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

Retrieves the cafe tree of 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
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`
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		The format of a NH (New Hampshire) request. Available only with the default setting to allow us to return the cafe tree with Taxa names appended with number of members and the p_value. example : homo_sapiens_3_0.123 where 3 is the number of members and 0.123 is the p value	`Preset with default cafe parameters`	`-`
object_type	`String`	Filter by feature type	`-`	`gene` `transcript`

Example Requests

/cafe/genetree/member/symbol/homo_sapiens/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 = '/cafe/genetree/member/symbol/homo_sapiens/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 = "/cafe/genetree/member/symbol/homo_sapiens/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 = "/cafe/genetree/member/symbol/homo_sapiens/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 = '/cafe/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' => '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 = "/cafe/genetree/member/symbol/homo_sapiens/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 <- "/cafe/genetree/member/symbol/homo_sapiens/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/cafe/genetree/member/symbol/homo_sapiens/BRCA2?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://staging.rest.ensembl.org/cafe/genetree/member/symbol/homo_sapiens/BRCA2?'  -O -

/cafe/genetree/member/symbol/homo_sapiens/BRCA2?nh_format=simple;content-type=text/x-nh

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://staging.rest.ensembl.org';
my $ext = '/cafe/genetree/member/symbol/homo_sapiens/BRCA2?nh_format=simple';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-nh' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{content}\n";

import requests, sys
 
server = "http://staging.rest.ensembl.org"
ext = "/cafe/genetree/member/symbol/homo_sapiens/BRCA2?nh_format=simple"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-nh"})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "http://staging.rest.ensembl.org"
ext = "/cafe/genetree/member/symbol/homo_sapiens/BRCA2?nh_format=simple"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-nh"})
 
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 = '/cafe/genetree/member/symbol/homo_sapiens/BRCA2?nh_format=simple'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-nh'})
 
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 = "/cafe/genetree/member/symbol/homo_sapiens/BRCA2?nh_format=simple";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-nh");
    
 
    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 <- "/cafe/genetree/member/symbol/homo_sapiens/BRCA2?nh_format=simple"
 
r <- GET(paste(server, ext, sep = ""), content_type("text/x-nh"))
 
stop_for_status(r)
 
 
print(content(r))

 
curl 'http://staging.rest.ensembl.org/cafe/genetree/member/symbol/homo_sapiens/BRCA2?nh_format=simple' -H 'Content-type:text/x-nh'

wget -q --header='Content-type:text/x-nh' 'http://staging.rest.ensembl.org/cafe/genetree/member/symbol/homo_sapiens/BRCA2?nh_format=simple'  -O -

Resource Information

Methods	GET
Response formats	nh json jsonp