-
Notifications
You must be signed in to change notification settings - Fork 5
Expand file tree
/
Copy pathbiology_sampledfeature_extension.html
More file actions
821 lines (803 loc) · 52.9 KB
/
biology_sampledfeature_extension.html
File metadata and controls
821 lines (803 loc) · 52.9 KB
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
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.3.450">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<title>biology_sampledfeature_extension</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
</style>
<script src="biology_sampledfeature_extension_files/libs/clipboard/clipboard.min.js"></script>
<script src="biology_sampledfeature_extension_files/libs/quarto-html/quarto.js"></script>
<script src="biology_sampledfeature_extension_files/libs/quarto-html/popper.min.js"></script>
<script src="biology_sampledfeature_extension_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="biology_sampledfeature_extension_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="biology_sampledfeature_extension_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="biology_sampledfeature_extension_files/libs/bootstrap/bootstrap.min.js"></script>
<link href="biology_sampledfeature_extension_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="biology_sampledfeature_extension_files/libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
</head>
<body>
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#concept-scheme-biology-extension-basic-taxon-classes-for-biological-entity" id="toc-concept-scheme-biology-extension-basic-taxon-classes-for-biological-entity" class="nav-link active" data-scroll-target="#concept-scheme-biology-extension-basic-taxon-classes-for-biological-entity"><span class="header-section-number">1</span> <strong>Concept scheme:</strong> Biology Extension: Basic taxon classes for biological entity</a>
<ul>
<li><a href="#biological-entity" id="toc-biological-entity" class="nav-link" data-scroll-target="#biological-entity"><span class="header-section-number">1.1</span> Biological entity</a>
<ul class="collapse">
<li><a href="#eukaryote" id="toc-eukaryote" class="nav-link" data-scroll-target="#eukaryote"><span class="header-section-number">1.1.1</span> Eukaryote</a>
<ul class="collapse">
<li><a href="#algae" id="toc-algae" class="nav-link" data-scroll-target="#algae"><span class="header-section-number">1.1.1.1</span> Algae</a></li>
<li><a href="#animalia" id="toc-animalia" class="nav-link" data-scroll-target="#animalia"><span class="header-section-number">1.1.1.2</span> Animalia</a></li>
<li><a href="#chromista" id="toc-chromista" class="nav-link" data-scroll-target="#chromista"><span class="header-section-number">1.1.1.3</span> Chromista</a></li>
<li><a href="#eukaryotic-microorganism" id="toc-eukaryotic-microorganism" class="nav-link" data-scroll-target="#eukaryotic-microorganism"><span class="header-section-number">1.1.1.4</span> Eukaryotic microorganism</a></li>
<li><a href="#fungi" id="toc-fungi" class="nav-link" data-scroll-target="#fungi"><span class="header-section-number">1.1.1.5</span> Fungi</a></li>
<li><a href="#plantae" id="toc-plantae" class="nav-link" data-scroll-target="#plantae"><span class="header-section-number">1.1.1.6</span> Plantae</a></li>
<li><a href="#protozoa" id="toc-protozoa" class="nav-link" data-scroll-target="#protozoa"><span class="header-section-number">1.1.1.7</span> Protozoa</a></li>
</ul></li>
<li><a href="#lichen" id="toc-lichen" class="nav-link" data-scroll-target="#lichen"><span class="header-section-number">1.1.2</span> Lichen</a></li>
<li><a href="#plasmid" id="toc-plasmid" class="nav-link" data-scroll-target="#plasmid"><span class="header-section-number">1.1.3</span> Plasmid</a></li>
<li><a href="#prokaryote" id="toc-prokaryote" class="nav-link" data-scroll-target="#prokaryote"><span class="header-section-number">1.1.4</span> Prokaryote</a>
<ul class="collapse">
<li><a href="#archaea" id="toc-archaea" class="nav-link" data-scroll-target="#archaea"><span class="header-section-number">1.1.4.1</span> Archaea</a></li>
<li><a href="#bacteria" id="toc-bacteria" class="nav-link" data-scroll-target="#bacteria"><span class="header-section-number">1.1.4.2</span> Bacteria</a></li>
</ul></li>
<li><a href="#virus" id="toc-virus" class="nav-link" data-scroll-target="#virus"><span class="header-section-number">1.1.5</span> Virus</a>
<ul class="collapse">
<li><a href="#other-virus" id="toc-other-virus" class="nav-link" data-scroll-target="#other-virus"><span class="header-section-number">1.1.5.1</span> Other Virus</a></li>
<li><a href="#phage" id="toc-phage" class="nav-link" data-scroll-target="#phage"><span class="header-section-number">1.1.5.2</span> Phage</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</nav>
</div>
<main class="content" id="quarto-document-content">
<p><span id="BiologyExtension:Basictaxonclassesforbiologicalentity"></span></p>
<section id="concept-scheme-biology-extension-basic-taxon-classes-for-biological-entity" class="level1" data-number="1">
<h1 data-number="1"><span class="header-section-number">1</span> <strong>Concept scheme:</strong> Biology Extension: Basic taxon classes for biological entity</h1>
<p>Vocabulary last modified: 2024-01-19</p>
<p>subtitle: This is a vocabulary to categorize sampled organisms (whole or part) according to taxonomic classes. Classes are based largely on taxonomy found in Wikipedia, particularly Whittaker’s five kingdom system (1969) (https://en.wikipedia.org/wiki/Kingdom_(biology), https://doi.org/10.1126%2Fscience.163.3863.150). The intended use is in iSamples cross domain categorization of material samples, recognizing that there are multiple view for taxonomy and cladistics for the tree of life. This is a high level view intended for cross domain purposes, not expert analysis. Other extension vocabularies should be used for other taxonomic schemes</p>
<p>Namespace: <a href="https://w3id.org/isample/biology/biosampledfeature/1.1/biologicentityvocabulary"><code>https://w3id.org/isample/biology/biosampledfeature/1.1/biologicentityvocabulary</code></a></p>
