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GET homology/symbol/:species/:symbol

Retrieves homology information (orthologues) by symbol

Parameters

Required

NameTypeDescriptionDefaultExample Values
species String Species name/alias - brugia_malayi_prjna10729
symbol String Symbol or display name of a gene - Bm994

Optional

NameTypeDescriptionDefaultExample Values
aligned Boolean Return the aligned string if true. Otherwise, return the original sequence (no insertions) 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
external_db String Filter by external database - EntrezGene
format Enum(full,condensed) Layout of the response full -
sequence Enum(none, cdna, protein) The type of sequence to bring back. Setting it to none results in no sequence being returned protein -
target_species String Filter by species. Supports all species aliases - brugia_malayi_prjna10729
target_taxon Integer Filter by taxon - 6279
6279
type Enum(orthologues, paralogues, projections, all) The type of homology to return from this call. Projections are orthology calls defined between alternative assemblies and the genes shared between them. Useful if you need only one type of homology back from the service all -

Example Requests

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


 {
  "data": [
    {
      "homologies": [
        {
          "taxonomy_level": "Onchocercidae",
          "target": {
            "perc_id": 38.5093,
            "align_seq": "MSEKMPLDRAERIEQHKHELISTDPQQNNLISTNYSA--SSSSSPPSTQQQRQNDKLLTEINKGIHLRHVIPNAHKQCISMLYDKKCEK-SSTTEKDSVKEDETKLEMEKSTDIGNVLLNAMRKRRLLVEFESSSISNEDGNERRLEQWSDSDDTDSNAGKFRN",
            "perc_pos": 49.6894,
            "taxon_id": 42156,
            "species": "litomosoides_sigmodontis_prjeb3075",
            "protein_id": "nLs.2.1.2.t06925-RA",
            "id": "nLs.2.1.2.g06925",
            "cigar_line": "37M2D50MD74M"
          },
          "dn_ds": null,
          "source": {
            "taxon_id": 6279,
            "species": "brugia_malayi_prjna10729",
            "protein_id": "Bm994.1",
            "id": "WBGene00221255",
            "cigar_line": "3D7M3D16M2D12M2D3MD42M4D37M32D",
            "align_seq": "---MQKQVKG---QQHVNELLPSVIQQED--PTNDSLSPLSSA--RCT-DQYQSDKLLAEIRNGVQLRHVIPNDHKQCAKMLYDKACEKKE----ENNINEKETKLETEKAINIGNILLNAMQKRRLLMHFG--------------------------------",
            "perc_id": 52.9915,
            "perc_pos": 68.3761
          },
          "method_link_type": "ENSEMBL_ORTHOLOGUES",
          "type": "ortholog_one2one"
        },
        {
          "method_link_type": "ENSEMBL_ORTHOLOGUES",
          "source": {
            "align_seq": "-------------MQKQVKG---QQHVNELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAEIRNGVQLRHVIPNDHKQCAKMLYDKACEKKE----ENNINEKETKLETEKA---INIGNILLNAMQKRRLLMHFG--------------------------",
            "perc_id": 53.8462,
            "perc_pos": 69.2308,
            "id": "WBGene00221255",
            "taxon_id": 6279,
            "species": "brugia_malayi_prjna10729",
            "protein_id": "Bm994.1",
            "cigar_line": "13D7M3D73M4D16M3D21M26D"
          },
          "type": "ortholog_one2one",
          "target": {
            "id": "nDi.2.2.2.g04666",
            "species": "dirofilaria_immitis_prjeb1797",
            "protein_id": "nDi.2.2.2.t04666",
            "taxon_id": 6287,
            "cigar_line": "94MD71M",
            "align_seq": "MQKVNKAAISDKQIKALLKRISQKEQVREFHAINIQGENSTNDQSLSSSSNHCNDQYQYDKLLTEIRNGIELRHVIPNEHKRCAKMLYDKTIEE-LFISGEDKINDKQIKLCEQKSTDDIDIENILINAMCKRRFAMRFESSSSDENVSGRELEHWYDADDGNDDE",
            "perc_id": 38.1818,
            "perc_pos": 49.0909
          },
          "dn_ds": null,
          "taxonomy_level": "Onchocercidae"
        },
        {
          "taxonomy_level": "Brugia",
          "dn_ds": null,
          "target": {
            "perc_pos": 86.4407,
            "align_seq": "MQKQVKRQQHVDELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAVS----------------VNVLTFEKY------------------------------------------",
            "perc_id": 79.661,
            "cigar_line": "50M16D9M42D",
