-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy path4_unique_identifiers.html
568 lines (506 loc) · 28.4 KB
/
4_unique_identifiers.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
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<title>Unique Identifiers in an Online Permit and Monitoring System to support the Nagoya Protocol</title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/flatly.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
a.sourceLine { display: inline-block; line-height: 1.25; }
a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
a.sourceLine:empty { height: 1.2em; position: absolute; }
.sourceCode { overflow: visible; }
code.sourceCode { white-space: pre; position: relative; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
code.sourceCode { white-space: pre-wrap; }
a.sourceLine { text-indent: -1em; padding-left: 1em; }
}
pre.numberSource a.sourceLine
{ position: relative; }
pre.numberSource a.sourceLine:empty
{ position: absolute; }
pre.numberSource a.sourceLine::before
{ content: attr(data-line-number);
position: absolute; left: -5em; text-align: right; vertical-align: baseline;
border: none; pointer-events: all;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
a.sourceLine::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
</head>
<body>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 60px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 65px;
margin-top: -65px;
}
.section h2 {
padding-top: 65px;
margin-top: -65px;
}
.section h3 {
padding-top: 65px;
margin-top: -65px;
}
.section h4 {
padding-top: 65px;
margin-top: -65px;
}
.section h5 {
padding-top: 65px;
margin-top: -65px;
}
.section h6 {
padding-top: 65px;
margin-top: -65px;
}
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<div class="container-fluid main-container">
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
});
});
</script>
<!-- code folding -->
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html"></a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">About</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
The Model
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="executive_summary.html">Executive Summary</a>
</li>
<li>
<a href="1_background.html">Background</a>
</li>
<li>
<a href="2_the_model.html">The Model</a>
</li>
<li>
<a href="3_principles.html">Core Principles</a>
</li>
<li>
<a href="4_unique_identifiers.html">Unique Identifiers</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Planning
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="5_workplan.html">Draft Workplan</a>
</li>
<li>
<a href="annex.html">Annex</a>
</li>
</ul>
</li>
<li>
<a href="presentations/schematics/index.html">Schematics</a>
</li>
<li>
<a href="resources.html">Publications</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Resources for Developers
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="kenya.html">Kenya Prototype</a>
</li>
<li>
<a href="researcher_identifiers.html">Researcher Identifiers</a>
</li>
<li>
<a href="literature.html">Scientific Literature</a>
</li>
<li>
<a href="geographic.html">Geographic</a>
</li>
<li>
<a href="patent.html">Patent Data</a>
</li>
<li>
<a href="taxonomy.html">Taxonomy</a>
</li>
<li>
<a href="taxonomic_dashboards.html">Taxonomic Dashboards</a>
</li>
<li>
<a href="mdm.html">Master Data Management</a>
</li>
<li>
<a href="dictionary.html">Data Dictionary</a>
</li>
</ul>
</li>
<li>
<a href="https://poldham.github.io/abs/index.html">ABS Monitoring Handbook</a>
</li>
<li>
<a href="https://www.pauloldham.net/">The Blog</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">Unique Identifiers in an Online Permit and Monitoring System to support the Nagoya Protocol</h1>
</div>
<p>##Introduction</p>
<p>This section discusses the use of unique identifiers for permits and related documents and the application of the principle of triple redundancy.<a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a></p>
<p>Unique identifiers associated with permits and associated documents will allow for sets of documents linked to a specific application to be stored within a retrievable register or file history. As such, unique identifiers will enable internal coherence within the permit system.</p>
<p>Unique identifiers linked to a permit and corresponding MAT (an ABS contract) are also the key to monitoring the outcomes of research and the genetic resources. We propose a system consisting of the following unique identifiers:</p>
<ol style="list-style-type: decimal">
<li>Country Codes, dates and unique numbers (e.g. BS20151234).</li>
<li>Bar codes.</li>
<li>QR Codes (Quick Response codes).</li>
<li>Html embed codes.</li>
</ol>
<p>In proposing the use of unique identifiers we also suggest the application of the principle of triple redundancy, notably in labelling. The principle of triple redundancy is a well established engineering principle that involves three different systems performing the same function. In the event that one system fails a second system takes over the same function. If the second system fails then the third system takes over. Given that the failure of all three systems is unlikely the function of a particular system within a wider system is maintained. It is important to note that triple redundancy does not guarantee that a system will not fail completely, rather it reduces the likelihood of failure.</p>