<p><strong>History</strong></p>
<ul>
<li><p>2024-01-19 SMR add cross reference to GBIF taxonomy backbone where mapping was apparent.</p></li>
<li><p>2024-04-12 SMR. Import of GEOME records show that many samples are classified as Kingdom Chromista, but this is missing from this vocabulary extension (https://github.com/isamplesorg/vocabularies/issues/17). Hierarchy and classes reviewed; deprecate Protista and make it an alternate name in Eukaryotic microorganism class and update definition; add Chromista; update scope notes for Eukaryote. Harmonize better with GBIF tree of life: Make Mycetozoa subclass of Protozoa, not subclass of Amoebozoa, add Other Protozoa class for logical completeness. increment version to 1.1; these are not breaking changes, but addition of new class and hierarchy adjustments in protozoa are more than incremental.</p></li>
<li><p>Based on draft DiSSCo specimen & collection classification, table 2, https://docs.google.com/document/d/19OPyOm9VF2qfI3M6RmJPvRfo8JlZ3tt0II05aGCyBHQ/ , with added classes to attempt a logical hierarchy.</p></li>
<li><p><a href="#biologicalentity">Biological entity</a></p>
<ul>
<li><a href="#eukaryote">Eukaryote</a>
<ul>
<li><a href="#algae">Algae</a></li>
<li><a href="#animalia">Animalia</a>
<ul>
<li><a href="#arthropod">Arthropod</a>
<ul>
<li><a href="#arachnid">Arachnid</a></li>
<li><a href="#crustacea">Crustaceans</a></li>
<li><a href="#hexapoda">Insect</a></li>
<li><a href="#myriapod">Myriapod</a></li>
<li><a href="#otherarthropod">Other arthropod</a></li>
</ul></li>
<li><a href="#mollusca">Mollusca</a></li>
<li><a href="#otherinvertebrate">Other invertebrate</a></li>
<li><a href="#porifera">Porifera</a></li>
<li><a href="#vertebrate">Vertebrate</a>
<ul>
<li><a href="#amphibian">Amphibian</a></li>
<li><a href="#bird">Bird</a></li>
<li><a href="#fish">Fish</a></li>
<li><a href="#mammal">Mammal</a></li>
<li><a href="#reptile">Reptile</a></li>
</ul></li>
</ul></li>
<li><a href="#chromista">Chromista</a></li>
<li><a href="#eukaryoticmicroorganism">Eukaryotic microorganism</a></li>
<li><a href="#fungi">Fungi</a>
<ul>
<li><a href="#macrofungi">Macrofungi</a></li>
<li><a href="#microfungi">Microfungi</a></li>
</ul></li>
<li><a href="#plantae">Plantae</a>
<ul>
<li><a href="#nonvascularplant">Non-vascular plant</a></li>
<li><a href="#otherplant">Other plant</a></li>
<li><a href="#vascularseedplant">Vascular seed plant</a></li>
<li><a href="#vascularsportplant">Vascular spore plant</a></li>
</ul></li>
<li><a href="#protozoa">Protozoa</a>
<ul>
<li><a href="#amoebozoa">Amoebozoa</a></li>
<li><a href="#mycetozoa">Mycetozoa</a></li>
<li><a href="#otherprotozoa">Other Protozoa</a></li>
</ul></li>
</ul></li>
<li><a href="#lichen">Lichen</a></li>
<li><a href="#plasmid">Plasmid</a></li>
<li><a href="#prokaryote">Prokaryote</a>
<ul>
<li><a href="#archaea">Archaea</a></li>
<li><a href="#bacteria">Bacteria</a></li>
</ul></li>
<li><a href="#virus">Virus</a>
<ul>
<li><a href="#othervirus">Other Virus</a></li>
<li><a href="#phage">Phage</a></li>
</ul></li>
</ul></li>
</ul>
<p><strong>Concepts</strong></p>
<p><span id="biologicalentity"></span></p>
<section id="biological-entity" class="level2" data-number="1.1">
<h2 data-number="1.1" data-anchor-id="biological-entity"><span class="header-section-number">1.1</span> Biological entity</h2>
<ul>
<li>Sampled feature is an organism. Use for samples that represent some species of organism as the proximate sampled feature for which the focus is not the environment that the organism inhabits.</li>
<li>Concept URI token: biologicalentity</li>
</ul>
<p><span id="eukaryote"></span></p>
<section id="eukaryote" class="level3" data-number="1.1.1">
<h3 data-number="1.1.1" data-anchor-id="eukaryote"><span class="header-section-number">1.1.1</span> Eukaryote</h3>
<ul>
<li><p>Child of: <a href="#biologicalentity"><code>biologicalentity</code></a></p></li>
<li><p>Organism whose cells have a nucleus. Includes all animals, plants, fungi, and many unicellular organisms (https://en.wikipedia.org/wiki/Eukaryote). Eucaryote membranes are flexible, and contain cholesterol. The membrane, nucleus, and structures are supported by cross-connecting protein filaments. Cells are ~10 times larger in radius relative to prokaryotes. Cells have several types of internal enclosed compartments. Cell walls, if present, are made from cellulose or chitin, in contrast to prokaryotes. Eukaryotes have novel modes of direct body movement and swimming, based on sensors, and the mode of reproduction uses sexual combination. Their DNA is linear but wound up into nucleosomes and then chromosomes. (https://doi.org/10.1016/B978-044452115-6/50050-6, table 7-2). Eukaryotes can be considered a chimera; a combination of archaeal and bacterial features that result in the cellular complexity and distinctive characteristics. (https://doi.org/10.1016/j.tim.2021.11.003).</p></li>
<li><p>Concept URI token: eukaryote</p></li>
</ul>
<p><span id="algae"></span></p>
<section id="algae" class="level4" data-number="1.1.1.1">
<h4 data-number="1.1.1.1" data-anchor-id="algae"><span class="header-section-number">1.1.1.1</span> Algae</h4>
<ul>
<li><p>Child of: <a href="#eukaryote"><code>eukaryote</code></a></p></li>
<li><p>Informal term for a large and diverse group of photosynthetic eukaryotic organisms. Included organisms range from unicellular microalgae, such as Chlorella, Prototheca and the diatoms, to multicellular forms, such as the giant kelp, a large brown alga which may grow up to 50 metres (160 ft) in length. Most are aquatic and autotrophic (they generate food internally) and lack many of the distinct cell and tissue types, such as stomata, xylem and phloem that are found in land plants. Includes red algae (Rhodophycophyta), brown algae (Phaeophycophyta), and green algae (Chlorophyta). https://en.wikipedia.org/wiki/Algae</p></li>
<li><p>Concept URI token: algae</p></li>
</ul>
<p><span id="animalia"></span></p>
</section>
<section id="animalia" class="level4" data-number="1.1.1.2">
