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updates and fixes for non-vertebrate prefixes
not sure if anyone other than us at Sanger has started using the non-vertebrate naming prefixes yet, but here are some updates and fixes from @richarddurbin. * ctenophores changed to "other animal phyla" * hemichordated removed from "other chordates" to be included in "other animal phyla" * bacteria was `c` now `y` * archea was `h` now `z` * platyhelminths was `y` now `h` * non-vascular plants was `z` now `c`
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‎VGP_specimen_naming_scheme.md

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@@ -70,33 +70,152 @@ If this scheme were to extend beyond vertebrates in the VGP, the below is a prop
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This is meant as a pragmatic division rather then a strict taxonomic one.
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| prefix | class | count | group | notes |
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|:-------|:-----------------------------|:-------|:----------|:------------------------------------------------------------------------------------------|
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| a | amphibians | 6439 | chordates | |
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| b | birds | 10301 | chordates | |
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| c | bacteria | 6468 | | |
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| d | dicots | 200000 | plants | not monophyletic |
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| e | echinoderm | 6753 | animals | |
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| f | fishes | 31862 | chordates | lobe-finned and ray finned = Osteichthyes = Teleostomi (excluding tetrapods) |
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| g | fungi | 123126 | | |
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| h | archea | 281 | | |
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| i | insects | 795000 | animals | |
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| j | jellyfish and other cnidaria | 9747 | animals | |
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| k | other chordates | 1926 | chordates | hemichordates, cephalochordates, urochordates (tunicates), jawless fish; not monophyletic |
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| l | monocots | 51595 | plants | 'l' for lily |
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| m | mammals | 4863 | chordates | |
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| n | nematodes | 3455 | animals | |
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| o | sponges | 8499 | animals | |
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| p | protists | 12695 | | defined here as eukaryotes not animals or plants or fungi; not monophyletic |
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| q | other arthropods | 120000 | animals | not insects; not monophyletic |
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| r | reptiles | 9789 | chordates | excluding birds |
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| s | sharks and relatives  | 1149 | chordates | Chondricthyes = Elasmobranchs and Chimaeras |
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| t | ctenophores | 165 | animals | |
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| u | algae | 2056 | plants | not monophyletic |
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| v | other vascular plants | 66717 | plants | ferns, cycads, conifers, gingko etc.; not monophyletic |
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| w | annelids (worms) | 12738 | animals | |
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| x | molluscs | 41646 | animals | the "scs" in "moluscs" sounds a bit like it contains an 'x' |
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| y | platyhelminths | 9164 | animals | |
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| z | non-vascular plants | 14222 | plants | mosses, liverworts, hornworts; not monophyletic |
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| - | viruses | | | '-' for missing |
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| prefix | class | count | group | notes |
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|:-------|:-----------------------------|:-------|:-----------------|:------------------------------------------------------------------------------------------|
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| a | amphibians | 6439 | chordates | |
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| b | birds | 10301 | chordates | |
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| c | non-vascular plants | 14222 | plants | |
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| d | dicotyledons | 200000 | plants | not monophyletic |
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| e | echinoderm | 6753 | other animals | |
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| f | fishes | 31862 | chordates | lobe-finned and ray finned = Osteichthyes = Teleostomi (excluding tetrapods) |
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| g | fungi | 123126 | other eukaryotes | |
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| h | platyhelminths | 9164 | other animals | |
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| i | insects | 795000 | other animals | |
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| j | jellyfish and other cnidaria | 9747 | other animals | |
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| k | other chordates | 1926 | chordates | cephalochordates, urochordates (tunicates), jawless fish; not monophyletic |
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| l | monocotyledons (lilies etc.) | 51595 | plants | 'l' for lily |
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| m | mammals | 4863 | chordates | |
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| n | nematodes | 3455 | other animals | |
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| o | sponges | 8499 | other animals | |
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| p | protists | 12695 | other eukaryotes | defined here as eukaryotes not animals or plants or fungi; not monophyletic |
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| q | other arthropods | 120000 | other animals | not insects; not monophyletic |
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| r | reptiles | 9789 | chordates | excluding birds |
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| s | sharks and relatives | 1149 | chordates | Chondricthyes = Elasmobranchs and Chimaeras |
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| t | other animal phyla | 165 | other animals | |
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| u | algae | 2056 | plants | not monophyletic |
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| v | other vascular plants | 66717 | plants | ferns, cycads, conifers, gingko etc.; not monophyletic |
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| w | annelids (worms) | 12738 | other animals | |
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| x | molluscs | 41646 | other animals | the "scs" in "moluscs" sounds a bit like it contains an 'x' |
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| y | bacteria | 6468 | prokaryotes | |
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| z | archea | 281 | prokaryotes | mosses, liverworts, hornworts; not monophyletic |
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| - | viruses | | | '-' for missing |
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Equivalently, presented by group:
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<table>
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<tr>
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<th>group</th>
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<th>prefix</th>
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<th>class</th>
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</tr>
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<tr>
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<td rowspan="7">chordates (including vertebrates)</td>
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<td>m</td>
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<td>mammals</td>
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</tr>
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<tr>
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<td>b</td>
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<td>birds</td>
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</tr>
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<tr>
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<td>r</td>
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<td>reptiles</td>
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</tr>
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<tr>
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<td>a</td>
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<td>amphibians</td>
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</tr>
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<tr>
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<td>f</td>
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<td>fishes</td>
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</tr>
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<tr>
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<td>s</td>
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<td>sharks</td>
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</tr>
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<tr>
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<td>k</td>
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<td>other chordates</td>
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</tr>
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<tr>
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<td rowspan="10">other animals</td>
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<td>e</td>
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<td>echinoderms</td>
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</tr>
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<tr>
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<td>x</td>
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<td>molluscs</td>
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</tr>
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<tr>
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<td>i</td>
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<td>insects</td>
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</tr>
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<tr>
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<td>q</td>
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<td>other arthropods</td>
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</tr>
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<tr>
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<td>w</td>
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<td>annelids (worms)</td>
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</tr>
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<tr>
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<td>n</td>
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<td>nematodes</td>
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</tr>
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<tr>
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<td>h</td>
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<td>platyhelminths</td>
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</tr>
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<tr>
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<td>j</td>
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<td>jellyfish and other cnidaria</td>
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</tr>
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<tr>
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<td>o</td>
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<td>sponges</td>
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</tr>
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<tr>
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<td>t</td>
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<td>other animal phyla</td>
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</tr>
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<tr>
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<td rowspan="5">plants</td>
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<td>d</td>
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<td>dicotyledons</td>
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</tr>
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<tr>
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<td>l</td>
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<td>monocotyledons</td>
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</tr>
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<tr>
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<td>v</td>
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<td>other vascular plants</td>
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</tr>
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<tr>
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<td>c</td>
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<td>non-vascular plants</td>
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</tr>
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<tr>
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<td>u</td>
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<td>algae</td>
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</tr>
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<tr>
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<td rowspan="2">other eukaryotes</td>
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<td>g</td>
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<td>fungi</td>
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</tr>
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<tr>
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<td>p</td>
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<td>protists</td>
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</tr>
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<tr>
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<td rowspan="2">prokaryotes</td>
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<td>y</td>
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<td>bacteria</td>
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</tr>
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<tr>
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<td>z</td>
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<td>archaea</td>
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</tr>
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</table>

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