Permalink
Browse files

Adding phylum Myzozoa to dataset

  • Loading branch information...
mdoering committed Jan 17, 2017
1 parent ff39658 commit afccc623414b7ff2be715bcce1e64fc1aa97ca86
Showing with 237 additions and 9 deletions.
  1. +6 −7 README.md
  2. +231 −2 algae.txt
View
@@ -1,9 +1,9 @@
# GBIF Algae Classification
-A classification for [all algae from kingdom down to families](algae.txt) distributed across the 3 kingdoms Plantae, Chromista and Protozoa.
+A classification for [all algae sensu latu from kingdom down to families](algae.txt) distributed across the 3 kingdoms Plantae, Chromista and Protozoa.
The project is setup so that the github zip represents a valid Darwin Core Checklist Archive, synonyms are included.
-This classification is aiming to fill the algae gaps in the current Catalog of Life which has no taxa within the following phyla:
- - Chromista: Cryptophyta, Haptophyta, Ochrophyta
+This classification is aiming to fill the gaps in the current Catalog of Life due to the removal of Algaebase. The CoL currently has no taxa within the following phyla:
+ - Chromista: Cryptophyta, Haptophyta, Ochrophyta, Myzozoa
- Plantae: Charophyta, Chlorophyta, Glaucophyta, Rhodophyta
- Protozoa: Euglenozoa
@@ -23,7 +23,7 @@ Chromista
*Cryptista
Foraminifera
*Haptophyta
- Miozoa
+ *Miozoa
*Ochrophyta
Oomycota
Radiozoa
@@ -59,6 +59,8 @@ For Protozoa we will only treat the "algae" phylum Euglenozoa:
- Cryptista aka Cryptophyta
- Haptophyta
- Ochrophyta
+ - Myzozoa (preferred over Miozoa, see [WoRMS](http://www.marinespecies.org/aphia.php?p=taxdetails&id=450030) and [Wikipedia](https://en.wikipedia.org/wiki/Myzozoa))
+ - Cercozoa
- Plantae
- Charophyta
- Chlorophyta
@@ -77,9 +79,6 @@ Classification down to families: [plantae](itis/itis-plantae.md), [chromista](it
### WoRMS
Classification down to families for the kingdoms: [plantae](worms/worms-3.txt), [chromista](worms/worms-7.txt) & [protozoa](worms/worms-5.txt)
-### Algaebase
-Hard to access and the bad guy who requested removal from CoL and prevends WoRMS from sharing
-
### Ruggiero 2015
See [PLOS article 10.1371/journal.pone.0119248](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119248)
Also available as strangely formatted [Excel spreadsheet](journal.pone.0119248.s002.XLSX).
View
233 algae.txt
@@ -1,4 +1,4 @@
-taxonID parentID acceptedID taxonRank scientificName isExtinct isMarine isTerrestrial isFreshwater
+taxonID parentNameUsageID acceptedNameUsageID taxonRank scientificName isExtinct isMarine isTerrestrial isFreshwater
1 Kingdom Plantae 1
100 1 Phylum Charophyta 1
1000 100 Class Charophyceae 1
@@ -978,10 +978,239 @@ taxonID parentID acceptedID taxonRank scientificName isExtinct isMarine isTerres
1069 113 Class Placidiophyceae
10875 1069 Order Placidiales
+450030 3 Phylum Myzozoa
+450030b 450030 Phylum Miozoa
+13 450030 Subphylum Mastigophora 1
+22565 450030 Subphylum Apicomplexa 1 1 1
+591163 22565 Class Apicomonadea
+591165 591163 Order Acrocoelida
+591166 591163 Order Colpodellida
+591164 22565 Order Chromerida
+582464 22565 Class Aconoidasida
+562845 582464 Class Haematozoa 1 1 1
+591168 582464 Order Haemospororida
+722976 591168 Family Plasmodiidae
+562847 582464 Order Piroplasmorida 1 1 1
+562848 562847 Family Haemohormidiidae 1 0 0
+394011 22565 Class Conoidasida
+582463 394011 Subclass Coccidiasina
+562794 582463 Class Coccidea 1 1 1
+562795 582463 Order Agamococcidiorida 1 0 0
