Perform lookups of identifiers and retrieve their external references in other databases
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
id | String | A Stable ID | - |
ENSG00000157764 |
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
all_levels | Boolean | Set to find all genetic features linked to the stable ID, and fetch all external references for them. Specifying this on a gene will also return values from its transcripts and translations | 0 |
1 |
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 |
db_type | String | Restrict the search to a database other than the default. Useful if you need to use a DB other than core | core |
core |
external_db | String | Filter by external database | - |
EntrezGene |
object_type | String | Filter by feature type | - |
gene transcript |
species | String | Species name/alias | - |
brugia_malayi_prjna10729 |
[
{
"info_type": "DEPENDENT",
"primary_id": "6095652",
"db_display_name": "WikiGene",
"version": "0",
"synonyms": [],
"description": "WH2 motif family protein",
"dbname": "WikiGene",
"display_id": "Bm994",
"info_text": ""
},
{
"db_display_name": "WormBase Gene",
"info_type": "DIRECT",
"primary_id": "WBGene00221255",
"display_id": "WBGene00221255",
"dbname": "wormbase_gene",
"info_text": "",
"version": "0",
"description": null,
"synonyms": []
},
{
"db_display_name": "WormBase Gene Sequence-name",
"primary_id": "WBGene00221255",
"info_type": "DIRECT",
"info_text": "",
"display_id": "Bm994",
"dbname": "wormbase_gseqname",
"description": null,
"synonyms": [],
"version": "0"
},
{
"synonyms": [
"Bm1_03535"
],
"description": "WH2 motif family protein",
"version": "0",
"info_text": "",
"display_id": "Bm994",
"dbname": "EntrezGene",
"db_display_name": "NCBI gene (formerly Entrezgene)",
"primary_id": "6095652",
"info_type": "DEPENDENT"
}
]
- use strict;
- use warnings;
- use HTTP::Tiny;
- my $http = HTTP::Tiny->new();
- my $server = 'https://parasite.wormbase.org';
- my $ext = '/rest-19/xrefs/id/WBGene00221255?';
- 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/xrefs/id/WBGene00221255?"
- 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/xrefs/id/WBGene00221255?"
- 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/xrefs/id/WBGene00221255?'
- 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/xrefs/id/WBGene00221255?";
- 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/xrefs/id/WBGene00221255?' -H 'Content-type:application/json'
- wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/xrefs/id/WBGene00221255?' -O -
[
{
"db_display_name": "GO",
"info_type": "DEPENDENT",
"primary_id": "GO:0005886",
"info_text": "",
"display_id": "GO:0005886",
"linkage_types": [
"IEA"
],
"dbname": "GO",
"description": "plasma membrane",
"synonyms": [],
"version": "0"
},
{
"version": "0",
"synonyms": [],
"description": "plasma membrane",
"linkage_types": [
"IEA"
],
"display_id": "GO:0005886",
"dbname": "GO",
"info_text": "InterPro",
"db_display_name": "GO",
"info_type": "DIRECT",
"primary_id": "GO:0005886"
},
{
"info_text": "EnsemblMetazoa",
"dbname": "GO",
"linkage_types": [
"IEA"
],
"display_id": "GO:0009410",
"description": "response to xenobiotic stimulus",
"synonyms": [],
"version": "0",
"primary_id": "GO:0009410",
"info_type": "DIRECT",
"db_display_name": "GO"
},
{
"db_display_name": "GO",
"info_type": "DIRECT",
"primary_id": "GO:0016020",
"description": "membrane",
"synonyms": [],
"version": "0",
"info_text": "UniProt",
"linkage_types": [
"IEA"
],
"display_id": "GO:0016020",
"dbname": "GO"
},
{
"version": "0",
"synonyms": [],
"description": "membrane",
"display_id": "GO:0016020",
"linkage_types": [
"IEA"
],
"dbname": "GO",
"info_text": "InterPro",
"db_display_name": "GO",
"primary_id": "GO:0016020",
"info_type": "DIRECT"
},
{
"db_display_name": "GO",
"info_type": "DEPENDENT",
"primary_id": "GO:0016020",
"display_id": "GO:0016020",
"linkage_types": [
"IEA"
],
"dbname": "GO",
"info_text": "",
"version": "0",
"synonyms": [],
"description": "membrane"
},
{
"primary_id": "GO:0030424",
"info_type": "DIRECT",
"db_display_name": "GO",
"synonyms": [],
"description": "axon",
"version": "0",
"info_text": "EnsemblMetazoa",
"dbname": "GO",
"display_id": "GO:0030424",
"linkage_types": [
"IEA"
]
}
]
- use strict;
- use warnings;
- use HTTP::Tiny;
- my $http = HTTP::Tiny->new();
- my $server = 'https://parasite.wormbase.org';
- my $ext = '/rest-19/xrefs/id/Bm4789.1?external_db=GO;object_type=transcript;all_levels=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 = "https://parasite.wormbase.org"
- ext = "/rest-19/xrefs/id/Bm4789.1?external_db=GO;object_type=transcript;all_levels=1"
- 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/xrefs/id/Bm4789.1?external_db=GO;object_type=transcript;all_levels=1"
- 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/xrefs/id/Bm4789.1?external_db=GO;object_type=transcript;all_levels=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 = "https://parasite.wormbase.org";
- String ext = "/rest-19/xrefs/id/Bm4789.1?external_db=GO;object_type=transcript;all_levels=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);
- }
- }
- curl 'https://parasite.wormbase.org/rest-19/xrefs/id/Bm4789.1?external_db=GO;object_type=transcript;all_levels=1' -H 'Content-type:application/json'
- wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/xrefs/id/Bm4789.1?external_db=GO;object_type=transcript;all_levels=1' -O -
Methods | GET |
Response formats | json xml jsonp |