mason/tools/sequence_metadata/api_sequence_metadata.mas

   1
   2 <& /util/import_javascript.mas, classes => [ 'jquery' ],  &>
   3
   4 <p>Sequence Metadata queries can be made using a public API (Application Programming Interface).  Below are the available
   5 endpoints related to sequence metadata that can be used to query the database using HTTP requests.</p>
   6
   7 <br />
   8
   9 <h3>Sequence Metadata Query</h3>
  10 <p class='sequence_metadata_description'>Perform a query of the stored sequence metadata for a specific parent feature (i.e., chromosome) using any combination of additional filter criteria, provided as query parameters.  The feature must be provided, either by the feature ID or by the feature and species names.  If either the start or end positions are given, the name of the reference genome for those positions must be provided.</p>
  11 <code class='sequence_metadata_method'>GET</code>&nbsp;
  12 <code class='sequence_metadata_path'><span class='sequence_metadata_host'></span>/ajax/sequence_metadata/query</code>
  13 <br /><br />
  14 <p><strong>Query Parameters:</strong></p>
  15 <table class='table table-striped sequence_metadata_query_params'>
  16     <thead>
  17         <tr>
  18             <th>Name</th>
  19             <th>Description</th>
  20             <th>Example</th>
  21         </tr>
  22     </thead>
  23     <tbody>
  24         <tr>
  25             <td>feature_id<br /><strong>REQUIRED</strong><br />if&nbsp;<code>feature_name</code> and&nbsp;<code>species_name</code> are not provided</td>
  26             <td>ID of the parent feature (i.e., chromosome) associated with the sequence metadata</td>
  27             <td><code>2881383</code></td>
  28         </tr>
  29         <tr>
  30             <td>feature_name<br /><strong>REQUIRED</strong><br />with&nbsp;<code>species_name</code> if&nbsp;<code>feature_id</code> is not provided</td>
  31             <td>Name of the parent feature (i.e., chromosome) associated with the sequence metadata</td>
  32             <td><code>1A</code></td>
  33         </tr>
  34         <tr>
  35             <td>species_name<br /><strong>REQUIRED</strong><br />with&nbsp;<code>feature_name</code> if&nbsp;<code>feature_id</code> is not provided</td>
  36             <td>Name of the species associated with the provided feature name</td>
  37             <td><code>Triticum aestivum</code></td>
  38         </tr>
  39         <tr>
  40             <td>start</td>
  41             <td>start position of the query range<br /><strong>default:</strong> 0</td>
  42             <td><code>1000000</code></td>
  43         </tr>
  44         <tr>
  45             <td>end</td>
  46             <td>end position of the query range<br /><strong>default:</strong> max of specified feature</td>
  47             <td><code>2000000</code></td>
  48         </tr>
  49         <tr>
  50             <td>reference_genome<br /><strong>REQUIRED</strong><br />if&nbsp;either&nbsp;<code>start</code> or&nbsp;<code>end</code> positions are provided</td>
  51             <td>Name of the reference genome used for the start and/or end positions</td>
  52             <td><code>RefSeq_v1</code></td>
  53         </tr>
  54         <tr>
  55             <td>type_id</td>
  56             <td>cvterm_id(s) of sequence metadata type(s) (comma separated list of multiple type_ids)<br /><strong>default:</strong> any</td>
  57             <td><code>86273</code><br /><code>86273,86275</code></td>
  58         </tr>
  59         <tr>
  60             <td>nd_protocol_id</td>
  61             <td>nd_protocol_id(s) of sequence metadata protocol(s) (comma separated list of multiple nd_protocol_ids)<br /><strong>default:</strong> any</td>
  62             <td><code>204</code><br /><code>204,207</code></td>
  63         </tr>
  64         <tr>
  65             <td>attribute</td>
  66             <td>
  67                 Filter results using the value of an attribute (score or any of the defined secondary attributes) from a specific protocol.