            "id": "BPAG_0000674301",
            "protein_id": "BPAG_0000674301-mRNA-1",
            "species": "brugia_pahangi_prjeb497",
            "taxon_id": 6280
          },
          "type": "ortholog_one2many",
          "source": {
            "species": "brugia_malayi_prjna10729",
            "protein_id": "Bm994.1",
            "taxon_id": 6279,
            "id": "WBGene00221255",
            "cigar_line": "117M",
            "align_seq": "MQKQVKGQQHVNELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAEIRNGVQLRHVIPNDHKQCAKMLYDKACEKKEENNINEKETKLETEKAINIGNILLNAMQKRRLLMHFG",
            "perc_id": 40.1709,
            "perc_pos": 43.5897
          },
          "method_link_type": "ENSEMBL_ORTHOLOGUES"
        },
        {
          "type": "ortholog_one2many",
          "source": {
            "perc_id": 39.3162,
            "align_seq": "MQKQVKGQQHVNELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAEIRNGVQLRHVIPNDHKQCAKMLYDKACEKKEENNINEKETKLETEKAINIGNILLNAMQKRRLLMHFG",
            "perc_pos": 43.5897,
            "id": "WBGene00221255",
            "taxon_id": 6279,
            "species": "brugia_malayi_prjna10729",
            "protein_id": "Bm994.1",
            "cigar_line": "117M"
          },
          "method_link_type": "ENSEMBL_ORTHOLOGUES",
          "taxonomy_level": "Brugia",
          "dn_ds": null,
          "target": {
            "cigar_line": "50M16D9M42D",
            "id": "BPAG_0000621901",
            "protein_id": "BPAG_0000621901-mRNA-1",
            "species": "brugia_pahangi_prjeb497",
            "taxon_id": 6280,
            "perc_pos": 86.4407,
            "align_seq": "MQKQVKRQQHIDELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAVS----------------VNVLTFEKY------------------------------------------",
            "perc_id": 77.9661
          }
        },
        {
          "taxonomy_level": "Onchocercidae",
          "target": {
            "id": "Wban_10481",
            "protein_id": "mrna-Wban_10481",
            "species": "wuchereria_bancrofti_prjna275548",
            "taxon_id": 6293,
            "cigar_line": "78MD38M",
            "perc_id": 86.2069,
            "align_seq": "MQSQVKRQQHVDELLPPVLQQKDPTNDSLSPSSFARCTDQYQSDKLLAQIRSGVQLRHVIPNDHKQCTKMLYDKACEK-EENNINEKEVKLETEKTIDIGNILLNAMHKRRLLMRFG",
            "perc_pos": 91.3793
          },
          "dn_ds": null,
          "source": {
            "taxon_id": 6279,
            "species": "brugia_malayi_prjna10729",
            "protein_id": "Bm994.1",
            "id": "WBGene00221255",
            "cigar_line": "117M",
            "perc_id": 85.4701,
            "align_seq": "MQKQVKGQQHVNELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAEIRNGVQLRHVIPNDHKQCAKMLYDKACEKKEENNINEKETKLETEKAINIGNILLNAMQKRRLLMHFG",
            "perc_pos": 90.5983
          },
          "method_link_type": "ENSEMBL_ORTHOLOGUES",
          "type": "ortholog_one2one"
        },
        {
          "taxonomy_level": "Onchocercidae",
          "dn_ds": null,
          "target": {
            "perc_pos": 61.2613,
            "align_seq": "------------------------MNDLSSSSHTDRYVDQNQNNKLLTEIRSRIHLRHVIPNEHKQCTKMLYDKTFDK-AIISNEDNVSKKETKLDEQKRIHAENLLINAMRKRRFVMRFESSSSDENETEQELEH",
            "perc_id": 45.045,
            "cigar_line": "24D54MD57M",
            "species": "onchocerca_volvulus_prjeb513",
            "protein_id": "OVOC2199.1",
            "taxon_id": 6282,
            "id": "WBGene00239008"
          },
          "type": "ortholog_one2one",
          "method_link_type": "ENSEMBL_ORTHOLOGUES",
          "source": {
            "id": "WBGene00221255",
            "species": "brugia_malayi_prjna10729",
            "protein_id": "Bm994.1",
            "taxon_id": 6279,
            "cigar_line": "80M4D37M15D",
            "perc_id": 42.735,
            "align_seq": "MQKQVKGQQHVNELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAEIRNGVQLRHVIPNDHKQCAKMLYDKACEKKE----ENNINEKETKLETEKAINIGNILLNAMQKRRLLMHFG---------------",
            "perc_pos": 58.1197
          }
        },
        {
          "type": "ortholog_one2one",