<h4 data-number="1.1.1.2" data-anchor-id="animalia"><span class="header-section-number">1.1.1.2</span> Animalia</h4>
<ul>
<li><p>Child of: <a href="#eukaryote"><code>eukaryote</code></a></p></li>
<li><p>Animals are distinguished from other eukaryotes based on several key characteristics, including: 1) animals are multicellular organisms 2) Animals are heterotrophic, they obtain their food by consuming other organisms or organic matter; 3) Animals lack cell walls; 4) Many animals have a nervous system; 5) Most animals reproduce sexually (Chat GPT)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/1"><https://www.gbif.org/species/1></a></p></li>
<li><p>Concept URI token: animalia</p></li>
</ul>
<p><span id="arthropod"></span></p>
<section id="arthropod" class="level5" data-number="1.1.1.2.1">
<h5 data-number="1.1.1.2.1" data-anchor-id="arthropod"><span class="header-section-number">1.1.1.2.1</span> Arthropod</h5>
<ul>
<li><p>Child of: <a href="#animalia"><code>animalia</code></a></p></li>
<li><p>invertebrate animals with an exoskeleton, a segmented body, and paired jointed appendages. Arthropods form the phylum Arthropoda. They are distinguished by their jointed limbs and cuticle made of chitin, often mineralised with calcium carbonate. The arthropod body plan consists of segments, each with a pair of appendages. Arthropods are bilaterally symmetrical and their body possesses an external skeleton. (https://en.wikipedia.org/wiki/Arthropod)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/54"><https://www.gbif.org/species/54></a></p></li>
<li><p>Concept URI token: arthropod</p></li>
</ul>
<p><span id="arachnid"></span></p>
<section id="arachnid" class="level6" data-number="1.1.1.2.1.1">
<h6 data-number="1.1.1.2.1.1" data-anchor-id="arachnid"><span class="header-section-number">1.1.1.2.1.1</span> Arachnid</h6>
<ul>
<li><p>Child of: <a href="#arthropod"><code>arthropod</code></a></p></li>
<li><p>a group of arthropods that share several key characteristics, including two main body segments, four pairs of legs, lack of antennae, simple eyes, and specialized feeding and defense structures called chelicerae (ChatGPT)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://en.wikipedia.org/wiki/Arachnid"><https://en.wikipedia.org/wiki/Arachnid></a></p></li>
<li><p><a href="https://www.gbif.org/species/367"><https://www.gbif.org/species/367></a></p></li>
<li><p>Concept URI token: arachnid</p></li>
</ul>
<p><span id="crustacea"></span></p>
</section>
<section id="crustaceans" class="level6" data-number="1.1.1.2.1.2">
<h6 data-number="1.1.1.2.1.2" data-anchor-id="crustaceans"><span class="header-section-number">1.1.1.2.1.2</span> Crustaceans</h6>
<ul>
<li><p>Child of: <a href="#arthropod"><code>arthropod</code></a></p></li>
<li><p>arthropod taxon which includes such animals as decapods, seed shrimp, branchiopods, fish lice, krill, remipedes, isopods, barnacles, copepods, amphipods and mantis shrimp. crustaceans have an exoskeleton, which they moult to grow. They are distinguished from other groups of arthropods, such as insects, myriapods and chelicerates, by the possession of biramous (two-parted) limbs, and by their larval forms, such as the nauplius stage of branchiopods and copepods. (https://en.wikipedia.org/wiki/Crustacean)</p></li>
<li><p>Concept URI token: crustacea</p></li>
</ul>
<p><span id="hexapoda"></span></p>
</section>
<section id="insect" class="level6" data-number="1.1.1.2.1.3">
<h6 data-number="1.1.1.2.1.3" data-anchor-id="insect"><span class="header-section-number">1.1.1.2.1.3</span> Insect</h6>
<ul>
<li><p>Child of: <a href="#arthropod"><code>arthropod</code></a></p></li>
<li><p>Include all hexapoda here; Insects are a group of hexapod arthropods characterized by having three main body segments (head, thorax, and abdomen), six legs, and wings in many species. All other hexapod arthropods, such as springtails and diplurans, are not classified as insects, but they share the same body plan of three main body segments and six legs. However, they lack wings and other features that are unique to insects. Therefore, all insects are hexapods, but not all hexapods are insects. (ChatGPT)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/174780701"><https://www.gbif.org/species/174780701></a></p></li>
<li><p><strong>Alternate labels:</strong> Hexapoda</p></li>
<li><p>Concept URI token: hexapoda</p></li>
</ul>
<p><span id="myriapod"></span></p>
</section>
<section id="myriapod" class="level6" data-number="1.1.1.2.1.4">
<h6 data-number="1.1.1.2.1.4" data-anchor-id="myriapod"><span class="header-section-number">1.1.1.2.1.4</span> Myriapod</h6>
<ul>
<li><p>Child of: <a href="#arthropod"><code>arthropod</code></a></p></li>
<li><p>Arthropods such as millipedes and centipedes. (https://en.wikipedia.org/wiki/Myriapoda). A group of arthropods that have long, segmented body with numerous pairs of legs, simple eyes, specialized mouthparts, and a primarily terrestrial habitat, which distinguishes them from other arthropod groups such as insects and crustaceans. (ChatGPT)</p></li>
<li><p>Concept URI token: myriapod</p></li>
</ul>
<p><span id="otherarthropod"></span></p>
</section>
<section id="other-arthropod" class="level6" data-number="1.1.1.2.1.5">
<h6 data-number="1.1.1.2.1.5" data-anchor-id="other-arthropod"><span class="header-section-number">1.1.1.2.1.5</span> Other arthropod</h6>
<ul>
<li><p>Child of: <a href="#arthropod"><code>arthropod</code></a></p></li>
<li><p>includes Chelicerata (horseshoe crabs, scorpions, and sea spiders), Trilobitomorpha ( extinct trilobites), and Pentastomida (parasitic arthropods that infect the respiratory systems of reptiles and mammals). (ChatGPT)</p></li>
<li><p>Concept URI token: otherarthropod</p></li>
</ul>
<p><span id="mollusca"></span></p>
</section>
</section>
<section id="mollusca" class="level5" data-number="1.1.1.2.2">
<h5 data-number="1.1.1.2.2" data-anchor-id="mollusca"><span class="header-section-number">1.1.1.2.2</span> Mollusca</h5>
<ul>
<li><p>Child of: <a href="#animalia"><code>animalia</code></a></p></li>
