Service logo

GET /phenotype/region/:species/:region

Return phenotype annotations that overlap a given genomic region.

Parameters

Required

NameTypeDescriptionDefaultExample Values
region String Query region. A maximum of 5Mb is allowed to be requested at any one time - 9:22125500-22136000:1
9:22125500-22136000:-1
9:22125500-22136000
species String Species name/alias - homo_sapiens
human

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
feature_type String Restrict to phenotype annotations from a specific feature type. - Variation
StructuralVariation
Gene
QTL
include_pubmed_id Boolean(0,1) Include the pubmed_ids 0 -
include_review_status Boolean(0,1) Include the review_status information 0 -
include_submitter Boolean(0,1) Include the submitter names 0 -
non_specified Boolean(0,1) Return non_specified phenotypes (records that did not provide a specific phenotype e.g. 'not provided') 1 -
only_phenotypes Boolean(0,1) Only returns associated phenotype description and mapped ontology accessions for a lighter output. 0 -
trait Boolean(0,1) Return phenotype/disease associations 1 -
tumour Boolean(0,1) Return mutations observed in tumour samples and the tumour type 1 -

Example Requests

/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation';
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 = "https://jan2020.rest.ensembl.org"
ext = "/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation"

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 = "https://jan2020.rest.ensembl.org"
ext = "/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation"

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='https://jan2020.rest.ensembl.org'
path = '/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation'

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 = "https://jan2020.rest.ensembl.org";
    String ext = "/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation";
    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 <- "https://jan2020.rest.ensembl.org"
ext <- "/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation"

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 'https://jan2020.rest.ensembl.org/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation' -H 'Content-type:application/json'


wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation'  -O -

/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;content-type=application/json;only_phenotypes=1


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/phenotype/region/homo_sapiens/9:22125500-22136000?only_phenotypes=1;feature_type=Variation';
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 = "https://jan2020.rest.ensembl.org"
ext = "/phenotype/region/homo_sapiens/9:22125500-22136000?only_phenotypes=1;feature_type=Variation"

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 = "https://jan2020.rest.ensembl.org"
ext = "/phenotype/region/homo_sapiens/9:22125500-22136000?only_phenotypes=1;feature_type=Variation"

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='https://jan2020.rest.ensembl.org'
path = '/phenotype/region/homo_sapiens/9:22125500-22136000?only_phenotypes=1;feature_type=Variation'

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 = "https://jan2020.rest.ensembl.org";
    String ext = "/phenotype/region/homo_sapiens/9:22125500-22136000?only_phenotypes=1;feature_type=Variation";
    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 <- "https://jan2020.rest.ensembl.org"
ext <- "/phenotype/region/homo_sapiens/9:22125500-22136000?only_phenotypes=1;feature_type=Variation"

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 'https://jan2020.rest.ensembl.org/phenotype/region/homo_sapiens/9:22125500-22136000?only_phenotypes=1;feature_type=Variation' -H 'Content-type:application/json'


wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/phenotype/region/homo_sapiens/9:22125500-22136000?only_phenotypes=1;feature_type=Variation'  -O -

Resource Information

MethodsGET
Response formatsjson
xml
jsonp