          "source": {
            "cigar_line": "13D35M2D3MD42M4D37M51D",
            "id": "WBGene00221255",
            "taxon_id": 6279,
            "species": "brugia_malayi_prjna10729",
            "protein_id": "Bm994.1",
            "perc_pos": 68.3761,
            "perc_id": 58.9744,
            "align_seq": "-------------MQKQVKGQQHVNELLPSVIQQEDPTNDSLSPLSSA--RCT-DQYQSDKLLAEIRNGVQLRHVIPNDHKQCAKMLYDKACEKKE----ENNINEKETKLETEKAINIGNILLNAMQKRRLLMHFG---------------------------------------------------"
          },
          "method_link_type": "ENSEMBL_ORTHOLOGUES",
          "dn_ds": null,
          "target": {
            "perc_pos": 44.9438,
            "align_seq": "MQKTNKPTVSGIHGQTLLKRIEHINELFPTNLQQNSSTNNSS--SSSLSS---TKQCQNDNLLVEIRSGVQLRHVIPNAHKQCIKMLYDNTCEK-LFITE----NENERKLETEKQTDIGNIILNAMRKRRLLMGFGQLAFIVFRFNDSMIKNDHCPLKSSSTSNEDGNERKLEQWSDTDDKGYGDDQ",
            "perc_id": 38.764,
            "cigar_line": "42M2D6M3D41MD5M4D84M",
            "species": "cercopithifilaria_johnstoni_prjeb47283",
            "protein_id": "rna-CJOHNSTONI_LOCUS9362",
            "taxon_id": 2874296,
            "id": "CJOHNSTONI_LOCUS9362"
          },
          "taxonomy_level": "Onchocercidae"
        }
      ],
      "id": "WBGene00221255"
    }
  ]
}
  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://parasite.wormbase.org';
  9. my $ext = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'application/json' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. use JSON;
  18. use Data::Dumper;
  19. if(length $response->{content}) {
  20.   my $hash = decode_json($response->{content});
  21.   local $Data::Dumper::Terse = 1;
  22.   local $Data::Dumper::Indent = 1;
  23.   print Dumper $hash;
  24.   print "\n";
  25. }
  26.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12. decoded = r.json()
  13. print repr(decoded)
  14.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12. decoded = r.json()
  13. print(repr(decoded))
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://parasite.wormbase.org'
  5. path = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15.   puts "Invalid response: #{response.code}"
  16.   puts response.body
  17.   exit
  18. end
  19.  
  20.  
  21. require 'rubygems'
  22. require 'json'
  23. require 'yaml'
  24.  
  25. result = JSON.parse(response.body)
  26. puts YAML::dump(result)
  27.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13.   public static void main(String[] args) throws Exception {
  14.     String server = "https://parasite.wormbase.org";
  15.     String ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?";
  16.     URL url = new URL(server + ext);
  17.  
  18.     URLConnection connection = url.openConnection();
  19.     HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20.     
  21.     httpConnection.setRequestProperty("Content-Type", "application/json");
  22.     
  23.  
  24.     InputStream response = connection.getInputStream();
  25.     int responseCode = httpConnection.getResponseCode();
  26.  
  27.     if(responseCode != 200) {
  28.       throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  29.     }
  30.  
  31.     String output;
  32.     Reader reader = null;
  33.     try {
  34.       reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  35.       StringBuilder builder = new StringBuilder();
  36.       char[] buffer = new char[8192];
  37.       int read;
  38.       while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  39.         builder.append(buffer, 0, read);
  40.       }
  41.       output = builder.toString();
  42.     } 
  43.     finally {
  44.         if (reader != null) try {
  45.           reader.close(); 
  46.         } catch (IOException logOrIgnore) {
  47.           logOrIgnore.printStackTrace();
  48.         }
  49.     }
  50.  
  51.     System.out.println(output);
  52.   }
  53. }
  54.  
  1.  
  2. curl 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?' -H 'Content-type:application/json'
  3.  
  1. wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?'  -O -
  2.  