+562796 562795 Family Gemmocystidae 1 0 0
+562798 562795 Family Rhytidocystidae 1 0 0
+394012 582463 Order Eucoccidiorida 1 1 1
+394013 394012 Suborder Adeleorina 1 1 1
+562809 394013 Family Adeleidae 1 1 1
+394014 394013 Family Haemogregarinidae 1 1 1
+562814 394012 Suborder Eimeriorina 1 0 1
+391853 562814 Family Aggregatidae 1 0 0
+562822 562814 Family Calyptosporidae 1 0 0
+562824 562814 Family Caryotrophidae 1 0 0
+391924 562814 Family Cryptosporidiidae 1 0 1
+562827 562814 Family Dactylosomatidae 1 0 1
+562830 562814 Family Dobellidae 1 0 0
+562832 562814 Family Eimeriidae 1 1 1
+562841 562814 Family Sarcocystidae 1 1 1
+562843 562814 Family Selenococcidiidae 1 0 0
+591167 582463 Order Ixorheorida
+562801 582463 Order Protococcidiorida 1 0 0
+562802 562801 Family Eleutheroschizonidae 1 0 0
+562806 562801 Family Grelliidae 1 0 0
+562673 394011 Subclass Gregarinasina 1 1 1
+562672 562673 Class Gregarinea 1 1 1
+562674 562673 Order Archigregarinorida 1 0 0
+562675 562674 Family Exoschizonidae 1 0 0
+562677 562674 Family Selenidioididae 1 0 0
+394869 562673 Order Eugregarinorida 1 1 1
+562682 394869 Suborder Aseptatorina 1 0 0
+562683 562682 Family Aikinetocystidae 1 0 0
+562688 562682 Family Ganymedidae 1 0 1
+562693 562682 Family Lecudinidae 1 0 0
+562731 562682 Family Monocystidae
+562734 562682 Family Selenidiidae 1 0 0
+562747 562682 Family Urosporidae 1 0 0
+562760 394869 Suborder Blastogregarinorina 1 0 0
+562761 562760 Family Siedleckiidae 1 0 0
+394870 394869 Suborder Septatorina 1 1 1
+562763 394870 Family Actinocephalidae 1 1 1
+394872 394870 Family Cephaloidophoridae 1 0 1
+562768 394870 Family Cephalolobidae 1 0 0
+562771 394870 Family Didymophoridae
+562773 394870 Family Gregarinidae 1
+562777 394870 Family Metameridae 1
+394871 394870 Superfamily Porosporicae
+465333 394870 Family Porosporidae 1 0 0
+562786 394870 Family Uradiophoridae 1 0 1
+562793 562673 Order Neogregarinorida
+562620 450030 Subphylum Dinozoa
+562668 562620 Order Chytridiodinida 1 0 0
+577294 562620 Family Adnatosphaeridiaceae
+577373 562620 Family Aeroligeraceae
+19542 562620 Class Dinophyceae 1
+147418 19542 Order Dinoflagellida 1
+21005 19542 Phylum Dinophyta 1
+590355 19542 Class Pyrrophyta
+231760 19542 Order Actiniscales 1
+591145 231760 Order Actiniscida
+109409 231760 Family Actiniscaceae 1
+744375 19542 Order Amphilothales
+744376 744375 Family Amphilothaceae
+109386 19542 Order Blastodiniales 1
+562636 109386 Order Blastodinida 1 0 1
+562637 109386 Family Apodinidae 1 0 0
+562640 109386 Family Blastodinidae 1 0 0
+562644 109386 Family Diplomorphidae 1 0 0
+562649 109386 Family Haplozoonidae 1 0 0
+345493 109386 Family Oodiniaceae 1
+562652 109386 Family Oodinidae 1 0 0
+562659 109386 Family Paradinophycidae 1 0 0
+231767 19542 Order Brachidiniales 1
+146214 231767 Order Brachydiniales 1
+493844 19542 Order Coccidiniales
+591146 493844 Order Coccidinida
+109400 493844 Family Chytriodiniaceae 1
+577497 493844 Family Syndiniaceae
+599630 19542 Order Desmomastigales
+599631 599630 Family Desmomastigaceae
+599632 599630 Family Protaspidaceae
+599633 599630 Family Spiromonadaceae
+836378 19542 Family Haplozoonaceae
+146204 19542 Subclass Dinophycidae 1
+109390 19542 Order Dinophysiales 1
+591154 109390 Order Dinophysida
+109405 109390 Family Amphisoleniaceae 1
+231771 109390 Family Citharistaceae 1
+231772 109390 Family Dinophysaceae 1
