Ensembl Rest API - GET taxonomy/name/:name

Search for a taxonomic id by a non-scientific name

Parameters

Required

Name	Type	Description	Default	Example Values
name	`String`	A non-scientific species name. Can include SQL wildcards	`-`	`Homo%25`

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`

Example Requests

/taxonomy/name/Homo%25?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 = '/taxonomy/name/Homo%2525?';
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 = "/taxonomy/name/Homo%25?"
 
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 = "/taxonomy/name/Homo%25?"
 
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 = '/taxonomy/name/Homo%2525?'
 
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 = "/taxonomy/name/Homo%2525?";
    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 <- "/taxonomy/name/Homo%25?"
 
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/taxonomy/name/Homo%2525?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/taxonomy/name/Homo%25?'  -O -

/taxonomy/name/human?content-type=application/json

 [
  {
    "children": [
      {
        "scientific_name": "Homo sapiens subsp. 'Denisova'",
        "tags": {
          "synonym": [
            "Homo sp. Altai"
          ],
          "equivalent_name": [
            "Homo sapiens ssp. 'Denisova'",
            "Homo sapiens ssp. Denisova"
          ],
          "common_name": [
            "Denisovan",
            "Denisovans"
          ],
          "genbank_common_name": [
            "Denisova hominin"
          ],
          "scientific_name": [
            "Homo sapiens subsp. 'Denisova'"
          ],
          "name": [
            "Homo sapiens subsp. 'Denisova'"
          ]
        },
        "name": "Homo sapiens subsp. 'Denisova'",
        "leaf": 1,
        "id": "741158"
      },
      {
        "scientific_name": "Homo sapiens neanderthalensis",
        "tags": {
          "scientific_name": [
            "Homo sapiens neanderthalensis"
          ],
          "genbank_common_name": [
            "Neandertal"
          ],
          "authority": [
            "Homo sapiens neanderthalensis King, 1864"
          ],
          "synonym": [
            "Homo neanderthalensis"
          ],
          "common_name": [
            "Neandertal man",
            "Neanderthal",
            "Neanderthal man"
          ],
          "type_material": [
            "Feldhofer 1",
            "Neanderthal 1"
          ],
          "name": [
            "Homo sapiens neanderthalensis"
          ]
        },
        "id": "63221",
        "leaf": 1,
        "name": "Homo sapiens neanderthalensis"
      }
    ],
    "parent": {
      "scientific_name": "Homo",
      "tags": {
        "scientific_name": [
          "Homo"
        ],
        "common_name": [
          "humans"
        ],
        "authority": [
          "Homo Linnaeus, 1758"
        ],
        "name": [
          "Homo"
        ]
      },
      "name": "Homo",
      "id": "9605",
      "leaf": 0
    },
    "tags": {
      "authority": [
        "Homo sapiens Linnaeus, 1758"
      ],
      "genbank_common_name": [
        "human"
      ],
      "scientific_name": [
        "Homo sapiens"
      ],
      "name": [
        "Homo sapiens"
      ]
    },
    "scientific_name": "Homo sapiens",
    "id": "9606",
    "leaf": 0,
    "name": "Homo sapiens"
  }
]

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/taxonomy/name/human?';
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 = "/taxonomy/name/human?"
 
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 = "/taxonomy/name/human?"
 
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 = '/taxonomy/name/human?'
 
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 = "/taxonomy/name/human?";
    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 <- "/taxonomy/name/human?"
 
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/taxonomy/name/human?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/taxonomy/name/human?'  -O -

Resource Information

Methods	GET
Response formats	json xml yaml jsonp