  68                 The query parameter value includes the attribute(s) and their properties (attribute name, protocol id, comparison type, comparison value - separated by a '|')
  69                 (multiple attribute filters separated by a ',')<br />
  70                 <strong>format:</strong> {attribute name}|{nd_protocol_id}|{comparison}|{value}<br />
  71                 <strong>comparison:</strong> 'eq' (equal), 'con' (contains), 'lt' (less than), 'lte' (less than or equal), 'gt' (greater than), 'gte' (greater than or equal)<br />
  72                 <strong>default:</strong> none
  73             </td>
  74             <td><code>score|207|gt|0</code><br /><code>score|207|gt|0,Trait|204|con|grain+yield</code></td>
  75         </tr>
  76         <tr>
  77             <td>format</td>
  78             <td>
  79                 The output format of the response<br />
  80                 <strong>format:</strong> 'JSON' (breedbase JSON format), 'GA4GH' (Global Alliance for Genomics &amp; Health JSON format), 'gff' (gff3 format)<br />
  81                 <strong>default:</strong> JSON
  82             </td>
  83             <td><code>JSON</code><br /><code>GA4GH</code><br /><code>gff</code></td>
  84         </tr>
  85     </tbody>
  86 </table>
  87 <br />
  88 <p><strong>Response:</strong></p>
  89 <p>An example response for each format:</p>
  90 <ul class="nav nav-tabs">
  91   <li class="active"><a data-toggle="tab" href="#sequence_metadata_response_json">JSON</a></li>
  92   <li><a data-toggle="tab" href="#sequence_metadata_response_ga4gh">GA4GH</a></li>
  93   <li><a data-toggle="tab" href="#sequence_metadata_response_gff">gff</a></li>
  94 </ul>
  95
  96 <div class="tab-content">
  97   <div id="sequence_metadata_response_json" class="tab-pane fade in active">
  98     <pre class='sequence_metadata_response'>
  99 {
 100   "results": [
 101     {
 102       "start": 1207522,
 103       "score": "0.0454952857260828",
 104       "nd_protocol_id": 204,
 105       "featureprop_json_id": 1253,
 106       "type_id": 86274,
 107       "feature_name": "chr1A",
 108       "attributes": {
 109         "qvalue": "0.0454952857260828",
 110         "pvalue": "0.00080725065468678",
 111         "zvalue": "3.350296620481",
 112         "ID": "RAC875_c20883_801",
 113         "Population": "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon",
 114         "Locus": "TraesCS1A02G002300",
 115         "Variable": "CO_321:0001138",
 116         "Trait": "SDS sedimentation"
 117       },
 118       "type_name": "GWAS Results",
 119       "end": 1207522,
 120       "nd_protocol_name": "T3 Automated GWAS",
 121       "feature_id": 2881383
 122     },
 123     {
 124       "type_name": "GWAS Results",
 125       "end": 1211006,
 126       "feature_name": "chr1A",
 127       "attributes": {
 128         "ID": "GENE-0014_317",
 129         "zvalue": "3.350296620481",
 130         "pvalue": "0.00080725065468678",
 131         "qvalue": "0.0454952857260828",
 132         "Trait": "SDS sedimentation",
 133         "Variable": "CO_321:0001138",
 134         "Locus": "TraesCS1A02G002300",
 135         "Population": "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon"
 136       },
 137       "nd_protocol_id": 204,
 138       "featureprop_json_id": 1253,
 139       "type_id": 86274,
 140       "start": 1211006,
 141       "score": "0.0454952857260828",
 142       "feature_id": 2881383,
 143       "nd_protocol_name": "T3 Automated GWAS"
 144     },
 145     {
 146       "attributes": {
 147         "Population": "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon",
 148         "Locus": "TraesCS1A02G002300",
 149         "Variable": "CO_321:0001138",
 150         "Trait": "SDS sedimentation",
 151         "qvalue": "0.0454952857260828",
 152         "pvalue": "0.00080725065468678",
 153         "zvalue": "3.350296620481",
 154         "ID": "GENE-0014_262"
 155       },
 156       "feature_name": "chr1A",
 157       "type_name": "GWAS Results",
