GET lookup/symbol/:species/:symbol

Find the species and database for a symbol in a linked external database

Parameters

Required

Name	Type	Description	Default	Example Values
species	`String`	Species name/alias	`-`	`brugia_malayi_prjna10729`
symbol	`String`	A name or symbol from an annotation source has been linked to a genetic feature	`-`	`Bm994`

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`
expand	`Boolean(0,1)`	Expands the search to include any connected features. e.g. If the object is a gene, its transcripts, translations and exons will be returned as well.	`NULL`	`-`
format	`Enum(full,condensed)`	Specify the layout of the response	`full`	`-`

Example Requests

/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?content-type=text/xml;expand=1

<opt>
  <data id="WBGene00221255" assembly_name="Bmal-4.0" biotype="protein_coding" canonical_transcript="Bm994.1." db_type="core" description="WH2 motif family protein  [Source:UniProtKB/TrEMBL;Acc:A0A4E9FZ75]" display_name="Bm994" end="484217" logic_name="wormbase" object_type="Gene" seq_region_name="Bm_007" source="WormBase" species="brugia_malayi_prjna10729" start="479867" strand="-1" version="1">
    <Transcript id="Bm994.1" Parent="WBGene00221255" assembly_name="Bmal-4.0" biotype="protein_coding" db_type="core" display_name="Bm994.1" end="484217" is_canonical="1" length="702" logic_name="wormbase" object_type="Transcript" seq_region_name="Bm_007" source="WormBase" species="brugia_malayi_prjna10729" start="479867" strand="-1">
      <Exon id="Bm994.1.e1" assembly_name="Bmal-4.0" db_type="core" end="484217" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="484063" strand="-1"/>
      <Exon id="Bm994.1.e2" assembly_name="Bmal-4.0" db_type="core" end="482912" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="482778" strand="-1"/>
      <Exon id="Bm994.1.e3" assembly_name="Bmal-4.0" db_type="core" end="480955" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="480754" strand="-1"/>
      <Exon id="Bm994.1.e4" assembly_name="Bmal-4.0" db_type="core" end="480301" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="480209" strand="-1"/>
      <Exon id="Bm994.1.e5" assembly_name="Bmal-4.0" db_type="core" end="479983" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="479867" strand="-1"/>
      <Translation id="Bm994.1" Parent="Bm994.1" db_type="core" end="480897" length="117" object_type="Translation" species="brugia_malayi_prjna10729" start="479867"/>
    </Transcript>
    <Transcript id="Bm994.2" Parent="WBGene00221255" assembly_name="Bmal-4.0" biotype="protein_coding" db_type="core" display_name="Bm994.2" end="482947" is_canonical="0" length="582" logic_name="wormbase" object_type="Transcript" seq_region_name="Bm_007" source="WormBase" species="brugia_malayi_prjna10729" start="479867" strand="-1">
      <Exon id="Bm994.2.e1" assembly_name="Bmal-4.0" db_type="core" end="482947" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="482778" strand="-1"/>
      <Exon id="Bm994.1.e3" assembly_name="Bmal-4.0" db_type="core" end="480955" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="480754" strand="-1"/>
      <Exon id="Bm994.1.e4" assembly_name="Bmal-4.0" db_type="core" end="480301" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="480209" strand="-1"/>
      <Exon id="Bm994.1.e5" assembly_name="Bmal-4.0" db_type="core" end="479983" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="479867" strand="-1"/>
      <Translation id="Bm994.2" Parent="Bm994.2" db_type="core" end="480897" length="117" object_type="Translation" species="brugia_malayi_prjna10729" start="479867"/>
    </Transcript>
    <Transcript id="Bm994.3" Parent="WBGene00221255" assembly_name="Bmal-4.0" biotype="protein_coding" db_type="core" display_name="Bm994.3" end="482281" is_canonical="0" length="524" logic_name="wormbase" object_type="Transcript" seq_region_name="Bm_007" source="WormBase" species="brugia_malayi_prjna10729" start="479867" strand="-1">
      <Exon id="Bm994.3.e1" assembly_name="Bmal-4.0" db_type="core" end="482281" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="482211" strand="-1"/>
      <Exon id="Bm994.3.e2" assembly_name="Bmal-4.0" db_type="core" end="480996" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="480754" strand="-1"/>
      <Exon id="Bm994.1.e4" assembly_name="Bmal-4.0" db_type="core" end="480301" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="480209" strand="-1"/>
      <Exon id="Bm994.1.e5" assembly_name="Bmal-4.0" db_type="core" end="479983" object_type="Exon" seq_region_name="Bm_007" species="brugia_malayi_prjna10729" start="479867" strand="-1"/>
      <Translation id="Bm994.3" Parent="Bm994.3" db_type="core" end="480897" length="117" object_type="Translation" species="brugia_malayi_prjna10729" start="479867"/>
    </Transcript>
  </data>
</opt>