/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?target_taxon=6279;format=condensed;content-type=application/json;target_species=brugia_pahangi_prjeb497;type=orthologues


 {
  "data": [
    {
      "id": "WBGene00221255",
      "homologies": [
        {
          "protein_id": "BPAG_0000674301-mRNA-1",
          "species": "brugia_pahangi_prjeb497",
          "id": "BPAG_0000674301",
          "method_link_type": "ENSEMBL_ORTHOLOGUES",
          "type": "ortholog_one2many",
          "taxonomy_level": "Brugia"
        },
        {
          "method_link_type": "ENSEMBL_ORTHOLOGUES",
          "type": "ortholog_one2many",
          "species": "brugia_pahangi_prjeb497",
          "protein_id": "BPAG_0000621901-mRNA-1",
          "id": "BPAG_0000621901",
          "taxonomy_level": "Brugia"
        }
      ]
    }
  ]
}
  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://parasite.wormbase.org';
  9. my $ext = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?target_taxon=6279;format=condensed;target_species=brugia_pahangi_prjeb497;type=orthologues';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'application/json' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. use JSON;
  18. use Data::Dumper;
  19. if(length $response->{content}) {
  20.   my $hash = decode_json($response->{content});
  21.   local $Data::Dumper::Terse = 1;
  22.   local $Data::Dumper::Indent = 1;
  23.   print Dumper $hash;
  24.   print "\n";
  25. }
  26.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?target_taxon=6279;format=condensed;target_species=brugia_pahangi_prjeb497;type=orthologues"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12. decoded = r.json()
  13. print repr(decoded)
  14.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?target_taxon=6279;format=condensed;target_species=brugia_pahangi_prjeb497;type=orthologues"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12. decoded = r.json()
  13. print(repr(decoded))
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://parasite.wormbase.org'
  5. path = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?target_taxon=6279;format=condensed;target_species=brugia_pahangi_prjeb497;type=orthologues'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15.   puts "Invalid response: #{response.code}"
  16.   puts response.body
  17.   exit
  18. end
  19.  
  20.  
  21. require 'rubygems'
  22. require 'json'
  23. require 'yaml'
  24.  
  25. result = JSON.parse(response.body)
  26. puts YAML::dump(result)
  27.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13.   public static void main(String[] args) throws Exception {
  14.     String server = "https://parasite.wormbase.org";
  15.     String ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?target_taxon=6279;format=condensed;target_species=brugia_pahangi_prjeb497;type=orthologues";
  16.     URL url = new URL(server + ext);
  17.  
  18.     URLConnection connection = url.openConnection();
  19.     HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20.     
  21.     httpConnection.setRequestProperty("Content-Type", "application/json");
  22.     
  23.  
  24.     InputStream response = connection.getInputStream();
  25.     int responseCode = httpConnection.getResponseCode();
  26.  
  27.     if(responseCode != 200) {
  28.       throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  29.     }
  30.  
  31.     String output;
  32.     Reader reader = null;
  33.     try {
  34.       reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  35.       StringBuilder builder = new StringBuilder();
  36.       char[] buffer = new char[8192];
  37.       int read;
  38.       while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  39.         builder.append(buffer, 0, read);
  40.       }
  41.       output = builder.toString();
  42.     } 
  43.     finally {
  44.         if (reader != null) try {
  45.           reader.close(); 
  46.         } catch (IOException logOrIgnore) {
  47.           logOrIgnore.printStackTrace();
  48.         }
  49.     }
  50.  
  51.     System.out.println(output);
  52.   }
  53. }
  54.  
  1.  
  2. curl 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?target_taxon=6279;format=condensed;target_species=brugia_pahangi_prjeb497;type=orthologues' -H 'Content-type:application/json'
  3.  
  1. wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?target_taxon=6279;format=condensed;target_species=brugia_pahangi_prjeb497;type=orthologues'  -O -
  2.  