 158       "end": 1211057,
 159       "start": 1211057,
 160       "score": "0.0454952857260828",
 161       "nd_protocol_id": 204,
 162       "featureprop_json_id": 1253,
 163       "type_id": 86274,
 164       "nd_protocol_name": "T3 Automated GWAS",
 165       "feature_id": 2881383
 166     },
 167     {
 168       "nd_protocol_name": "T3 Automated GWAS",
 169       "feature_id": 2881383,
 170       "feature_name": "chr1A",
 171       "attributes": {
 172         "Trait": "SDS sedimentation",
 173         "Locus": "TraesCS1A02G002500",
 174         "Population": "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon",
 175         "Variable": "CO_321:0001138",
 176         "ID": "RAC875_c95364_59",
 177         "qvalue": "0.0454952857260828",
 178         "pvalue": "0.00080725065468678",
 179         "zvalue": "3.350296620481"
 180       },
 181       "end": 1234797,
 182       "type_name": "GWAS Results",
 183       "score": "0.0454952857260828",
 184       "start": 1234797,
 185       "type_id": 86274,
 186       "featureprop_json_id": 1253,
 187       "nd_protocol_id": 204
 188     },
 189     {
 190       "nd_protocol_name": "T3 Automated GWAS",
 191       "feature_id": 2881383,
 192       "score": "0.0394888300035745",
 193       "start": 1342766,
 194       "type_id": 86274,
 195       "featureprop_json_id": 1253,
 196       "nd_protocol_id": 204,
 197       "feature_name": "chr1A",
 198       "attributes": {
 199         "pvalue": "0.000513039677027759",
 200         "zvalue": "3.4738542266235",
 201         "qvalue": "0.0394888300035745",
 202         "ID": "Kukri_c2408_857",
 203         "Variable": "CO_321:0001138",
 204         "Population": "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon",
 205         "Locus": "TraesCS1A02G002700",
 206         "Trait": "SDS sedimentation"
 207       },
 208       "end": 1342766,
 209       "type_name": "GWAS Results"
 210     }
 211   ]
 212 }
 213     </pre>
 214   </div>
 215   <div id="sequence_metadata_response_ga4gh" class="tab-pane fade">
 216     <pre class='sequence_metadata_response'>
 217 {
 218   "features": [
 219     {
 220       "attributes": {
 221         "qvalue": [
 222           "0.0454952857260828"
 223         ],
 224         "pvalue": [
 225           "0.00080725065468678"
 226         ],
 227         "zvalue": [
 228           "3.350296620481"
 229         ],
 230         "ID": [
 231           "RAC875_c20883_801"
 232         ],
 233         "Locus": [
 234           "TraesCS1A02G002300"
 235         ],
 236         "Population": [
 237           "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon"
 238         ],
 239         "Variable": [
 240           "CO_321:0001138"
 241         ],
 242         "bb_metadata": {
 243           "nd_protocol_name": [
 244             "T3 Automated GWAS"
 245           ],
 246           "type_name": [
 247             "GWAS Results"
 248           ],
 249           "nd_protocol_id": [
 250             204
 251           ],
 252           "type_id": [
 253             86274
 254           ]
 255         },
 256         "Trait": [
 257           "SDS sedimentation"
 258         ],
 259         "score": [
 260           "0.0454952857260828"
 261         ]
 262       },
 263       "parent_id": 2881383,
 264       "end": 1207522,
 265       "feature_set_id": 204,
 266       "reference_name": "chr1A",
 267       "start": 1207522,
 268       "id": "1253.0"
 269     },
 270     {
 271       "feature_set_id": 204,
 272       "start": 1211006,
 273       "id": "1253.1",
 274       "reference_name": "chr1A",
 275       "parent_id": 2881383,
 276       "end": 1211006,
 277       "attributes": {
 278         "bb_metadata": {
 279           "nd_protocol_name": [
 280             "T3 Automated GWAS"
 281           ],
 282           "type_name": [
 283             "GWAS Results"
 284           ],
 285           "nd_protocol_id": [
 286             204
 287           ],
 288           "type_id": [
 289             86274
 290           ]
 291         },