<li><p>animals that have a soft body with a mantle, a radula (ribbon-like structure covered in tiny teeth that is used to scrape food), a muscular foot, an open circulatory system, and a visceral mass that contains the internal organs, including the digestive, excretory, and reproductive systems. (ChatGPT)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/52"><https://www.gbif.org/species/52></a></p></li>
<li><p><strong>Alternate labels:</strong> bivalves, cephalopods, gastropods,</p></li>
<li><p>Concept URI token: mollusca</p></li>
</ul>
<p><span id="otherinvertebrate"></span></p>
</section>
<section id="other-invertebrate" class="level5" data-number="1.1.1.2.3">
<h5 data-number="1.1.1.2.3" data-anchor-id="other-invertebrate"><span class="header-section-number">1.1.1.2.3</span> Other invertebrate</h5>
<ul>
<li><p>Child of: <a href="#animalia"><code>animalia</code></a></p></li>
<li><p>Includes Cnidaria (jellyfish, coral, anemones), Echinodermata (starfish, sea urchins, sea cucumbers), Nematoda (roundworms), Platyhelminthes (flatworms), Annelida (segmented worms), Ctenophora (comb jellies), Brachiopoda (lamp shells), Bryozoa (moss animals), Chaetognatha (arrow worms), Hemichordata (acorn worms), Xenacoelomorpha (simple-bodied worms) (ChatGPT)</p></li>
<li><p>Concept URI token: otherinvertebrate</p></li>
</ul>
<p><span id="porifera"></span></p>
</section>
<section id="porifera" class="level5" data-number="1.1.1.2.4">
<h5 data-number="1.1.1.2.4" data-anchor-id="porifera"><span class="header-section-number">1.1.1.2.4</span> Porifera</h5>
<ul>
<li><p>Child of: <a href="#animalia"><code>animalia</code></a></p></li>
<li><p>multicellular animals that have bodies full of pores and channels allowing water to circulate through them, consisting of jelly-like mesohyl sandwiched between two thin layers of cells. (https://en.wikipedia.org/wiki/Sponge)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/105"><https://www.gbif.org/species/105></a></p></li>
<li><p><strong>Alternate labels:</strong> sponges</p></li>
<li><p>Concept URI token: porifera</p></li>
</ul>
<p><span id="vertebrate"></span></p>
</section>
<section id="vertebrate" class="level5" data-number="1.1.1.2.5">
<h5 data-number="1.1.1.2.5" data-anchor-id="vertebrate"><span class="header-section-number">1.1.1.2.5</span> Vertebrate</h5>
<ul>
<li><p>Child of: <a href="#animalia"><code>animalia</code></a></p></li>
<li><p>Animals that have a vertebral column, a cranium, an endoskeleton, a well-developed muscular system, and an advanced nervous system (ChatGPT);</p></li>
<li><p>Concept URI token: vertebrate</p></li>
</ul>
<p><span id="amphibian"></span></p>
<section id="amphibian" class="level6" data-number="1.1.1.2.5.1">
<h6 data-number="1.1.1.2.5.1" data-anchor-id="amphibian"><span class="header-section-number">1.1.1.2.5.1</span> Amphibian</h6>
<ul>
<li><p>Child of: <a href="#vertebrate"><code>vertebrate</code></a></p></li>
<li><p>Vertebrates that have a dual life cycle, semi-permeable skin, absence of scales and claws, a three-chambered heart, and dependence on water for reproduction and survival (ChatGPT)</p></li>
<li><p>Concept URI token: amphibian</p></li>
</ul>
<p><span id="bird"></span></p>
</section>
<section id="bird" class="level6" data-number="1.1.1.2.5.2">
<h6 data-number="1.1.1.2.5.2" data-anchor-id="bird"><span class="header-section-number">1.1.1.2.5.2</span> Bird</h6>
<ul>
<li><p>Child of: <a href="#vertebrate"><code>vertebrate</code></a></p></li>
<li><p>Vertebrates that have feathers, lightweight, hollow bones, a beak, an efficient respiratory system, and are warm-blooded. (ChatGPT)</p></li>
<li><p>Concept URI token: bird</p></li>
</ul>
<p><span id="fish"></span></p>
</section>
<section id="fish" class="level6" data-number="1.1.1.2.5.3">
<h6 data-number="1.1.1.2.5.3" data-anchor-id="fish"><span class="header-section-number">1.1.1.2.5.3</span> Fish</h6>
<ul>
<li><p>Child of: <a href="#vertebrate"><code>vertebrate</code></a></p></li>
<li><p>Vertebrates that have gills, scales, fins, are cold-blooded, and commonly have a swim bladder; includes jawless fish, cartilaginous fish and bony fish. (ChatGPT)</p></li>
<li><p>Concept URI token: fish</p></li>
</ul>
<p><span id="mammal"></span></p>
</section>
<section id="mammal" class="level6" data-number="1.1.1.2.5.4">
<h6 data-number="1.1.1.2.5.4" data-anchor-id="mammal"><span class="header-section-number">1.1.1.2.5.4</span> Mammal</h6>
<ul>
<li><p>Child of: <a href="#vertebrate"><code>vertebrate</code></a></p></li>
<li><p>vertebrates that have mammary glands, hair or fur, three middle ear bones, specialized teeth, and are warm-blooded. (ChatGPT)</p></li>
<li><p>Concept URI token: mammal</p></li>
</ul>
<p><span id="reptile"></span></p>
</section>
<section id="reptile" class="level6" data-number="1.1.1.2.5.5">
<h6 data-number="1.1.1.2.5.5" data-anchor-id="reptile"><span class="header-section-number">1.1.1.2.5.5</span> Reptile</h6>
<ul>
<li><p>Child of: <a href="#vertebrate"><code>vertebrate</code></a></p></li>
<li><p>Vertebrates that have scaly skin and claws, amniotic eggs, are cold- blooded, and are ectothermic (ChatGPT)</p></li>
<li><p>Concept URI token: reptile</p></li>
</ul>
<p><span id="chromista"></span></p>
</section>
</section>
</section>
<section id="chromista" class="level4" data-number="1.1.1.3">
<h4 data-number="1.1.1.3" data-anchor-id="chromista"><span class="header-section-number">1.1.1.3</span> Chromista</h4>
<ul>
<li><p>Child of: <a href="#eukaryote"><code>eukaryote</code></a></p></li>
<li><p>Chromists are unified by a shared common ancestral body plan with</p></li>
</ul>
<ol type="1">
