-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
449 lines (413 loc) · 25.9 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
<!DOCTYPE html>
<html lang="en">
<head>
<title>CFDE Home</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta charset="UTF-8">
<link rel="stylesheet" href="./css/style.css" type="text/css"/>
<link rel="stylesheet" href="./css/index.css" type="text/css"/>
<script src="/chaise/lib/navbar/navbar.app.js"></script>
<link rel="stylesheet" href="./css/components/normalize.css" type="text/css">
<link rel="stylesheet" href="./css/components/bootstrap.min.css" type="text/css">
<link rel="shortcut icon" type="image/png" href="./images/icons/CFDE-icon-1.png?v=2"/>
<link rel="stylesheet" href="./css/fonts.css" type="text/css"/>
<link rel="stylesheet" href="./css/components/all.min.css"/>
<style>
/* customize carousel */
.carousel-item > div {
background-color: #ffffff;
}
.carousel-caption h5, p {
color: black;
}
.carousel-caption h5, p {
text-shadow: none;
}
.carousel-control-next,
.carousel-control-prev /*, .carousel-indicators */ {
filter: invert(100%);
align-items: flex-middle;
bottom: 0%;
top: 60%;
}
.carousel-indicators li {
filter: invert(100%);
}
</style>
</head>
<body>
<div id="wrap-navbar">
<navbar></navbar>
</div>
<main class="main">
<div class="top_content">
<div class="top_content_section_left">
<div class="section_left_page_info">
<h1>Common Fund Data Ecosystem Search Portal</h1>
<h2>Find files, biosamples, or subjects from Common Fund data sets</h2>
</div>
</div>
</div><!-- End Top Content-->
<div class="content">
<div class="content__top">
<div class="content__left">
<div class="data_header">
<p>Start your search</p>
</div>
<div class="data_content">
<h5>Click to search by:</h5>
<div class="browse_by_feature">
<div id="browse-by-feature-container">
<p>
<a href="/chaise/recordset/#1/CFDE:anatomy" style="color:#c0653d" title="Search for all the biosamples taken from a specific anatomical region and their related files">
<i class="fas fa-solid fa-lungs fa-4x"></i>
<br/>Anatomy
<br/><span id="anatomy_count"/>
</a>
</p>
<p>
<a href="/chaise/recordset/#1/CFDE:assay_type" style="color:#138eae" title="Search for all the biosamples that have had a specific procedure or measurement taken, and their related files">
<i class="fas fa-solid fa-eye-dropper fa-4x"></i>
<br/>Assay
<br/><span id="assay_count"> </span>
</a>
</p>
<p>
<a href="/chaise/recordset/#1/CFDE:file" style="color:#96c93e" title="Search for digital objects containing metadata or data (images, sequences, etc) that result from assays">
<i class="fas fa-solid fa-file fa-4x"></i>
<br/>File
<br/><span id="file_count"> </span>
</a>
</p>
</div>
<div id="search-by-container">
<p>
<a href="/chaise/recordset/#1/CFDE:biosample" style="color: #eb7e23" title="Search for tissue samples and other physical specimens">
<i class="fas fa-solid fa-vial fa-4x""></i>
<br/>Biosample
<br/><span id="biosample_count"> </span>
</a>
</p>
<p>
<a href="/chaise/recordset/#1/CFDE:subject" style="color:#aa8ec2" title="Search for specific organisms that biosamples are taken from">
<i class="fas fa-solid fa-user fa-4x"></i>
<br/>Subject
<br/><span id="subject_count"> </span>
</a>
</p>
</div>
<div id="search-by-misc">
<p>
<a href="/chaise/recordset/#1/CFDE:disease" style="color:#f0593b" title="">
<i class="fas fa-solid fa-virus fa-4x"></i>
<br/>Disease
<br/><span id="disease_count"> </span>
</a>
</p>
<p>
<a href="/chaise/recordset/#1/CFDE:gene" style="color: #76c8ed" title="">
<i class="fas fa-solid fa-dna fa-4x""></i>
<br/>Gene
<br/><span id="gene_count"> </span>
</a>
</p>
<p>
<a href="/chaise/recordset/#1/CFDE:compound" style="color:#80cbb3" title="">
<i class="fas fa-solid fa-pills fa-4x"></i>
<br/>Compound
<br/><span id="compound_count"> </span>
</a>
</p>
</div>
<div style="clear: both"></div>
</div>
</div>
</div>
<div class="content__right">
<div class="data_header snapshot">
<p id="summary_view_title" class="snapshot_head">Preview the data</p>
<p id="last_updated" class="last-updated"></p>
</div>
<div class="data_content">
<div id="sbc1-container">
<div id="chart-inner-container">
<svg id="sbc1"></svg>
</div>
</div>
<div id="sbc1-group-by-and-legend-container" style="display: none;">
<div id="sbc1-group-by-container">
<label for="group-by" class="form-label">Color key:</label>
<select class="custom-select" id="sbc1-group-by" name="groupby" style="display: none;">
<option value="anatomy">Anatomy</option>
<option selected value="assay_type">Assay</option>
<option value="dcc">CF Program</option>
<option value="data_type">Data Type</option>
<option value="disease">Disease</option>
<option value="ethnicity">Ethnicity</option>
<option value="race">Race</option>
<option value="sex">Sex</option>
<option value="species">Species</option>
</select>
</div>
<div id="sbc1_container"></div>
</div>
<div id="form-controls">
<form>
<div class="container" style="width: 100%;">
<div class="row">
<div class="col-md-3" id="sbc1-y-axis-container">
<label for="y-axis" class="form-label">Y-axis</label>
<select class="custom-select" id="sbc1-y-axis" name="y-axis">
<option value="volume">Data volume</option>
<option value="collections">Collection count</option>
<option value="files">File count</option>
<option value="samples">Sample count</option>