 292         "score": [
 293           "0.0454952857260828"
 294         ],
 295         "Trait": [
 296           "SDS sedimentation"
 297         ],
 298         "Population": [
 299           "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon"
 300         ],
 301         "Locus": [
 302           "TraesCS1A02G002300"
 303         ],
 304         "Variable": [
 305           "CO_321:0001138"
 306         ],
 307         "ID": [
 308           "GENE-0014_317"
 309         ],
 310         "qvalue": [
 311           "0.0454952857260828"
 312         ],
 313         "zvalue": [
 314           "3.350296620481"
 315         ],
 316         "pvalue": [
 317           "0.00080725065468678"
 318         ]
 319       }
 320     },
 321     {
 322       "feature_set_id": 204,
 323       "start": 1211057,
 324       "reference_name": "chr1A",
 325       "id": "1253.2",
 326       "parent_id": 2881383,
 327       "end": 1211057,
 328       "attributes": {
 329         "Population": [
 330           "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon"
 331         ],
 332         "Locus": [
 333           "TraesCS1A02G002300"
 334         ],
 335         "Variable": [
 336           "CO_321:0001138"
 337         ],
 338         "bb_metadata": {
 339           "nd_protocol_name": [
 340             "T3 Automated GWAS"
 341           ],
 342           "type_name": [
 343             "GWAS Results"
 344           ],
 345           "type_id": [
 346             86274
 347           ],
 348           "nd_protocol_id": [
 349             204
 350           ]
 351         },
 352         "score": [
 353           "0.0454952857260828"
 354         ],
 355         "Trait": [
 356           "SDS sedimentation"
 357         ],
 358         "qvalue": [
 359           "0.0454952857260828"
 360         ],
 361         "pvalue": [
 362           "0.00080725065468678"
 363         ],
 364         "zvalue": [
 365           "3.350296620481"
 366         ],
 367         "ID": [
 368           "GENE-0014_262"
 369         ]
 370       }
 371     },
 372     {
 373       "feature_set_id": 204,
 374       "start": 1234797,
 375       "reference_name": "chr1A",
 376       "id": "1253.3",
 377       "end": 1234797,
 378       "parent_id": 2881383,
 379       "attributes": {
 380         "score": [
 381           "0.0454952857260828"
 382         ],
 383         "Trait": [
 384           "SDS sedimentation"
 385         ],
 386         "bb_metadata": {
 387           "type_name": [
 388             "GWAS Results"
 389           ],
 390           "nd_protocol_name": [
 391             "T3 Automated GWAS"
 392           ],
 393           "nd_protocol_id": [
 394             204
 395           ],
 396           "type_id": [
 397             86274
 398           ]
 399         },
 400         "Variable": [
 401           "CO_321:0001138"
 402         ],
 403         "Population": [
 404           "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon"
 405         ],
 406         "Locus": [
 407           "TraesCS1A02G002500"
 408         ],
 409         "ID": [
 410           "RAC875_c95364_59"
 411         ],
 412         "zvalue": [
 413           "3.350296620481"
 414         ],
 415         "pvalue": [
 416           "0.00080725065468678"
 417         ],
 418         "qvalue": [
 419           "0.0454952857260828"
 420         ]
 421       }
 422     },
 423     {
 424       "feature_set_id": 204,
 425       "start": 1342766,
 426       "reference_name": "chr1A",
 427       "id": "1253.4",
 428       "attributes": {
 429         "Locus": [
 430           "TraesCS1A02G002700"
 431         ],
 432         "Population": [
 433           "TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon"
 434         ],
 435         "Variable": [
 436           "CO_321:0001138"
 437         ],
 438         "bb_metadata": {
 439           "nd_protocol_name": [
 440             "T3 Automated GWAS"
 441           ],
 442           "type_name": [
 443             "GWAS Results"
