POST variation/:species/

Uses a list of variant identifiers (e.g. rsID) to return the variation features including optional genotype, phenotype and population data

Parameters

Required

NameTypeDescriptionDefaultExample Values
species String Species name/alias for the whole batch of symbols - arabidopsis_thaliana
Arabidopsis thaliana

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
genotypes Boolean(0,1) Include individual genotypes 0 -
phenotypes Boolean(0,1) Include phenotypes 0 -
pops Boolean(0,1) Include population allele frequencies 0 -
population_genotypes Boolean(0,1) Include population genotype frequencies 0 -

Message

Content-typeFormatExample
application/json{ "ids": array }{ "ids" : ["ENSVATH12367443", "ENSVATH00550254" ] }

Example Requests

/variation/arabidopsis_thaliana


{ "ids" : ["ENSVATH12367443", "ENSVATH00550254" ] }
        
use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://rest.ensemblgenomes.org';
my $ext = '/variation/arabidopsis_thaliana';
my $response = $http->request('POST', $server.$ext, {
  headers => { 
  	'Content-type' => 'application/json',
  	'Accept' => 'application/json'
  },
  content => '{ "ids" : ["ENSVATH12367443", "ENSVATH00550254" ] }'
});

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.ensemblgenomes.org"
ext = "/variation/arabidopsis_thaliana"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
r = requests.post(server+ext, headers=headers, data='{ "ids" : ["ENSVATH12367443", "ENSVATH00550254" ] }')

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

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

import requests, sys

server = "http://rest.ensemblgenomes.org"
ext = "/variation/arabidopsis_thaliana"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
r = requests.post(server+ext, headers=headers, data='{ "ids" : ["ENSVATH12367443", "ENSVATH00550254" ] }')

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

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

require 'net/http'
require 'uri'

server='http://rest.ensemblgenomes.org'
path = '/variation/arabidopsis_thaliana'

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

request = Net::HTTP::Post.new(path, {'Content-Type' => 'application/json', 'Accept' => 'application/json'})
request.body = '{ "ids" : ["ENSVATH12367443", "ENSVATH00550254" ] }'

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;
import java.io.DataOutputStream;


public class EnsemblRest {

  public static void main(String[] args) throws Exception {
    String server = "http://rest.ensemblgenomes.org";
    String ext = "/variation/arabidopsis_thaliana";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    String postBody = "{ \"ids\" : [\"ENSVATH12367443\", \"ENSVATH00550254\" ] }";
    httpConnection.setRequestMethod("POST");
    httpConnection.setRequestProperty("Content-Type", "application/json");
    httpConnection.setRequestProperty("Accept", "application/json");
    httpConnection.setRequestProperty("Content-Length", Integer.toString(postBody.getBytes().length));
    httpConnection.setUseCaches(false);
    httpConnection.setDoInput(true);
    httpConnection.setDoOutput(true);

    DataOutputStream wr = new DataOutputStream(httpConnection.getOutputStream());
    wr.writeBytes(postBody);
    wr.flush();
    wr.close();
    

    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.ensemblgenomes.org"
ext <- "/variation/arabidopsis_thaliana"
r <- POST(paste(server, ext, sep = ""), content_type("application/json"), accept("application/json"), body = '{ "ids" : ["ENSVATH12367443", "ENSVATH00550254" ] }')

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.ensemblgenomes.org/variation/arabidopsis_thaliana' -H 'Content-type:application/json' \
-H 'Accept:application/json' -X POST -d '{ "ids" : ["ENSVATH12367443", "ENSVATH00550254" ] }'

wget -q --header='Content-type:application/json' --header='Accept:application/json' \
--post-data='{ "ids" : ["ENSVATH12367443", "ENSVATH00550254" ] }' \
'http://rest.ensemblgenomes.org/variation/arabidopsis_thaliana'  -O -

Resource Information

MethodsPOST
Response formatsjson
xml
jsonp