Ensembl Rest API - GET genetree/member/symbol/:species/:symbol

Retrieves the gene tree that contains the gene identified by a 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)	`0`	`-`
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	`0`	`-`
clusterset_id	`String`	Name of the gene-tree resource being queried. Common values are "default" for the standard multi-clade trees (which exclude all non-reference strains) and "murinae" for the trees spanning all mouse strains. By default, the most inclusive analysis will be selected	`-`	`default` `murinae`
compara	`String`	Name of the compara database to use. Multiple comparas exist on a server for separate species divisions	`vertebrates`	`vertebrates`
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` `otherfeatures`
external_db	`String`	Filter by external database	`-`	`HGNC`
nh_format	`Enum(full, display_label_composite, simple, species, species_short_name, ncbi_taxon, ncbi_name, njtree, phylip)`	The format of a NH (New Hampshire) request.	`simple`	`-`
object_type	`String`	Filter by feature type	`-`	`gene` `transcript`
prune_species	`String`	Prune the tree by species. Supports all species aliases. Will return a tree with only the species given	`-`	`human` `cow`
prune_taxon	`Integer`	Prune the tree by taxon. Will return a tree with only the taxons given	`-`	`9606` `10090`
sequence	`Enum(none, cdna, protein)`	The type of sequence to bring back. Setting it to none results in no sequence being returned	`protein`	`-`

Example Requests

/genetree/member/symbol/homo_sapiens/BRCA2?prune_species=cow;content-type=text/x-orthoxml%2Bxml;prune_taxon=9526

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/genetree/member/symbol/homo_sapiens/BRCA2?prune_species=cow;prune_taxon=9526';
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 = "https://jan2020.rest.ensembl.org"
ext = "/genetree/member/symbol/homo_sapiens/BRCA2?prune_species=cow;prune_taxon=9526"
 
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 = "https://jan2020.rest.ensembl.org"
ext = "/genetree/member/symbol/homo_sapiens/BRCA2?prune_species=cow;prune_taxon=9526"
 
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='https://jan2020.rest.ensembl.org'
path = '/genetree/member/symbol/homo_sapiens/BRCA2?prune_species=cow;prune_taxon=9526'
 
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 = "https://jan2020.rest.ensembl.org";
    String ext = "/genetree/member/symbol/homo_sapiens/BRCA2?prune_species=cow;prune_taxon=9526";
    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 <- "https://jan2020.rest.ensembl.org"
ext <- "/genetree/member/symbol/homo_sapiens/BRCA2?prune_species=cow;prune_taxon=9526"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/x-orthoxml+xml"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'https://jan2020.rest.ensembl.org/genetree/member/symbol/homo_sapiens/BRCA2?prune_species=cow;prune_taxon=9526' -H 'Content-type:text/x-orthoxml+xml'

wget -q --header='Content-type:text/x-orthoxml+xml' 'https://jan2020.rest.ensembl.org/genetree/member/symbol/homo_sapiens/BRCA2?prune_species=cow;prune_taxon=9526'  -O -

/genetree/member/symbol/homo_sapiens/BRCA2?content-type=text/x-phyloxml%2Bxml

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/genetree/member/symbol/homo_sapiens/BRCA2?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-phyloxml+xml' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{status} $response->{reason}\n";

import requests, sys
 
server = "https://jan2020.rest.ensembl.org"
ext = "/genetree/member/symbol/homo_sapiens/BRCA2?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "https://jan2020.rest.ensembl.org"
ext = "/genetree/member/symbol/homo_sapiens/BRCA2?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='https://jan2020.rest.ensembl.org'
path = '/genetree/member/symbol/homo_sapiens/BRCA2?'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-phyloxml+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://jan2020.rest.ensembl.org";
    String ext = "/genetree/member/symbol/homo_sapiens/BRCA2?";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-phyloxml+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 <- "https://jan2020.rest.ensembl.org"
ext <- "/genetree/member/symbol/homo_sapiens/BRCA2?"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/x-phyloxml+xml"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'https://jan2020.rest.ensembl.org/genetree/member/symbol/homo_sapiens/BRCA2?' -H 'Content-type:text/x-phyloxml+xml'

wget -q --header='Content-type:text/x-phyloxml+xml' 'https://jan2020.rest.ensembl.org/genetree/member/symbol/homo_sapiens/BRCA2?'  -O -

Resource Information

Methods	GET
Response formats	phyloxml orthoxml nh json jsonp