<option selected value="subjects">Subject count</option>
</select>
</div>
<div class="col-md-3" id="sbc1-x-axis-container">
<label for="x-axis" class="form-label">X-axis</label>
<select class="custom-select" id="sbc1-x-axis" name="x-axis">
<option value="anatomy">Anatomy</option>
<option value="assay_type">Assay</option>
<option value="dcc">CF Program</option>
<option selected value="data_type">Data Type</option>
<option value="disease">Disease</option>
<option value="ethnicity">Ethnicity</option>
<option value="race">Race</option>
<option value="sex">Sex</option>
<option value="species">Species</option>
</select>
</div>
<div class="col-md-3" id="sbc1-scale-container">
<label for="scale" class="form-label">Scale</label>
<select class="custom-select" id="sbc1-scale" name="scale">
<option value="Linear">Linear</option>
<option selected value="log">Logarithmic</option>
</select>
</div>
<div class="col-md-3" id="sbc1-download-button-container">
<p id="sbc1-export" class="export-button"><a href="javascript: export_chart_data('sbc1')"><img src='images/download_button.png' style='width: 125px; height: 32px;' title='Export chart'></a></p>
</div>
</div>
</div>
</form>
</div>
</div> <!--end data_content-->
</div>
</div>
<div class="content__bottom">
<div class="content__col left">
<div class="data_header">
<p>Searchable Common Fund data sets</p>
</div>
<div class="data_content">
<div style="display: flex; flex-direction: row; flex-wrap: wrap; justify-content: space-around;">
<div style="padding-bottom: 20px;"><div style="background: black; padding: 0.5em"><a target="_blank" href="https://exrna.org"><img width="170px" src="images/exrna-logo-white.png"></a></div></div>
<div style="padding-bottom: 20px;"><a target="_blank" href="https://gtexportal.org/home/"><img width="100px" src="images/GTEX.png"></a></div>
<div style="flex-basis: 100%; height: 0px;"></div>
<div style="padding-bottom: 20px;"><a target="_blank" href="https://hmpdacc.org"><img width="150px" src="images/HMP.png"></a></div>
<div style="padding-bottom: 20px;"><a target="_blank" href="https://hubmapconsortium.org"><img width="170px" src="images/hubmap-logo.png"></a></div>
<div style="flex-basis: 100%; height: 0px;"></div>
<div style="padding-bottom: 20px;"><a target="_blank" href="https://www.druggablegenome.net/"><img width="170px" src="images/IDG-logo.png"></a></div>
<div style="padding-bottom: 20px;"><a target="_blank" href="https://lincsproject.org/"><img width="170px" src="images/LINCS.png"></a></div>
<div style="flex-basis: 100%; height: 0px;"></div>
<div style="padding-bottom: 15px;"><a target="_blank" href="https://portal.kidsfirstdrc.org/dashboard"><img width="150px" src="images/KidsFirst.png"></a></div>
<div style="padding-bottom: 15px;"><a target="_blank" href="https://www.metabolomicsworkbench.org"><img width="170px" src="images/Metabolomics.png"></a></div>
<div style="flex-basis: 100%; height: 0px;"></div>
<div style="padding-top: 28px;"><div style="background: #2f78b7; padding: 0.5em"><a target="_blank" href="https://www.glygen.org"><img width="170px" src="images/glygen-logo.svg"></a></div></div>
<div style="padding-right: 20px;"><a target="_blank" href="http://dcic.4dnucleome.org"><img width="100px" src="images/4dn_logo.png"></a></div>
<div style="flex-basis: 100%; height: 0px;"></div>
<div style="padding-bottom: 0px; padding-left: 20px;"><a target="_blank" href="https://sparc.science"><img width="170px" src="images/SPARC-logo.png"></a></div>
<div style="padding-top: 28px;"><a target="_blank" href="https://motrpac-data.org"><img width="220px" src="images/MoTrPAC-logo.svg"></a></div>
</div>
</div>
</div>
<div class="content__col right" style="border: none;">
<div style='border: 1px solid #cccccc;'>
<div class="data_header">
<p>Highlighted videos</p>
</div>
<div class="data_content">
<div id="carouselExampleCaptions" class="carousel slide">
<ol class="carousel-indicators">
<li data-target="#carouselExampleCaptions" data-slide-to="0" class="active"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="1"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="2"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="3"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="4"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="5"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="6"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="7"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="8"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="9"></li>
<li data-target="#carouselExampleCaptions" data-slide-to="10"></li>
</ol>
<div class="carousel-inner" pause="hover">
<div class="carousel-item active">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/cWZPTjG5_Us" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>CFDE Overview</h5>
<p>Learn how the Common Fund Data Ecosystem is developing an online portal that will allow researchers to access and work across multiple NIH Common Fund program data sets within a digital cloud environment.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/aN8n2I1pROk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>Portal Overview</h5>