 444           ],
 445           "type_id": [
 446             86274
 447           ],
 448           "nd_protocol_id": [
 449             204
 450           ]
 451         },
 452         "Trait": [
 453           "SDS sedimentation"
 454         ],
 455         "score": [
 456           "0.0394888300035745"
 457         ],
 458         "qvalue": [
 459           "0.0394888300035745"
 460         ],
 461         "zvalue": [
 462           "3.4738542266235"
 463         ],
 464         "pvalue": [
 465           "0.000513039677027759"
 466         ],
 467         "ID": [
 468           "Kukri_c2408_857"
 469         ]
 470       },
 471       "parent_id": 2881383,
 472       "end": 1342766
 473     }
 474   ]
 475 }
 476     </pre>
 477   </div>
 478   <div id="sequence_metadata_response_gff" class="tab-pane fade">
 479     <pre class='sequence_metadata_response'>
 480 chr1A   .       .       1207522 1207522 0.0454952857260828      .       .       Trait="SDS sedimentation";Variable=CO_321:0001138;Population="TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon";Locus=TraesCS1A02G002300;ID=RAC875_c20883_801;pvalue=0.00080725065468678;zvalue=3.350296620481;qvalue=0.0454952857260828
 481 chr1A   .       .       1211006 1211006 0.0454952857260828      .       .       ID=GENE-0014_317;pvalue=0.00080725065468678;zvalue=3.350296620481;qvalue=0.0454952857260828;Trait="SDS sedimentation";Variable=CO_321:0001138;Locus=TraesCS1A02G002300;Population="TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon"
 482 chr1A   .       .       1211057 1211057 0.0454952857260828      .       .       Population="TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon";Locus=TraesCS1A02G002300;Variable=CO_321:0001138;Trait="SDS sedimentation";qvalue=0.0454952857260828;zvalue=3.350296620481;pvalue=0.00080725065468678;ID=GENE-0014_262
 483 chr1A   .       .       1234797 1234797 0.0454952857260828      .       .       ID=RAC875_c95364_59;pvalue=0.00080725065468678;zvalue=3.350296620481;qvalue=0.0454952857260828;Trait="SDS sedimentation";Variable=CO_321:0001138;Population="TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon";Locus=TraesCS1A02G002500
 484 chr1A   .       .       1342766 1342766 0.0394888300035745      .       .       ID=Kukri_c2408_857;qvalue=0.0394888300035745;pvalue=0.000513039677027759;zvalue=3.4738542266235;Trait="SDS sedimentation";Population="TCAP90K_SpringAM_panel x SW-AMPanel_2012_Saskatoon";Locus=TraesCS1A02G002700;Variable=CO_321:0001138
 485     </pre>
 486   </div>
 487 </div>
 488
 489 <br /><br /><br />
 490
 491 <h3>Get Features</h3>
 492 <p class='sequence_metadata_description'>Get all of the parent features (i.e., chromosomes) associated with loaded sequence metadata</p>
 493 <code class='sequence_metadata_method'>GET</code>&nbsp;
 494 <code class='sequence_metadata_path'><span class='sequence_metadata_host'></span>/ajax/sequence_metadata/features</code>
 495 <br /><br />
 496 <p><strong>Response:</strong></p>
 497 <p>An example response in JSON format:</p>
 498 <pre class='sequence_metadata_response'>
 499 {
 500   "features": [
 501     {
 502       "feature_name": "chr1A",
 503       "organism_id": 109397,
 504       "feature_id": 2881383,
 505       "type_name": "chromosome",
 506       "organism_name": "Triticum aestivum",
 507       "type_id": 75732
 508     },
 509     {
 510       "organism_name": "Triticum aestivum",
 511       "type_id": 75732,
 512       "feature_id": 2881384,
 513       "type_name": "chromosome",
 514       "feature_name": "chr1B",
 515       "organism_id": 109397
 516     },
 517     {
 518       "feature_name": "chr1D",
 519       "organism_id": 109397,
 520       "feature_id": 2881385,
 521       "type_name": "chromosome",
 522       "organism_name": "Triticum aestivum",
 523       "type_id": 75732
 524     },
 525     {
 526       "type_id": 75732,
 527       "organism_name": "Triticum aestivum",
 528       "type_name": "chromosome",
 529       "feature_id": 2881386,
 530       "organism_id": 109397,
