Return phenotype annotations that overlap a given genomic region.
Name | Type | Description | Default | Example 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 |
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 |
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 | - |
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'http://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 = "http://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 = "http://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='http://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 = "http://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 <- "http://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 'http://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' 'http://jan2020.rest.ensembl.org/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation' -O -
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'http://jan2020.rest.ensembl.org'; my $ext = '/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;only_phenotypes=1'; 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://jan2020.rest.ensembl.org" ext = "/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;only_phenotypes=1" 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://jan2020.rest.ensembl.org" ext = "/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;only_phenotypes=1" 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://jan2020.rest.ensembl.org' path = '/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;only_phenotypes=1' 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://jan2020.rest.ensembl.org"; String ext = "/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;only_phenotypes=1"; 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://jan2020.rest.ensembl.org" ext <- "/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;only_phenotypes=1" 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://jan2020.rest.ensembl.org/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;only_phenotypes=1' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'http://jan2020.rest.ensembl.org/phenotype/region/homo_sapiens/9:22125500-22136000?feature_type=Variation;only_phenotypes=1' -O -
Methods | GET |
Response formats | json xml jsonp |