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?expand=1';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/xml' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{status} $response->{reason}\n";

import requests, sys
 
server = "https://parasite.wormbase.org"
ext = "/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?expand=1"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/xml", "Accept" : ""})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "https://parasite.wormbase.org"
ext = "/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?expand=1"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/xml", "Accept" : ""})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='https://parasite.wormbase.org'
path = '/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?expand=1'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/xml'})
 
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 = "https://parasite.wormbase.org";
    String ext = "/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?expand=1";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/xml");
    
 
    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);
  }
}

 
curl 'https://parasite.wormbase.org/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?expand=1' -H 'Content-type:text/xml'

wget -q --header='Content-type:text/xml' 'https://parasite.wormbase.org/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?expand=1'  -O -

/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?content-type=application/json

 {
  "id": "WBGene00221255",
  "species": "brugia_malayi_prjna10729",
  "biotype": "protein_coding",
  "strand": -1,
  "end": 484217,
  "db_type": "core",
  "assembly_name": "Bmal-4.0",
  "object_type": "Gene",
  "seq_region_name": "Bm_007",
  "start": 479867,
  "source": "WormBase",
  "display_name": "Bm994",
  "canonical_transcript": "Bm994.1.",
  "logic_name": "wormbase",
  "description": "WH2 motif family protein  [Source:UniProtKB/TrEMBL;Acc:A0A4E9FZ75]",
  "version": 1
}

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?';
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://parasite.wormbase.org"
ext = "/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
decoded = r.json()
print repr(decoded)

import requests, sys
 
server = "https://parasite.wormbase.org"
ext = "/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
decoded = r.json()
print(repr(decoded))

require 'net/http'
require 'uri'
 
server='https://parasite.wormbase.org'
path = '/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?'
 
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://parasite.wormbase.org";
    String ext = "/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?";
    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);
  }
}

 
curl 'https://parasite.wormbase.org/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?'  -O -

/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?format=condensed;db_type=core;content-type=text/xml

<opt>
  <data id="WBGene00221255" db_type="core" object_type="Gene" species="brugia_malayi_prjna10729" version="1"/>
</opt>

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?db_type=core;format=condensed';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/xml' }
});
 
die "Failed!\n" unless $response->{success};
 
 
print "$response->{status} $response->{reason}\n";

import requests, sys
 
server = "https://parasite.wormbase.org"
ext = "/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?db_type=core;format=condensed"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/xml", "Accept" : ""})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "https://parasite.wormbase.org"
ext = "/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?db_type=core;format=condensed"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/xml", "Accept" : ""})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='https://parasite.wormbase.org'
path = '/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?db_type=core;format=condensed'
 
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
 
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/xml'})
 
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 = "https://parasite.wormbase.org";
    String ext = "/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?db_type=core;format=condensed";
    URL url = new URL(server + ext);
 
    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/xml");
    
 
    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);
  }
}

 
curl 'https://parasite.wormbase.org/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?db_type=core;format=condensed' -H 'Content-type:text/xml'

wget -q --header='Content-type:text/xml' 'https://parasite.wormbase.org/rest-19/lookup/symbol/brugia_malayi_prjna10729/Bm994?db_type=core;format=condensed'  -O -

Resource Information

Methods	GET
Response formats	json xml jsonp