<p>The principle of triple redundancy is particularly relevant to an online permit and monitoring system in connection with the use of unique identifiers to maintain the link between a permit, mutually agreed terms and samples of biological material that are subsequently deposited with a collection, transferred to a collection in a third country and potentially utilized by third parties.</p>
<p>The problem that triple redundancy helps to address is in ensuring the maintenance of the connection between a permit and a document containing MAT (an ABS contract) and the materials that are collected and transferred. These materials may be either physical or electronic (e.g. DNA and amino acid sequence data). The scope of genetic resources is likely to be defined in domestic ABS legislation.</p>
<div id="country-code-identifiers" class="section level3">
<h3>Country Code Identifiers</h3>
<p>All countries possess a unique two letter country code defined in international standard ISO3166-1 alpha 2 (e.g. see <a href="https://en.wikipedia.org/wiki/ISO_3166-1">this Wikipedia entry</a> and the <a href="https://www.iso.org/obp/ui/#search">ISO browsing platform</a> and select Country codes and search).</p>
<p>For example, the standard two letter country code for the Bahamas is BS, Kenya is KE, Uganda is UG and South Africa is ZA. If these country codes are combined with a date (YYYYMMDD) and a unique number (1234) a unique identifier will be generated. In this case we will simply use the year (YYYY) to generate the following identifiers.</p>
<ul>
<li>BS20151234</li>
<li>KE20151234</li>
<li>UG20151234</li>
<li>ZA20151234</li>
</ul>
<p>What is clear from this is that a single and distinctive unique identifier (country - year - number) has been created for each permit and corresponding MAT that is immediately distinguishable using the country code from similar numbers issued by other authorities. The combination of the country code, the date and a numeric identifier (country - YYYMMDD - number) is already used very successfully to keep track of approximately 90 million patent documents in countries around the world and is recommended. The example below is for a patent application from the United States that makes reference to collections from the Bahamas and can be viewed on the main worldwide patent database <a href="http://worldwide.espacenet.com/publicationDetails/biblio;jsessionid=J6iiTFoqvaPnW3CcNQbj9A-N.espacenet_levelx_prod_0?FT=D&date=20011206&DB=EPODOC&locale=en_EP&CC=US&NR=2001049387A1&KC=A1&ND=4">espacenet</a> operated by the European Patent Office <a href="http://worldwide.espacenet.com/publicationDetails/biblio;jsessionid=J6iiTFoqvaPnW3CcNQbj9A-N.espacenet_levelx_prod_0?FT=D&date=20011206&DB=EPODOC&locale=en_EP&CC=US&NR=2001049387A1&KC=A1&ND=4">here</a>.</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_Espacenet1.png" /></p>
<p>In this example we can see that the unique document identifier US2001049387A1 consists of the following [US] – the country code – [2001] the year of application – [049387] – the unique numeric identifier, and [A1] known as the “kind code” for the type of document (in this case a patent application).</p>
<p>The strength of this system is that the components combine into a unique identifier that is:</p>
<ol style="list-style-type: lower-alpha">
<li>distinctive, and;</li>
<li>easy to retrieve.</li>
</ol>
<p>The relevance of this type of numbering system becomes apparent when we consider the section of this patent application that makes reference to biological collections in a country. In this case the example is from the Bahamas (See the first paragraph highlighted or read directly <a href="http://worldwide.espacenet.com/publicationDetails/description;jsessionid=J6iiTFoqvaPnW3CcNQbj9A-N.espacenet_levelx_prod_0?CC=US&NR=2001049387A1&KC=A1&FT=D&ND=3&date=20011206&DB=EPODOC&locale=en_EP">here</a>).</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_Espacenet_specimen.png" /></p>
<p>In this case, the applicants make reference to a sponge specimen 23-XI-98-3-002 and a HBOI CatNo. 003:00973. Under the proposal advanced in this document the ABS domestic legislation, permit and associated MAT could require recipients of a permit to disclose the permit number (e.g. BS20151234) in the description section of any patent application arising from the research.<a href="#fn2" class="footnote-ref" id="fnref2"><sup>2</sup></a>.</p>
</div>
<div id="unique-identifiers-and-registers" class="section level2">
<h2>Unique Identifiers and Registers</h2>