<li>a skeleton comprising cortical alveoli with subpellicular microtubules and a microtubule bypassing band distinct from the three major microtubule centriolar roots inherited from excavate protozoa, and (2) chloroplasts of red algal origin inside the endomembrane system with unique membrane topology and derlin-based periplastid protein import machinery. Chromists are distinguished from Plantae because of more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs. The kingdom includes highly divergent cytoskeletons and trophic modes. Chromista comprise eight distinctive phyla (Cavalier-Smith, 2018) and includes a majority of marine algae and of heterotrophic protists, various human disease agents such as malaria parasites, and agricultural pathogens like potato blight and sugar beet rhizomania disease. They have a greater range of body plans and lifestyles than the entire plant kingdom and more phyla than kingdoms Fungi or Protozoa.</li>
</ol>
<ul>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/4"><https://www.gbif.org/species/4></a></p></li>
<li><p><strong>Alternate labels:</strong> KINGDOM CHROMISTA (Ruggerio et al., 2015)</p></li>
<li><p>Concept URI token: chromista</p></li>
</ul>
<p><span id="eukaryoticmicroorganism"></span></p>
</section>
<section id="eukaryotic-microorganism" class="level4" data-number="1.1.1.4">
<h4 data-number="1.1.1.4" data-anchor-id="eukaryotic-microorganism"><span class="header-section-number">1.1.1.4</span> Eukaryotic microorganism</h4>
<ul>
<li><p>Child of: <a href="#eukaryote"><code>eukaryote</code></a></p></li>
<li><p>Unclassified Eukaryote single-cell organisms; might be microfungi, microalgae, Protista or Chromista.</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://en.wikipedia.org/wiki/Protist"><https://en.wikipedia.org/wiki/Protist></a></p></li>
<li><p><strong>Alternate labels:</strong> Protista</p></li>
<li><p>Concept URI token: eukaryoticmicroorganism</p></li>
</ul>
<p><span id="fungi"></span></p>
</section>
<section id="fungi" class="level4" data-number="1.1.1.5">
<h4 data-number="1.1.1.5" data-anchor-id="fungi"><span class="header-section-number">1.1.1.5</span> Fungi</h4>
<ul>
<li><p>Child of: <a href="#eukaryote"><code>eukaryote</code></a></p></li>
<li><p>eukaryotic organisms that contain chitin in their cell walls, are heterotrophs (they obtain their nutrients by absorbing organic material from their environment, either as decomposers, parasites, or symbionts) , lack chloroplasts, reproduce both sexually and asexually, and can take on a variety of growth forms, including single-celled yeasts, multicellular molds, and complex, specialized fruiting bodies. (ChatGPT). Biologists use the term ‘fungus’ to include eukaryotic, spore-bearing, achlorophyllous organisms that generally reproduce sexually and asexually. They are usually made up of filamentous, branched somatic structures which are typically surrounded by cell walls containing chitin or cellulose, or both of these substances. (https://plantlet.org/lower-fungi-higher-fungi/)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/5"><https://www.gbif.org/species/5></a></p></li>
<li><p>Concept URI token: fungi</p></li>
</ul>
<p><span id="macrofungi"></span></p>
<section id="macrofungi" class="level5" data-number="1.1.1.5.1">
<h5 data-number="1.1.1.5.1" data-anchor-id="macrofungi"><span class="header-section-number">1.1.1.5.1</span> Macrofungi</h5>
<ul>
<li><p>Child of: <a href="#fungi"><code>fungi</code></a></p></li>
<li><p>Macrofungi refers to all fungi that produce visible fruiting bodies. These fungi are evolutionarily and ecologically very divergent. Evolutionarily, they belong to two main phyla, Ascomycota and Basidiomycota, and many of them have relatives that cannot form visible fruiting bodies.(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6106070/)</p></li>
<li><p>Concept URI token: macrofungi</p></li>
</ul>
<p><span id="microfungi"></span></p>
</section>
<section id="microfungi" class="level5" data-number="1.1.1.5.2">
<h5 data-number="1.1.1.5.2" data-anchor-id="microfungi"><span class="header-section-number">1.1.1.5.2</span> Microfungi</h5>
<ul>
<li><p>Child of: <a href="#fungi"><code>fungi</code></a></p></li>
<li><p>Microfungi or micromycetes are fungi—eukaryotic organisms such as molds, mildews and rusts, which have microscopic spore-producing structures. They exhibit tube tip-growth and have cell walls composed of chitin, a polymer of N-acetylglucosamine. Microfungi are a paraphyletic group, distinguished from macrofungi only by the absence of a large, multicellular fruiting body. Include moulds, yeasts. (https://en.wikipedia.org/wiki/Microfungi)</p></li>
<li><p><strong>Alternate labels:</strong> micromycetes</p></li>
<li><p>Concept URI token: microfungi</p></li>
</ul>
<p><span id="plantae"></span></p>
</section>
</section>
<section id="plantae" class="level4" data-number="1.1.1.6">
<h4 data-number="1.1.1.6" data-anchor-id="plantae"><span class="header-section-number">1.1.1.6</span> Plantae</h4>
<ul>
<li><p>Child of: <a href="#eukaryote"><code>eukaryote</code></a></p></li>
<li><p>Plants are eukaryotes that have cell walls made of cellulose, specialized organelles called chloroplasts, which contain chlorophyll and other pigments that allow plants to perform photosynthesis and produce their own food; a unique life cycle that involves alternating between a haploid gametophyte stage and a diploid sporophyte stage; specialized regions called apical meristems at the tips of their roots and shoots, which allow for growth and the development of new tissues; specialized structures for reproduction, including flowers, cones, and spores, and most plants have specialized tissues called xylem and phloem, which transport water, nutrients, and other substances throughout the plant. (ChatGPT). Subdivision here follows Margulis and Schwartz 2001.</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/6"><https://www.gbif.org/species/6></a></p></li>
<li><p><strong>Source:</strong> Margulis L, Schwartz KV. Five kingdoms: an illustrated guide to the phyla of life on earth, third edition, New York, WH Freeman and Company, 2001.</p></li>
<li><p>Concept URI token: plantae</p></li>
</ul>
<p><span id="nonvascularplant"></span></p>
<section id="non-vascular-plant" class="level5" data-number="1.1.1.6.1">
<h5 data-number="1.1.1.6.1" data-anchor-id="non-vascular-plant"><span class="header-section-number">1.1.1.6.1</span> Non-vascular plant</h5>
<ul>
<li><p>Child of: <a href="#plantae"><code>plantae</code></a></p></li>