/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?content-type=application/json;type=orthologues;target_species=brugia_pahangi_prjeb497;sequence=cdna;target_taxon=6279


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://parasite.wormbase.org';
  9. my $ext = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;target_species=brugia_pahangi_prjeb497;target_taxon=6279;sequence=cdna';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'application/json' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. use JSON;
  18. use Data::Dumper;
  19. if(length $response->{content}) {
  20.   my $hash = decode_json($response->{content});
  21.   local $Data::Dumper::Terse = 1;
  22.   local $Data::Dumper::Indent = 1;
  23.   print Dumper $hash;
  24.   print "\n";
  25. }
  26.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;target_species=brugia_pahangi_prjeb497;target_taxon=6279;sequence=cdna"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12. decoded = r.json()
  13. print repr(decoded)
  14.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;target_species=brugia_pahangi_prjeb497;target_taxon=6279;sequence=cdna"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12. decoded = r.json()
  13. print(repr(decoded))
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://parasite.wormbase.org'
  5. path = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;target_species=brugia_pahangi_prjeb497;target_taxon=6279;sequence=cdna'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15.   puts "Invalid response: #{response.code}"
  16.   puts response.body
  17.   exit
  18. end
  19.  
  20.  
  21. require 'rubygems'
  22. require 'json'
  23. require 'yaml'
  24.  
  25. result = JSON.parse(response.body)
  26. puts YAML::dump(result)
  27.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13.   public static void main(String[] args) throws Exception {
  14.     String server = "https://parasite.wormbase.org";
  15.     String ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;target_species=brugia_pahangi_prjeb497;target_taxon=6279;sequence=cdna";
  16.     URL url = new URL(server + ext);
  17.  
  18.     URLConnection connection = url.openConnection();
  19.     HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20.     
  21.     httpConnection.setRequestProperty("Content-Type", "application/json");
  22.     
  23.  
  24.     InputStream response = connection.getInputStream();
  25.     int responseCode = httpConnection.getResponseCode();
  26.  
  27.     if(responseCode != 200) {
  28.       throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  29.     }
  30.  
  31.     String output;
  32.     Reader reader = null;
  33.     try {
  34.       reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  35.       StringBuilder builder = new StringBuilder();
  36.       char[] buffer = new char[8192];
  37.       int read;
  38.       while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  39.         builder.append(buffer, 0, read);
  40.       }
  41.       output = builder.toString();
  42.     } 
  43.     finally {
  44.         if (reader != null) try {
  45.           reader.close(); 
  46.         } catch (IOException logOrIgnore) {
  47.           logOrIgnore.printStackTrace();
  48.         }
  49.     }
  50.  
  51.     System.out.println(output);
  52.   }
  53. }
  54.  
  1.  
  2. curl 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;target_species=brugia_pahangi_prjeb497;target_taxon=6279;sequence=cdna' -H 'Content-type:application/json'
  3.  
  1. wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;target_species=brugia_pahangi_prjeb497;target_taxon=6279;sequence=cdna'  -O -
  2.  

/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?format=condensed;type=orthologues;content-type=text/xml