 531       "feature_name": "chr2A"
 532     },
 533     {
 534       "type_name": "chromosome",
 535       "feature_id": 2881387,
 536       "organism_id": 109397,
 537       "feature_name": "chr2B",
 538       "organism_name": "Triticum aestivum",
 539       "type_id": 75732
 540     },
 541     {
 542       "organism_id": 109397,
 543       "feature_name": "chr2D",
 544       "type_name": "chromosome",
 545       "feature_id": 2881388,
 546       "organism_name": "Triticum aestivum",
 547       "type_id": 75732
 548     },
 549     {
 550       "organism_name": "Triticum aestivum",
 551       "type_id": 75732,
 552       "feature_name": "chr3A",
 553       "organism_id": 109397,
 554       "feature_id": 2881389,
 555       "type_name": "chromosome"
 556     },
 557     {
 558       "type_name": "chromosome",
 559       "feature_id": 2881390,
 560       "organism_id": 109397,
 561       "feature_name": "chr3B",
 562       "type_id": 75732,
 563       "organism_name": "Triticum aestivum"
 564     },
 565     {
 566       "type_id": 75732,
 567       "organism_name": "Triticum aestivum",
 568       "feature_name": "chr3D",
 569       "organism_id": 109397,
 570       "feature_id": 2881391,
 571       "type_name": "chromosome"
 572     },
 573     {
 574       "feature_name": "chr4A",
 575       "organism_id": 109397,
 576       "feature_id": 2881392,
 577       "type_name": "chromosome",
 578       "type_id": 75732,
 579       "organism_name": "Triticum aestivum"
 580     },
 581     {
 582       "feature_name": "chr4B",
 583       "organism_id": 109397,
 584       "feature_id": 2881393,
 585       "type_name": "chromosome",
 586       "organism_name": "Triticum aestivum",
 587       "type_id": 75732
 588     },
 589     {
 590       "organism_name": "Triticum aestivum",
 591       "type_id": 75732,
 592       "organism_id": 109397,
 593       "feature_name": "chr4D",
 594       "type_name": "chromosome",
 595       "feature_id": 2881394
 596     },
 597     {
 598       "feature_name": "chr5A",
 599       "organism_id": 109397,
 600       "feature_id": 2881395,
 601       "type_name": "chromosome",
 602       "organism_name": "Triticum aestivum",
 603       "type_id": 75732
 604     },
 605     {
 606       "feature_id": 2881396,
 607       "type_name": "chromosome",
 608       "feature_name": "chr5B",
 609       "organism_id": 109397,
 610       "organism_name": "Triticum aestivum",
 611       "type_id": 75732
 612     },
 613     {
 614       "organism_id": 109397,
 615       "feature_name": "chr5D",
 616       "type_name": "chromosome",
 617       "feature_id": 2881397,
 618       "type_id": 75732,
 619       "organism_name": "Triticum aestivum"
 620     },
 621     {
 622       "type_id": 75732,
 623       "organism_name": "Triticum aestivum",
 624       "feature_id": 2881398,
 625       "type_name": "chromosome",
 626       "feature_name": "chr6A",
 627       "organism_id": 109397
 628     },
 629     {
 630       "organism_id": 109397,
 631       "feature_name": "chr6B",
 632       "type_name": "chromosome",
 633       "feature_id": 2881399,
 634       "organism_name": "Triticum aestivum",
 635       "type_id": 75732
 636     },
 637     {
 638       "organism_name": "Triticum aestivum",
 639       "type_id": 75732,
 640       "organism_id": 109397,
 641       "feature_name": "chr6D",
 642       "type_name": "chromosome",
 643       "feature_id": 2881400
 644     },
 645     {
 646       "organism_name": "Triticum aestivum",
 647       "type_id": 75732,
 648       "feature_id": 2881401,
 649       "type_name": "chromosome",
 650       "feature_name": "chr7A",
 651       "organism_id": 109397
 652     },
 653     {
 654       "type_id": 75732,
 655       "organism_name": "Triticum aestivum",
 656       "organism_id": 109397,
 657       "feature_name": "chr7B",
 658       "type_name": "chromosome",
 659       "feature_id": 2881402
 660     },
 661     {
 662       "organism_name": "Triticum aestivum",
 663       "type_id": 75732,
 664       "organism_id": 109397,