<li><p>Non-vascular plants that do not have specialized tissues for transporting water and nutrients; includes mosses, Marchantiophyta (liverworts), and Anthocerotophyta (hornworts). (ChatGPT)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/35"><https://www.gbif.org/species/35></a></p></li>
<li><p><strong>Alternate labels:</strong> Bryophyte</p></li>
<li><p>Concept URI token: nonvascularplant</p></li>
</ul>
<p><span id="otherplant"></span></p>
</section>
<section id="other-plant" class="level5" data-number="1.1.1.6.2">
<h5 data-number="1.1.1.6.2" data-anchor-id="other-plant"><span class="header-section-number">1.1.1.6.2</span> Other plant</h5>
<ul>
<li><p>Child of: <a href="#plantae"><code>plantae</code></a></p></li>
<li><p>plants that do not fit in other plant sub class. Includes Lycopodiophyta (clubmosses) and Equisetophyta (horsetails)</p></li>
<li><p>Concept URI token: otherplant</p></li>
</ul>
<p><span id="vascularseedplant"></span></p>
</section>
<section id="vascular-seed-plant" class="level5" data-number="1.1.1.6.3">
<h5 data-number="1.1.1.6.3" data-anchor-id="vascular-seed-plant"><span class="header-section-number">1.1.1.6.3</span> Vascular seed plant</h5>
<ul>
<li><p>Child of: <a href="#plantae"><code>plantae</code></a></p></li>
<li><p>Plant that produces seeds, hence the alternative name seed plant. Spermatophytes are a subset of the embryophytes or land plants. They include most familiar types of plants, including all flowers and most trees, but exclude some other types of plants such as ferns, mosses, algae. (https://en.wikipedia.org/wiki/Spermatophyte). Includes Gymnosperms (naked-seed plants) and Angiosperms (flowering plants).</p></li>
<li><p><strong>Alternate labels:</strong> spermatophyte</p></li>
<li><p><strong>Source:</strong> https://en.wikipedia.org/wiki/Seed_plant</p></li>
<li><p>Concept URI token: vascularseedplant</p></li>
</ul>
<p><span id="vascularsportplant"></span></p>
</section>
<section id="vascular-spore-plant" class="level5" data-number="1.1.1.6.4">
<h5 data-number="1.1.1.6.4" data-anchor-id="vascular-spore-plant"><span class="header-section-number">1.1.1.6.4</span> Vascular spore plant</h5>
<ul>
<li><p>Child of: <a href="#plantae"><code>plantae</code></a></p></li>
<li><p>a vascular plant (with xylem and phloem) that disperses spores; they produce neither flowers nor seeds, Includes Ferns, horsetails (often treated as ferns), and lycophytes (clubmosses, spikemosses, and quillworts)</p></li>
<li><p><strong>Alternate labels:</strong> Pteridophyte</p></li>
<li><p><strong>Source:</strong> https://en.wikipedia.org/wiki/Pteridophyte</p></li>
<li><p>Concept URI token: vascularsportplant</p></li>
</ul>
<p><span id="protozoa"></span></p>
</section>
</section>
<section id="protozoa" class="level4" data-number="1.1.1.7">
<h4 data-number="1.1.1.7" data-anchor-id="protozoa"><span class="header-section-number">1.1.1.7</span> Protozoa</h4>
<ul>
<li><p>Child of: <a href="#eukaryote"><code>eukaryote</code></a></p></li>
<li><p>A single-celled eukaryote, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic tissues and debris (predominantly heterotrophic). Historically, protozoans were regarded as ‘one-celled animals’, because they often possess animal-like behaviours, such as motility and predation, and lack a cell wall, as found in plants and many algae. (https://en.wikipedia.org/wiki/Protozoa)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/7"><https://www.gbif.org/species/7></a></p></li>
<li><p><strong>Alternate labels:</strong> KINGDOM PROTOZOA (Ruggerio et al., 2015)</p></li>
<li><p>Concept URI token: protozoa</p></li>
</ul>
<p><span id="amoebozoa"></span></p>
<section id="amoebozoa" class="level5" data-number="1.1.1.7.1">
<h5 data-number="1.1.1.7.1" data-anchor-id="amoebozoa"><span class="header-section-number">1.1.1.7.1</span> Amoebozoa</h5>
<ul>
<li><p>Child of: <a href="#protozoa"><code>protozoa</code></a></p></li>
<li><p>a diverse group of organisms that share certain characteristics, such as the ability to move using pseudopodia, temporary extensions of the cell membrane and cytoplasm that allow the cell to crawl or engulf food particles, the lack of rigid cell walls, presence of mitochondria, which are organelles that generate energy for the cell through cellular respiration (chatGPT)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/7509337"><https://www.gbif.org/species/7509337></a></p></li>
<li><p>Concept URI token: amoebozoa</p></li>
</ul>
<p><span id="mycetozoa"></span></p>
</section>
<section id="mycetozoa" class="level5" data-number="1.1.1.7.2">
<h5 data-number="1.1.1.7.2" data-anchor-id="mycetozoa"><span class="header-section-number">1.1.1.7.2</span> Mycetozoa</h5>
<ul>
<li><p>Child of: <a href="#protozoa"><code>protozoa</code></a></p></li>
<li><p>Mycetozoa includes the slime molds, which are a group of organisms that have both amoeboid and fungal-like characteristics. The Mycetozoa can be further subdivided into two groups: the plasmodial slime molds and the cellular slime molds. Myxomycetes has most child orders; they are class of slime molds. Myxomycetes have a complex life cycle involving the formation of spore-bearing structures called fruiting bodies, which is a key feature that distinguishes them from other amoebae. All species pass through several, very different morphologic phases, such as microscopic individual cells, slimy amorphous organisms visible with the naked eye and conspicuously shaped fruit bodies. Although they are monocellular, they can reach immense widths and weights. (https://en.wikipedia.org/wiki/Mycetozoa). (ChatGPT)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/33"><https://www.gbif.org/species/33></a></p></li>
<li><p><strong>Alternate labels:</strong> Myxomycota</p></li>
<li><p>Concept URI token: mycetozoa</p></li>
</ul>
<p><span id="otherprotozoa"></span></p>
</section>
<section id="other-protozoa" class="level5" data-number="1.1.1.7.3">
<h5 data-number="1.1.1.7.3" data-anchor-id="other-protozoa"><span class="header-section-number">1.1.1.7.3</span> Other Protozoa</h5>