<opt>
  <data>
    <data id="WBGene00221255">
      <homologies id="nLs.2.1.2.g06925" method_link_type="ENSEMBL_ORTHOLOGUES" protein_id="nLs.2.1.2.t06925-RA" species="litomosoides_sigmodontis_prjeb3075" taxonomy_level="Onchocercidae" type="ortholog_one2one"/>
      <homologies id="nDi.2.2.2.g04666" method_link_type="ENSEMBL_ORTHOLOGUES" protein_id="nDi.2.2.2.t04666" species="dirofilaria_immitis_prjeb1797" taxonomy_level="Onchocercidae" type="ortholog_one2one"/>
      <homologies id="BPAG_0000674301" method_link_type="ENSEMBL_ORTHOLOGUES" protein_id="BPAG_0000674301-mRNA-1" species="brugia_pahangi_prjeb497" taxonomy_level="Brugia" type="ortholog_one2many"/>
      <homologies id="BPAG_0000621901" method_link_type="ENSEMBL_ORTHOLOGUES" protein_id="BPAG_0000621901-mRNA-1" species="brugia_pahangi_prjeb497" taxonomy_level="Brugia" type="ortholog_one2many"/>
      <homologies id="Wban_10481" method_link_type="ENSEMBL_ORTHOLOGUES" protein_id="mrna-Wban_10481" species="wuchereria_bancrofti_prjna275548" taxonomy_level="Onchocercidae" type="ortholog_one2one"/>
      <homologies id="WBGene00239008" method_link_type="ENSEMBL_ORTHOLOGUES" protein_id="OVOC2199.1" species="onchocerca_volvulus_prjeb513" taxonomy_level="Onchocercidae" type="ortholog_one2one"/>
      <homologies id="CJOHNSTONI_LOCUS9362" method_link_type="ENSEMBL_ORTHOLOGUES" protein_id="rna-CJOHNSTONI_LOCUS9362" species="cercopithifilaria_johnstoni_prjeb47283" taxonomy_level="Onchocercidae" type="ortholog_one2one"/>
    </data>
  </data>
</opt>
  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://parasite.wormbase.org';
  9. my $ext = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;format=condensed';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'text/xml' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. print "$response->{status} $response->{reason}\n";
  18.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;format=condensed"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/xml", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12.  
  13. print r.text
  14.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;format=condensed"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/xml", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12.  
  13. print(r.text)
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://parasite.wormbase.org'
  5. path = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;format=condensed'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/xml'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15.   puts "Invalid response: #{response.code}"
  16.   puts response.body
  17.   exit
  18. end
  19.  
  20.  
  21. puts response.body
  22.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13.   public static void main(String[] args) throws Exception {
  14.     String server = "https://parasite.wormbase.org";
  15.     String ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;format=condensed";
  16.     URL url = new URL(server + ext);
  17.  
  18.     URLConnection connection = url.openConnection();
  19.     HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20.     
  21.     httpConnection.setRequestProperty("Content-Type", "text/xml");
  22.     
  23.  
  24.     InputStream response = connection.getInputStream();
  25.     int responseCode = httpConnection.getResponseCode();
  26.  
  27.     if(responseCode != 200) {
  28.       throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  29.     }
  30.  
  31.     String output;
  32.     Reader reader = null;
  33.     try {
  34.       reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  35.       StringBuilder builder = new StringBuilder();
  36.       char[] buffer = new char[8192];
  37.       int read;
  38.       while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  39.         builder.append(buffer, 0, read);
  40.       }
  41.       output = builder.toString();
  42.     } 
  43.     finally {
  44.         if (reader != null) try {
  45.           reader.close(); 
  46.         } catch (IOException logOrIgnore) {
  47.           logOrIgnore.printStackTrace();
  48.         }
  49.     }
  50.  
  51.     System.out.println(output);
  52.   }
  53. }
  54.  
  1.  
  2. curl 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;format=condensed' -H 'Content-type:text/xml'
  3.  
  1. wget -q --header='Content-type:text/xml' 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?type=orthologues;format=condensed'  -O -
  2.  

/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?content-type=text/x-orthoxml%2Bxml