 665       "feature_name": "chr7D",
 666       "type_name": "chromosome",
 667       "feature_id": 2881403
 668     },
 669     {
 670       "organism_id": 109397,
 671       "feature_name": "chrUn",
 672       "type_name": "chromosome",
 673       "feature_id": 2881426,
 674       "type_id": 75732,
 675       "organism_name": "Triticum aestivum"
 676     },
 677     {
 678       "feature_id": 2881427,
 679       "type_name": "chromosome",
 680       "feature_name": "UNK",
 681       "organism_id": 109397,
 682       "organism_name": "Triticum aestivum",
 683       "type_id": 75732
 684     }
 685   ]
 686 }
 687 </pre>
 688
 689 <br /><br /><br />
 690
 691 <h3>Get Data Types</h3>
 692 <p class='sequence_metadata_description'>Get all of the sequence metadata data types supported by the database</p>
 693 <code class='sequence_metadata_method'>GET</code>&nbsp;
 694 <code class='sequence_metadata_path'><span class='sequence_metadata_host'></span>/ajax/sequence_metadata/types</code>
 695 <br /><br />
 696 <p><strong>Response:</strong></p>
 697 <p>An example response in JSON format:</p>
 698 <pre class='sequence_metadata_response'>
 699 {
 700   "types": [
 701     {
 702       "type_name": "Gene Annotation",
 703       "type_id": 86273,
 704       "type_definition": "Provides sequence features (gene, mRNA, UTR, exon, CDS) and annotations based on alignments of biological evidence."
 705     },
 706     {
 707       "type_name": "GWAS Results",
 708       "type_id": 86274,
 709       "type_definition": "Report of quantitative trait loci (QTLs) indentified by running rrBLUP analysis on phenotype trials and genotype trials within the T3 database."
 710     },
 711     {
 712       "type_id": 86275,
 713       "type_definition": "Report of chromatine accessibility score. The report can be used to prioritize genomic variants and explain phenotypes. (https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-02093-1)",
 714       "type_name": "MNase"
 715     }
 716   ]
 717 }
 718 </pre>
 719
 720 <br /><br /><br />
 721
 722 <h3>Get Protocols</h3>
 723 <p class='sequence_metadata_description'>Get all of the existing sequence metadata protocols</p>
 724 <code class='sequence_metadata_method'>GET</code>&nbsp;
 725 <code class='sequence_metadata_path'><span class='sequence_metadata_host'></span>/ajax/sequence_metadata/protocols</code>
 726 <br /><br />
 727 <p><strong>Response:</strong></p>
 728 <p>An example response in JSON format:</p>
 729 <pre class='sequence_metadata_response'>
 730 {
 731   "protocols": [
 732     {
 733       "nd_protocol_id": 204,
 734       "nd_protocol_description": "Description of T3 Automated GWAS",
 735       "nd_protocol_properties": {
 736         "reference_genome": "RefSeq_v1",
 737         "score_description": "none",
 738         "sequence_metadata_type": "GWAS Results",
 739         "attribute_descriptions": {
 740           "ID": "unique region identifier",
 741           "pvalue": "significance level",
 742           "zvalue": "number of standard deviations (used for meta analysis)",
 743           "qvalue": "pvalue adjusted for false discovery rate",
 744           "Trait": "Trait name",
 745           "Variable": "Trait ontology variable identifier",
 746           "Population": ".",
 747           "Locus": "Ensembl Gene ID"
 748         },
 749         "sequence_metadata_type_id": "86274"
 750       },
 751       "nd_protocol_name": "T3 Automated GWAS"
 752     },
 753     {
 754       "nd_protocol_name": "Variant Effect Predictor",
 755       "nd_protocol_description": "VEP Description",
 756       "nd_protocol_id": 205,
 757       "nd_protocol_properties": {
 758         "sequence_metadata_type": "Gene Annotation",
 759         "score_description": "none",
 760         "reference_genome": "RefSeq_v1",
 761         "sequence_metadata_type_id": "86273",
 762         "attribute_descriptions": {
 763           "Consequence": ".",
 764           "Name": ".",
 765           "ID": ".",
 766           "Impact": "."