<p>A overview of the portal for navigation of cross-project data using a flexible metadata standard for describing experimental resources in biomedicine and related fields.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/i0qWaa8chNQ" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>Data Submission Tools and Processes</h5>
<p>This video covers the process of submitting data to the Common Fund Data Ecosystem portal.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/QST9HtwzwjE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>C2M2 Compatibility Test</h5>
<p>The CFDE C2M2 FAIR Datapackage Assessment Appyter enables DCCs to test the FAIRness of their C2M2 compatible data packages before uploading to the CFDE portal for ingestion.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/3ePYK1YvwQU" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>Content Registry and Knowledge Base</h5>
<p>The Knowledge Base in the Common Fund Data Ecosystem's search portal hosts additional information on pages.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/bNoZ47QoRWc" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>A re-usable Solution for Knowledge Management C2M2</h5>
<p>An overview of the Knowledge Management C2M2 model for finding biomedical data using the Common Fund Data Ecosystem portal.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/ijrivk3G9-Y" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>Knowledge Graph</h5>
<p>The ability to access, via a human interface or an API, a vast, semantically-coherent knowledge graph integrated from data and relationships generated from different Common Fund projects.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/3eIBdcNngrA" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>Genes and Variants</h5>
<p>Researchers can use the Gene-Centric Appyter to query a gene or variant of interest across all Common Fund Data Ecosystem groups for information returned in a summary report.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/w7IKp4wQ1VM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>Drugs and Birth Defects</h5>
<p>This video demonstrates ways for researchers to easily assemble collated and organized information on genes of interest using the ReproTox Knowledge Graph.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/Z1hybV-V6ck" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>Cancer Research</h5>
<p>This video describes a precision therapy use case focused on pediatric cancer using RNA-seq data from Kids First and GTEx.</p>
</div>
</div>
<div class="carousel-item">
<div class="d-block w-100" style="width: 480px; height: 460px; text-align: center;">
<iframe style="width:480px; height: 240px; margin: 0 auto;" src="https://www.youtube.com/embed/_6KQZ6eUHAE" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
</div>
<div class="carousel-caption d-none d-md-block">
<h5>Assessment of Genetic Variants in Human Disease</h5>
<p>This video illustrates how CFDE resources are used to analyze whole genome sequencing data for the study of regulatory non-coding variants in congenital heart disease.</p>
</div>
</div>
</div>
<a class="carousel-control-prev" href="#carouselExampleCaptions" role="button" data-slide="prev">
<span class="carousel-control-prev-icon" aria-hidden="true"></span>
<span class="sr-only">Previous</span>
</a>
<a class="carousel-control-next" href="#carouselExampleCaptions" role="button" data-slide="next">
<span class="carousel-control-next-icon" aria-hidden="true"></span>
<span class="sr-only">Next</span>
</a>
</div>
</div>
</div>
<div style='border: 1px solid #cccccc; margin-top: 1em;'>
<div class="data_header">
<p>Funding</p>
</div>
<div class="data_content">
<!--insert NIH logo-->
<a href="http://nih.gov" target="_blank"><img width="380px" src="images/nih.png" title="NIH"></a>
</div>
</div>
</div>
</div>
</div>
</main>
<div id="export-modal" class="modal">
<div class="modal-dialog modal-dialog-centered">
<div class="modal-content">
<div class="modal-header">
<h5>Choose how you wish to export this chart</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<div class="row justify-content-center export-row">
<button id="export-png" type="button" class="btn btn-primary">Export as PNG</button>
</div>
<div class="row justify-content-center export-row">
<button id="export-svg" type="button" class="btn btn-primary">Export as SVG</button>
</div>
<div class="row justify-content-center export-row">
<button id="export-csv" type="button" class="btn btn-primary">Export data as CSV</button>
</div>
</div>
</div>
</div>
</div>
<footer><!-- Footer text/content --></footer>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-LNZN3CXFQK"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-LNZN3CXFQK');
</script>
<script src="js/components/jquery-3.5.1.min.js?ts=1616433204"></script>
<script src="js/components/bootstrap-4.5.0.min.js?ts=1616433204"></script>
<script src="js/components/d3-5.16.0.min.js?ts=1616433204"></script>
<script src="js/components/saveSvgAsPng.js?ts=1604093612"></script>
<script src="js/components/d3-save-svg.min.js?ts=1604093612"></script>
<script src="js/stacked-bar-graph.js?ts=1676582078"></script>
<script src="js/lz-string.min.js?ts=1607186913"></script>
<script src="js/config.js?ts=1619458908"></script>
<script src="js/index.js?ts=1676582078"></script>
</body>
</html>