<ul>
<li><p>Child of: <a href="#protozoa"><code>protozoa</code></a></p></li>
<li><p>Protozoa is not Amoebozoa or Mycetozoa. Includes phylum Euglenozoa and Microsporidia prominently among others.</p></li>
<li><p>Concept URI token: otherprotozoa</p></li>
</ul>
<p><span id="lichen"></span></p>
</section>
</section>
</section>
<section id="lichen" class="level3" data-number="1.1.2">
<h3 data-number="1.1.2" data-anchor-id="lichen"><span class="header-section-number">1.1.2</span> Lichen</h3>
<ul>
<li><p>Child of: <a href="#biologicalentity"><code>biologicalentity</code></a></p></li>
<li><p>A composite organism that arises from algae or cyanobacteria living among filaments of multiple fungi species in a mutualistic relationship. (https://en.wikipedia.org/wiki/Lichen). Lichens are not classified under a specific kingdom as they are a symbiotic association between a fungus and either an alga or a cyanobacterium. The fungal partner belongs to the kingdom Fungi, while the algal or cyanobacterial partner belongs to either the kingdom Plantae or the kingdom Bacteria, respectively. (ChatGPT)</p></li>
<li><p>Concept URI token: lichen</p></li>
</ul>
<p><span id="plasmid"></span></p>
</section>
<section id="plasmid" class="level3" data-number="1.1.3">
<h3 data-number="1.1.3" data-anchor-id="plasmid"><span class="header-section-number">1.1.3</span> Plasmid</h3>
<ul>
<li><p>Child of: <a href="#biologicalentity"><code>biologicalentity</code></a></p></li>
<li><p>A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. While chromosomes are large and contain all the essential genetic information for living under normal conditions, plasmids are usually very small and contain only additional genes that may be useful in certain situations or conditions. (https://en.wikipedia.org/wiki/Plasmid)</p></li>
<li><p>Concept URI token: plasmid</p></li>
</ul>
<p><span id="prokaryote"></span></p>
</section>
<section id="prokaryote" class="level3" data-number="1.1.4">
<h3 data-number="1.1.4" data-anchor-id="prokaryote"><span class="header-section-number">1.1.4</span> Prokaryote</h3>
<ul>
<li><p>Child of: <a href="#biologicalentity"><code>biologicalentity</code></a></p></li>
<li><p>single-celled organisms that lack a nucleus and other membrane-bound organelles. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor. Almost all prokaryotes have a cell wall, a protective structure that allows them to survive in extreme conditions, which is located outside of their plasma membrane. Archaea and bacteria cannot reproduce sexually.</p></li>
<li><p><strong>Alternate labels:</strong> Monera, SUPERKINGDOM PROKARYOTA (Ruggerio et al, 2015),</p></li>
<li><p>Concept URI token: prokaryote</p></li>
</ul>
<p><span id="archaea"></span></p>
<section id="archaea" class="level4" data-number="1.1.4.1">
<h4 data-number="1.1.4.1" data-anchor-id="archaea"><span class="header-section-number">1.1.4.1</span> Archaea</h4>
<ul>
<li><p>Child of: <a href="#prokaryote"><code>prokaryote</code></a></p></li>
<li><p>archaeal cell walls are composed of polysaccharides (sugars). they never have peptidoglycan in their cell walls, their cell membranes contain lipids of unique composition (glycerol molecules are mirror images of those found in other cells, and form ether linkages to isoprenoid side chains), and their 16S ribosomal- RNA nucleotide sequences are unlike those of bacteria. (https://quizlet.com/234154298/archaea-and-bacteria-flash-cards/). The common characteristics of Archaebacteria known to date are these:</p></li>
</ul>
<ol type="1">
<li>the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls, with in many cases, replacement by a largely proteinaceous coat; (3) the occurrence of ether linked lipids built from phytanyl chains and (4) in all cases known so far, their occurrence only in unusual habitats. (https://pubmed.ncbi.nlm.nih.gov/691075/)</li>
</ol>
<ul>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/2"><https://www.gbif.org/species/2></a></p></li>
<li><p><strong>Alternate labels:</strong> Archaebacteria, KINGDOM ARCHAEA (Ruggerio et al. 2015),</p></li>
<li><p>Concept URI token: archaea</p></li>
</ul>
<p><span id="bacteria"></span></p>
</section>
<section id="bacteria" class="level4" data-number="1.1.4.2">
<h4 data-number="1.1.4.2" data-anchor-id="bacteria"><span class="header-section-number">1.1.4.2</span> Bacteria</h4>
<ul>
<li><p>Child of: <a href="#prokaryote"><code>prokaryote</code></a></p></li>
<li><p>a large domain of prokaryotic microorganisms. Bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. The bacterial cell is surrounded by a cell membrane, which is made primarily of phospholipids. This membrane encloses the contents of the cell and acts as a barrier to hold nutrients, proteins and other essential components of the cytoplasm within the cell. Bacterial cell walls are composed of peptidoglycan, a complex of protein and sugars, while archaeal cell walls are composed of polysaccharides (sugars). (https://en.wikipedia.org/wiki/Bacteria)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/3"><https://www.gbif.org/species/3></a></p></li>
<li><p><strong>Alternate labels:</strong> Eubacteria, KINGDOM BACTERIA (Ruggerio et al., 2015),</p></li>
<li><p>Concept URI token: bacteria</p></li>
</ul>
<p><span id="virus"></span></p>
</section>
</section>
<section id="virus" class="level3" data-number="1.1.5">
<h3 data-number="1.1.5" data-anchor-id="virus"><span class="header-section-number">1.1.5</span> Virus</h3>
<ul>
<li><p>Child of: <a href="#biologicalentity"><code>biologicalentity</code></a></p></li>
<li><p>A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Realms are Adnaviria, Duplodnaviria, Monodnaviria, Riboviria, Ribozyviria, Varidnaviria (https://en.wikipedia.org/wiki/Virus). Viruses are not cells at all, so they are neither prokaryotes nor eukaryotes. (https://bio.libretext s.org/Bookshelves/Introductory_and_General_Biology/Book)</p></li>
<li><p>See Also:</p></li>
<li><p><a href="https://www.gbif.org/species/8"><https://www.gbif.org/species/8></a></p></li>