 767         }
 768       }
 769     },
 770     {
 771       "nd_protocol_description": "IWGSC Assembly Description",
 772       "nd_protocol_id": 206,
 773       "nd_protocol_properties": {
 774         "sequence_metadata_type_id": "86273",
 775         "attribute_descriptions": {
 776           "logic_name": "source of the gene annotation",
 777           "description": "annotation of feature, can describe function",
 778           "Parent": "parent of the feature, used to group exons into transcripts and transcripts into genes",
 779           "rank": ".",
 780           "ensemble_phase": ".",
 781           "Name": "display name for feature",
 782           "Alias": "a secondary name for the feature",
 783           "biotype": "type of feature",
 784           "exon_id": "unique identifier for exon",
 785           "gene_id": "another form of the ID for a feature",
 786           "constitutive": "exon that are not spliced out",
 787           "ID": "unique identifier for feature (gene)",
 788           "transcript_id": "a splice variant of a gene",
 789           "ensemble_end_phase": ".",
 790           "protein_id": "unique identifier for protein"
 791         },
 792         "sequence_metadata_type": "Gene Annotation",
 793         "score_description": "none",
 794         "reference_genome": "RefSeq_v1"
 795       },
 796       "nd_protocol_name": "IWGSC Assembly"
 797     },
 798     {
 799       "nd_protocol_description": "MNase Open Chromatin description",
 800       "nd_protocol_id": 207,
 801       "nd_protocol_properties": {
 802         "sequence_metadata_type_id": "86275",
 803         "attribute_descriptions": {
 804           "ID": "unique region identifier"
 805         },
 806         "sequence_metadata_type": "MNase",
 807         "score_description": "open chromatin score",
 808         "reference_genome": "RefSeq_v1"
 809       },
 810       "nd_protocol_name": "MNase Open Chromatin"
 811     }
 812   ]
 813 }
 814 </pre>
 815
 816
 817 <br /><br /><br />
 818
 819 <p>
 820     <strong>Error:</strong> If an error is encountered processing the request, the response will return a JSON object with an <code>error</code> property containing an error message:<br />
 821     <code>{"error":"The requested query is too large to perform at once. Try filtering the data by including fewer data types/protocols and/or a smaller sequence range."}</code>
 822 <p>
 823
 824
 825
 826 <script type="text/javascript">
 827     jQuery(document).ready(function() {
 828         set_host();
 829     });
 830
 831     /**
 832      * Get and set the host for the API paths
 833      */
 834     function set_host() {
 835         let host = window.location.protocol + '//' + window.location.host;
 836         jQuery('.sequence_metadata_host').html(host);
 837     }
 838 </script>
 839
 840
 841 <style>
 842     code.sequence_metadata_method {
 843         font-size: 14px;
 844         font-weight: 700;
 845         color: #096927;
 846         background: #C3E9CE;
 847     }
 848     code.sequence_metadata_path {
 849         font-size: 14px;
 850         font-weight: 700;
 851         color: #000;
 852         background: #eee;
 853     }
 854     code.sequence_metadata_path > span.sequence_metadata_host {
 855         color: #aaa;
 856     }
 857     p.sequence_metadata_description {
 858         margin-top: -5px;
 859         margin-bottom: 15px;
 860     }
 861     table.sequence_metadata_query_params {
 862         margin-top: 10px;
 863     }
 864     table.sequence_metadata_query_params code {
 865         background: none;
 866         color: #333;
 867         font-size: 12px;
 868     }
 869     pre.sequence_metadata_response {
 870       max-height: 500px;
 871       overflow-y: auto;
 872     }
 873 </style>