<?xml version="1.0" encoding="UTF-8"?><orthoXML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://orthoXML.org/2011/" xsi:schemaLocation="http://orthoXML.org http://orthoXML.org/0.3/orthoxml.xsd" version="0.3" origin="Ensembl" originVersion="111">
  <species NCBITaxId="6279" name="brugia_malayi_prjna10729">
    <database name="111" version="Bmal-4.0/2022-01-WormBase">
      <genes>
        <gene id="822707" geneId="WBGene00221255" protId="Bm994.1"/>
      </genes>
    </database>
  </species>
  <species NCBITaxId="42156" name="litomosoides_sigmodontis_prjeb3075">
    <database name="111" version="nLs.2.1/2014-05-WormBase">
      <genes>
        <gene id="3238125" geneId="nLs.2.1.2.g06925" protId="nLs.2.1.2.t06925-RA"/>
      </genes>
    </database>
  </species>
  <species NCBITaxId="6287" name="dirofilaria_immitis_prjeb1797">
    <database name="111" version="nDi.2.2/2021-04-WormBase">
      <genes>
        <gene id="616001" geneId="nDi.2.2.2.g04666" protId="nDi.2.2.2.t04666"/>
      </genes>
    </database>
  </species>
  <species NCBITaxId="6280" name="brugia_pahangi_prjeb497">
    <database name="111" version="B_pahangi_Glasgow_v1_5_4/2016-03-WormBase">
      <genes>
        <gene id="4955073" geneId="BPAG_0000674301" protId="BPAG_0000674301-mRNA-1"/>
        <gene id="4941162" geneId="BPAG_0000621901" protId="BPAG_0000621901-mRNA-1"/>
      </genes>
    </database>
  </species>
  <species NCBITaxId="6293" name="wuchereria_bancrofti_prjna275548">
    <database name="111" version="ASM528172v1/2023-09-WormBase">
      <genes>
        <gene id="4705267" geneId="Wban_10481" protId="mrna-Wban_10481"/>
      </genes>
    </database>
  </species>
  <species NCBITaxId="6282" name="onchocerca_volvulus_prjeb513">
    <database name="111" version="ASM49940v2/2021-03-WormBase">
      <genes>
        <gene id="2666872" geneId="WBGene00239008" protId="OVOC2199.1"/>
      </genes>
    </database>
  </species>
  <species NCBITaxId="2874296" name="cercopithifilaria_johnstoni_prjeb47283">
    <database name="111" version="SD210906/2021-11-WormBase">
      <genes>
        <gene id="1725229" geneId="CJOHNSTONI_LOCUS9362" protId="rna-CJOHNSTONI_LOCUS9362"/>
      </genes>
    </database>
  </species>
  <scores>
    <scoreDef id="bootstrap" desc="Reliability of the branch"/>
    <scoreDef id="duplication_confidence_score" desc="Reliability of the duplication"/>
    <scoreDef id="n" desc="Number of non-synonymous mutations"/>
    <scoreDef id="s" desc="Number of synonymous mutations"/>
    <scoreDef id="dn" desc="Rate of non-synonymous mutations"/>
    <scoreDef id="ds" desc="Rate of synonymous mutations"/>
    <scoreDef id="lnl" desc="Likelihood of the n/s scores"/>
    <scoreDef id="dnds_ratio" desc="dN/dS ratio"/>
    <scoreDef id="goc_score" desc="Gene order conservation score"/>
    <scoreDef id="wga_coverage" desc="Whole genome alignment coverage"/>
    <scoreDef id="perc_identity" desc="Percentage of identity of this protein to the alignment"/>
  </scores>
  <groups>
    <orthologGroup id="32189331">
      <property name="taxon_name" value="Onchocercidae"/>
      <property name="taxon_id" value="6296"/>
      <property name="description" value="ortholog_one2one"/>
      <property name="is_tree_compliant" value="1"/>
      <property name="is_high_confidence" value="1"/>
      <geneRef id="822707">
        <score id="perc_identity" value="52.9915"/>
      </geneRef>
      <geneRef id="3238125">
        <score id="perc_identity" value="38.5093"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="32261053">
      <property name="taxon_name" value="Onchocercidae"/>
      <property name="taxon_id" value="6296"/>
      <property name="description" value="ortholog_one2one"/>
      <property name="is_tree_compliant" value="1"/>
      <property name="is_high_confidence" value="1"/>
      <geneRef id="822707">
        <score id="perc_identity" value="53.8462"/>
      </geneRef>
      <geneRef id="616001">
        <score id="perc_identity" value="38.1818"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="32298874">
      <property name="taxon_name" value="Brugia"/>
      <property name="taxon_id" value="6278"/>
      <property name="description" value="ortholog_one2many"/>
      <property name="is_tree_compliant" value="1"/>
      <property name="is_high_confidence" value="1"/>
      <geneRef id="822707">
        <score id="perc_identity" value="40.1709"/>
      </geneRef>
      <geneRef id="4955073">
        <score id="perc_identity" value="79.661"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="32298875">
      <property name="taxon_name" value="Brugia"/>
      <property name="taxon_id" value="6278"/>
      <property name="description" value="ortholog_one2many"/>