<li><p>Concept URI token: virus</p></li>
</ul>
<p><span id="othervirus"></span></p>
<section id="other-virus" class="level4" data-number="1.1.5.1">
<h4 data-number="1.1.5.1" data-anchor-id="other-virus"><span class="header-section-number">1.1.5.1</span> Other Virus</h4>
<ul>
<li><p>Child of: <a href="#virus"><code>virus</code></a></p></li>
<li><p>Virus that is not a member of order Caudovirales (e.g., bacteriophage T4, lambda phage).</p></li>
<li><p>Concept URI token: othervirus</p></li>
</ul>
<p><span id="phage"></span></p>
</section>
<section id="phage" class="level4" data-number="1.1.5.2">
<h4 data-number="1.1.5.2" data-anchor-id="phage"><span class="header-section-number">1.1.5.2</span> Phage</h4>
<ul>
<li><p>Child of: <a href="#virus"><code>virus</code></a></p></li>
<li><p>A bacteriophage, also known informally as a phage, is a duplodnaviria virus that infects and replicates within bacteria and archaea. Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes (e.g. MS2) and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. (https://en.wikipedia.org/wiki/Bacteriophage). Includes all virus in order Caudovirales (e.g., bacteriophage T4, lambda phage).</p></li>
<li><p><strong>Alternate labels:</strong> bacteriophage</p></li>
<li><p>Concept URI token: phage</p></li>
</ul>
</section>
</section>
</section>
</section>
</main>
<!-- /main column -->
<script id="quarto-html-after-body" type="application/javascript">
window.document.addEventListener("DOMContentLoaded", function (event) {
const toggleBodyColorMode = (bsSheetEl) => {
const mode = bsSheetEl.getAttribute("data-mode");
const bodyEl = window.document.querySelector("body");
if (mode === "dark") {
bodyEl.classList.add("quarto-dark");
bodyEl.classList.remove("quarto-light");
} else {
bodyEl.classList.add("quarto-light");
bodyEl.classList.remove("quarto-dark");
}
}
const toggleBodyColorPrimary = () => {
const bsSheetEl = window.document.querySelector("link#quarto-bootstrap");
if (bsSheetEl) {
toggleBodyColorMode(bsSheetEl);
}
}
toggleBodyColorPrimary();
const isCodeAnnotation = (el) => {
for (const clz of el.classList) {
if (clz.startsWith('code-annotation-')) {
return true;
}
}
return false;
}
const clipboard = new window.ClipboardJS('.code-copy-button', {
text: function(trigger) {
const codeEl = trigger.previousElementSibling.cloneNode(true);
for (const childEl of codeEl.children) {
if (isCodeAnnotation(childEl)) {
childEl.remove();
}
}
return codeEl.innerText;
}
});
clipboard.on('success', function(e) {
// button target
const button = e.trigger;
// don't keep focus
button.blur();
// flash "checked"
button.classList.add('code-copy-button-checked');
var currentTitle = button.getAttribute("title");
button.setAttribute("title", "Copied!");
let tooltip;
if (window.bootstrap) {
button.setAttribute("data-bs-toggle", "tooltip");
button.setAttribute("data-bs-placement", "left");
button.setAttribute("data-bs-title", "Copied!");
tooltip = new bootstrap.Tooltip(button,
{ trigger: "manual",
customClass: "code-copy-button-tooltip",
offset: [0, -8]});
tooltip.show();
}
setTimeout(function() {
if (tooltip) {
tooltip.hide();
button.removeAttribute("data-bs-title");
button.removeAttribute("data-bs-toggle");
button.removeAttribute("data-bs-placement");
}
button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
// clear code selection
e.clearSelection();
});
function tippyHover(el, contentFn) {
const config = {
allowHTML: true,
content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
};
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
for (var i=0; i<noterefs.length; i++) {
const ref = noterefs[i];
tippyHover(ref, function() {
// use id or data attribute instead here
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
});
}
let selectedAnnoteEl;
const selectorForAnnotation = ( cell, annotation) => {
let cellAttr = 'data-code-cell="' + cell + '"';
let lineAttr = 'data-code-annotation="' + annotation + '"';
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
return selector;
}
const selectCodeLines = (annoteEl) => {
const doc = window.document;
const targetCell = annoteEl.getAttribute("data-target-cell");
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
const lineIds = lines.map((line) => {
return targetCell + "-" + line;
})
let top = null;
let height = null;
let parent = null;
if (lineIds.length > 0) {
//compute the position of the single el (top and bottom and make a div)
const el = window.document.getElementById(lineIds[0]);
top = el.offsetTop;
height = el.offsetHeight;
parent = el.parentElement.parentElement;
if (lineIds.length > 1) {
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
height = bottom - top;
}
if (top !== null && height !== null && parent !== null) {
// cook up a div (if necessary) and position it
let div = window.document.getElementById("code-annotation-line-highlight");
if (div === null) {
div = window.document.createElement("div");
div.setAttribute("id", "code-annotation-line-highlight");
div.style.position = 'absolute';
parent.appendChild(div);
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
gutterDiv.style.position = 'absolute';
const codeCell = window.document.getElementById(targetCell);
const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
}
gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
}
selectedAnnoteEl = annoteEl;
}
};
const unselectCodeLines = () => {
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
}
});
selectedAnnoteEl = undefined;
};
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
annoteDlNode.addEventListener('click', (event) => {
const clickedEl = event.target;
if (clickedEl !== selectedAnnoteEl) {
unselectCodeLines();
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
if (activeEl) {
activeEl.classList.remove('code-annotation-active');
}
selectCodeLines(clickedEl);
clickedEl.classList.add('code-annotation-active');
} else {
// Unselect the line
unselectCodeLines();
clickedEl.classList.remove('code-annotation-active');
}
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
</div> <!-- /content -->
</body></html>