<p>An important feature of this system as deployed within patent databases is that the unique identifier is used to store all documents that relate to a particular application over time. In this case the United States application was also filed in Europe at the European Patent Office and this document can be identified in the <a href="http://worldwide.espacenet.com/publicationDetails/inpadocPatentFamily;jsessionid=J6iiTFoqvaPnW3CcNQbj9A-N.espacenet_levelx_prod_0?CC=US&NR=2001049387A1&KC=A1&FT=D&ND=3&date=20011206&DB=EPODOC&locale=en_EP">patent family</a> of the US document. European Patent Application <a href="http://worldwide.espacenet.com/publicationDetails/biblio?DB=EPODOC&II=6&ND=4&adjacent=true&locale=en_EP&FT=D&date=20021127&CC=EP&NR=1259502A2&KC=A2">EP1259502A2</a> was filed prior to the introduction of the year into the identifier. However, for our purposes the document is important because in Europe it is possible to access all documents linked to that application, including formal communications between the patent office and applicants in the <a href="https://register.epo.org/application?number=EP01920158&tab=main">European Patent Register</a>. The figure below displays the list of documents linked to this identifier and can be accessed <a href="https://register.epo.org/application?number=EP01920158&lng=en&tab=doclist">here</a>.</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_espacenet_register.png" /></p>
<p>It is immediately clear that the use of this unique identifier system allows all documents related to that identifier to be linked together into an electronic register (file history) for each application. We propose a very similar system where a unique identifier is used to link all documents arising from a permit application both internally within the system and for samples, publications and patent applications arising from the research. Specifically, the use of the unique identifier in labels for samples and specimens would facilitate the monitoring of compliance by users.</p>
<p>This type of unique identifier is simple, easy to use and robust over time. For that reason it is recommended as the first component of a triple system.</p>
<div id="simple-barcodes" class="section level3">
<h3>Simple Barcodes</h3>
<p>A second system is the standard bar code which can be optically scanned to reveal basic information. The bar code system was developed in the 1960s and became ubiquitous for tracking and scanning products from the 1970s onwards. A range of bar code types are available along with free bar code generators. A simple example using a free tool is provided below. This bar code could be attached to documents and samples with basic information that could be encoded into the bar code. The advantage of a simple bar code is that it can be scanned by a machine.</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_barcode.gif" /></p>
</div>
<div id="quick-response-codes-qr-codes" class="section level3">
<h3>Quick Response Codes (QR Codes)</h3>
<p>The third system is QR (Quick Response) codes which provide a much greater level of embedded detail than bar codes and can be used to embed geographic and other information. An example is provided below.</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_QR_code.gif" /></p>
<p>The information in this QR code can be read using free software on a smart phone such as an iPhone, Android phone, or tablet, as can be seen in the image below (using QRReader on the iPhone). QR codes are normally open. However, encryption of data may potentially be desirable so that only authorised users (police, customs, port authorities) can scan the contents.</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_qr_results.png" /></p>
<p>The combination of the three systems would meet the requirement for triple redundancy. The main issue is not likely to be the means to generate the identifiers and codes but with ensuring that both authorities and applicants consistently use the identifiers and codes in documentation (including sample documentation) linked to a permit and associated MAT.</p>
<p>Finally, the use of identifiers is likely to be desirable in cases where ABS domestic frameworks include DNA and amino acid sequence data arising from research under a permit and associated MAT. This requires further exploration but is briefly considered below.</p>
</div>
</div>
<div id="dna-and-amino-acid-sequences" class="section level2">
<h2>DNA and Amino Acid Sequences</h2>
<p>Additional options include a requirement to use the basic unique identifier (BS20151234) in the documentation entered into databases for DNA and amino acid sequence data or html embed codes (for web publications).</p>
<p>In the case of DNA data an example of the existing use of identifiers, and the ability to monitor DNA sequence and amino acid information is provided by the <a href="http://www.boldsystems.org">Barcode of Life Database (BOLD)</a>.</p>
<p>Information using species names or identifiers can be retrieved using the <code>taxize</code> package in R using <a href="https://www.rstudio.com">RStudio</a> which generates the following link for a search for a species name.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(taxize) <span class="co"># load the taxize package</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw">get_boldid</span>(<span class="dt">searchterm =</span> <span class="st">"Prunus africana"</span>) <span class="co"># search for the dna barcode id for a species</span></a></code></pre></div>
<pre><code>##
