 |
| 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 | - |
use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://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://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://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://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://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://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://rest.ensembl.org/homology/symbol/human/BRCA2?' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'http://rest.ensembl.org/homology/symbol/human/BRCA2?' -O -
use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/homology/symbol/human/BRCA2?target_taxon=10090;target_species=bos_taurus;format=condensed;type=orthologues';
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.ensembl.org"
ext = "/homology/symbol/human/BRCA2?target_taxon=10090;target_species=bos_taurus;format=condensed;type=orthologues"
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.ensembl.org"
ext = "/homology/symbol/human/BRCA2?target_taxon=10090;target_species=bos_taurus;format=condensed;type=orthologues"
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.ensembl.org'
path = '/homology/symbol/human/BRCA2?target_taxon=10090;target_species=bos_taurus;format=condensed;type=orthologues'
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.ensembl.org";
String ext = "/homology/symbol/human/BRCA2?target_taxon=10090;target_species=bos_taurus;format=condensed;type=orthologues";
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://rest.ensembl.org"
ext <- "/homology/symbol/human/BRCA2?target_taxon=10090;target_species=bos_taurus;format=condensed;type=orthologues"
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://rest.ensembl.org/homology/symbol/human/BRCA2?target_taxon=10090;target_species=bos_taurus;format=condensed;type=orthologues' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'http://rest.ensembl.org/homology/symbol/human/BRCA2?target_taxon=10090;target_species=bos_taurus;format=condensed;type=orthologues' -O -
use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/homology/symbol/human/BRCA2?sequence=cdna;type=orthologues;target_taxon=10090;target_species=bos_taurus';
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.ensembl.org"
ext = "/homology/symbol/human/BRCA2?sequence=cdna;type=orthologues;target_taxon=10090;target_species=bos_taurus"
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.ensembl.org"
ext = "/homology/symbol/human/BRCA2?sequence=cdna;type=orthologues;target_taxon=10090;target_species=bos_taurus"
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.ensembl.org'
path = '/homology/symbol/human/BRCA2?sequence=cdna;type=orthologues;target_taxon=10090;target_species=bos_taurus'
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.ensembl.org";
String ext = "/homology/symbol/human/BRCA2?sequence=cdna;type=orthologues;target_taxon=10090;target_species=bos_taurus";
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://rest.ensembl.org"
ext <- "/homology/symbol/human/BRCA2?sequence=cdna;type=orthologues;target_taxon=10090;target_species=bos_taurus"
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://rest.ensembl.org/homology/symbol/human/BRCA2?sequence=cdna;type=orthologues;target_taxon=10090;target_species=bos_taurus' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'http://rest.ensembl.org/homology/symbol/human/BRCA2?sequence=cdna;type=orthologues;target_taxon=10090;target_species=bos_taurus' -O -
use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/homology/symbol/human/BRCA2?type=orthologues;format=condensed';
my $response = $http->get($server.$ext, {
headers => { 'Content-type' => 'text/xml' }
});
die "Failed!\n" unless $response->{success};
print "$response->{content}\n";
import requests, sys
server = "http://rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?type=orthologues;format=condensed"
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://rest.ensembl.org"
ext = "/homology/symbol/human/BRCA2?type=orthologues;format=condensed"
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://rest.ensembl.org'
path = '/homology/symbol/human/BRCA2?type=orthologues;format=condensed'
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://rest.ensembl.org";
String ext = "/homology/symbol/human/BRCA2?type=orthologues;format=condensed";
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://rest.ensembl.org"
ext <- "/homology/symbol/human/BRCA2?type=orthologues;format=condensed"
r <- GET(paste(server, ext, sep = ""), content_type("text/xml"))
stop_for_status(r)
print(content(r))
curl 'http://rest.ensembl.org/homology/symbol/human/BRCA2?type=orthologues;format=condensed' -H 'Content-type:text/xml'
wget -q --header='Content-type:text/xml' 'http://rest.ensembl.org/homology/symbol/human/BRCA2?type=orthologues;format=condensed' -O -
use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://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->{content}\n";
import requests, sys
server = "http://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://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://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://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://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://rest.ensembl.org/homology/symbol/human/BRCA2?' -H 'Content-type:text/x-orthoxml+xml'
wget -q --header='Content-type:text/x-orthoxml+xml' 'http://rest.ensembl.org/homology/symbol/human/BRCA2?' -O -