      <property name="is_tree_compliant" value="1"/>
      <property name="is_high_confidence" value="1"/>
      <geneRef id="822707">
        <score id="perc_identity" value="39.3162"/>
      </geneRef>
      <geneRef id="4941162">
        <score id="perc_identity" value="77.9661"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="32364192">
      <property name="taxon_name" value="Onchocercidae"/>
      <property name="taxon_id" value="6296"/>
      <property name="description" value="ortholog_one2one"/>
      <property name="is_tree_compliant" value="1"/>
      <property name="is_high_confidence" value="1"/>
      <geneRef id="822707">
        <score id="perc_identity" value="85.4701"/>
      </geneRef>
      <geneRef id="4705267">
        <score id="perc_identity" value="86.2069"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="32530446">
      <property name="taxon_name" value="Onchocercidae"/>
      <property name="taxon_id" value="6296"/>
      <property name="description" value="ortholog_one2one"/>
      <property name="is_tree_compliant" value="1"/>
      <property name="is_high_confidence" value="1"/>
      <geneRef id="822707">
        <score id="perc_identity" value="42.735"/>
      </geneRef>
      <geneRef id="2666872">
        <score id="perc_identity" value="45.045"/>
      </geneRef>
    </orthologGroup>
    <orthologGroup id="33430110">
      <property name="taxon_name" value="Onchocercidae"/>
      <property name="taxon_id" value="6296"/>
      <property name="description" value="ortholog_one2one"/>
      <property name="is_tree_compliant" value="1"/>
      <property name="is_high_confidence" value="1"/>
      <geneRef id="822707">
        <score id="perc_identity" value="58.9744"/>
      </geneRef>
      <geneRef id="1725229">
        <score id="perc_identity" value="38.764"/>
      </geneRef>
    </orthologGroup>
  </groups>
</orthoXML>
  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://parasite.wormbase.org';
  9. my $ext = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'text/x-orthoxml+xml' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. print "$response->{status} $response->{reason}\n";
  18.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-orthoxml+xml", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12.  
  13. print r.text
  14.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-orthoxml+xml", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12.  
  13. print(r.text)
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://parasite.wormbase.org'
  5. path = '/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-orthoxml+xml'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15.   puts "Invalid response: #{response.code}"
  16.   puts response.body
  17.   exit
  18. end
  19.  
  20.  
  21. puts response.body
  22.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13.   public static void main(String[] args) throws Exception {
  14.     String server = "https://parasite.wormbase.org";
  15.     String ext = "/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?";
  16.     URL url = new URL(server + ext);
  17.  
  18.     URLConnection connection = url.openConnection();
  19.     HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20.     
  21.     httpConnection.setRequestProperty("Content-Type", "text/x-orthoxml+xml");
  22.     
  23.  
  24.     InputStream response = connection.getInputStream();
  25.     int responseCode = httpConnection.getResponseCode();
  26.  
  27.     if(responseCode != 200) {
  28.       throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  29.     }
  30.  
  31.     String output;
  32.     Reader reader = null;
  33.     try {
  34.       reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  35.       StringBuilder builder = new StringBuilder();
  36.       char[] buffer = new char[8192];
  37.       int read;
  38.       while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  39.         builder.append(buffer, 0, read);
  40.       }
  41.       output = builder.toString();
  42.     } 
  43.     finally {
  44.         if (reader != null) try {
  45.           reader.close(); 
  46.         } catch (IOException logOrIgnore) {
  47.           logOrIgnore.printStackTrace();
  48.         }
  49.     }
  50.  
  51.     System.out.println(output);
  52.   }
  53. }
  54.  
  1.  
  2. curl 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?' -H 'Content-type:text/x-orthoxml+xml'
  3.  
  1. wget -q --header='Content-type:text/x-orthoxml+xml' 'https://parasite.wormbase.org/rest-19/homology/symbol/brugia_malayi_prjna10729/Bm994?'  -O -
  2.  

Resource Information

MethodsGET
Response formatsjson
xml
orthoxml
jsonp