## Retrieving data for taxon 'Prunus africana'</code></pre>
<pre><code>## [1] "191949"
## attr(,"class")
## [1] "boldid"
## attr(,"match")
## [1] "found"
## attr(,"multiple_matches")
## [1] FALSE
## attr(,"pattern_match")
## [1] FALSE
## attr(,"uri")
## [1] "http://boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=191949"</code></pre>
<p>More information from the URL can then be accessed in R as a data table or through the BOLD website. On the BOLD website this produces a list of sequence related records. The image below is viewable <a href="http://boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=191949">here</a>.</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_bold_1.png" /></p>
<p>Selecting <code>Access Published & Released Data</code> produces the following list of <a href="http://boldsystems.org/index.php/Public_SearchTerms?query=%22Prunus%20africana%22%5Btax%5D">records</a>.</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_bold_2.png" /></p>
<p>The final record in this list includes a specimen image and the <a href="http://boldsystems.org/index.php/Public_RecordView?processid=KNPA139-08">following information</a>.</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_bold_3.png" /></p>
<p>A significant amount of information is contained in this record, including the record number, sample ID, Museum ID, where the specimen is located along with where the material was collected, by whom, along with the sequence listing. A link is also provided to the Sequence ID and <a href="http://www.ncbi.nlm.nih.gov/nuccore/JQ024985">GenBank Accession number</a> as seen below.</p>
<p><img src="/Users/pauloldham17inch/Desktop/Permit%20System/abs_permits/images/figx_bold_genbank_3.png" /></p>
<p>As this demonstrates, it is increasingly possible to rapidly access sequence and associated record information for a particular species or list of species. Given the presence of multiple ID fields it appears reasonable to assume that the simple permit identifier (e.g. BS21051234) in sequence records arising from research could be included in the conditions of the permit and associated MAT. This could readily lead to the creation of an archive of electronic records for biodiversity in a country that contain known sequence data. Uses of such sequences could then become amenable to monitoring using the relevant IDs or sequence searching for identical or similar sequences using BLAST (Basic Local Alignment Search Tool) and associated tools.</p>
<div id="conclusion" class="section level3">
<h3>Conclusion</h3>
<p>In this section we have discussed the use of unique identifiers and the application of the principle of triple redundancy as part of the design of the online permit and monitoring system. Unique identifiers using standardised country codes, dates and sequences of numbers allow for the construction of an internal permit system that establishes and maintains links between a permit application and associated documents (MAT) and communications. This system already works well for millions of patent documents. The principle of triple redundancy was then applied to the generation of labels containing identifiers that could be used to maintain links between the original permit and samples, publications, patent applications, and sequence data originating from the grant of a permit under an ABS framework. The use of free tools (such as <code>taxize</code> in R) allows this information to be readily retrieved from a range of different data sources. While requiring further elaboration, the use of unique identifiers combined with the principle of triple redundancy provides a route to cost effective monitoring and is recommended.</p>
</div>
</div>
<div class="footnotes">
<hr />
<ol>
<li id="fn1"><p>The research in this paper was conducted with the support of <a href="http://www.best.gov.bs">The Bahamas Environment, Science & Technology Commission (BEST)</a> of the Government of the Bahamas under the UNEP/GEF project “Strengthening Access and Benefit Sharing (ABS) in the Bahamas” as set out in <em>Oldham, P (2015) Concepts for an Electronic Monitoring Tool. UNEP/GEF project “Strengthening Access and Benefit Sharing (ABS) in the Bahamas”</em>. The present paper was written with the additional support of <a href="http://www.abs-initiative.info">The ABS Capacity Development Initiative</a> through the <a href="https://www.giz.de/en/html/index.html">Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ)</a>. The views expressed are solely those of the authors and should not be interpreted as reflecting the views of the Government of the Bahamas, the ABS Initiative or GIZ.<a href="#fnref1" class="footnote-back">↩</a></p></li>
<li id="fn2"><p>See Oldham and Burton (2010) Defusing Disclosure in Patent Applications, <a href="https://www.cbd.int/doc/meetings/cop/cop-10/information/cop-10-inf-44-en.pdf">UNEP/CBD/COP/10/INF/44</a> and Oldham, Hall and Forero (2013) <a href="http://dx.doi.org/10.1371/journal.pone.0078737">Biological Diversity in the Patent System. PLOS ONE</a>)<a href="#fnref2" class="footnote-back">↩</a></p></li>
</ol>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>