+162493 231772 Family Dinophysidae 1
+109406 109390 Family Dinophysiaceae 1
+231781 109390 Family Oxyphysaceae
+146206 19542 Subclass Ebriophycidae 1
+146210 19542 Subclass Ellobiophycidae 1
+109391 19542 Order Gonyaulacales 1
+591157 109391 Order Gonyaulacida
+231796 109391 Family Amphidomataceae 1
+109421 109391 Family Ceratiaceae 1
+109422 109391 Family Ceratocoryaceae 1
+109425 109391 Family Cladopyxidaceae 1
+109408 109391 Family Goniodomataceae 1
+109439 109408 Family Triadiniaceae 1
+109428 109391 Family Gonyaulacaceae 1
+109429 109391 Family Heterodiniaceae 1
+109431 109391 Family Ostreopsidaceae 1
+836360 109391 Family Protoceratiaceae
+109436 109391 Family Pyrophacaceae 1
+109392 19542 Order Gymnodiniales 1
+591158 109392 Order Gymnodiniida
+231768 109392 Family Brachidiniaceae 1
+109443 231768 Family Brachydiniaceae 1
+109410 109392 Family Gymnodiniaceae 1
+155552 109410 Family Gymnodiniidae
+599662 109392 Family Hemidiniaceae
+599664 109392 Family Kareniaceae
+109413 109392 Family Polykrikaceae 1
+150278 109413 Family Polykrikidae
+162515 109392 Family Pronoctilucaceae
+178558 162515 Family Pronoctilucidae
+146249 109392 Family Ptychodiscaceae 1
+577245 109392 Family Tovelliaceae
+109415 109392 Family Warnowiaceae 1
+368684 19542 Order Lophodiniales 1
+591148 368684 Order Lophodinida
+109412 368684 Family Lophodiniaceae 1
+150280 109412 Family Lophodiniidae
+109393 19542 Order Noctilucales 1
+591144 109393 Order Noctilucida
+146252 109393 Family Kofoidiniaceae 1
+109417 109393 Family Leptodiscaceae 1
+109418 109393 Family Noctilucaceae 1
+231795 109393 Family Protodiniferaceae 1
+146254 19542 Order Oxyrrhinales 1
+591162 146254 Order Oxyrrhida
+146255 146254 Family Oxyrrhinaceae 1
+109394 19542 Order Peridiniales 1
+591151 109394 Order Peridiniida
+109419 109394 Family Archaesphaerodiniopsidaceae 1
+109420 109394 Family Calciodinellaceae 1
+599684 109394 Family Centrodiniaceae
+231797 109394 Family Ceratocorythaceae 1
+109423 109394 Family Ceratoperidiniaceae 1
+593652 109394 Family Congruentidiaceae
+109426 109394 Family Crypthecodiniaceae 1
+109427 109394 Family Dinosphaeraceae 1
+146253 109394 Family Glenodiniaceae 1
+370356 109394 Family Glenodiniopsidaceae 1
+231800 109394 Family Heterocapsaceae 1
+109430 109394 Family Kolkwitziellaceae 1
+493895 109394 Family Lessardiaceae
+109432 109394 Family Oxytoxaceae 1
+150284 109432 Family Oxytoxidae
+109433 109394 Family Peridiniaceae 1
+150282 109433 Family Peridiniidae
+246596 109394 Family Pfiesteriaceae 1
+836367 109394 Family Phthanoperidiniaceae
+109434 109394 Family Podolampaceae 1
+231806 109394 Family Podolampadaceae 1
+109435 109394 Family Protoperidiniaceae 1
+231846 109435 Family Diplopsaliaceae
+231845 109435 Family Kolkwitziellaceae
+109437 109394 Family Thecadiniaceae 1
+493845 19542 Subclass Peridiniphycidae
+109395 19542 Order Phytodiniales 1
+109396 19542 Order Prorocentrales 1
+591152 109396 Order Prorocentrida
+231849 109396 Family Haplodiniaceae
+109442 109396 Family Prorocentraceae 1
+150274 109442 Family Prorocentridae
+109398 19542 Order Pyrocystales 1
+591149 109398 Order Pyrocystida
+109444 109398 Family Pyrocystaceae 1
+109399 19542 Order Suessiales 1
+591160 109399 Order Suessiida
+599712 109399 Family Biecheleriaceae
+599713 109399 Family Borghiellaceae
+231813 109399 Family Suessiaceae
+109445 109399 Family Symbiodiniaceae 1
+146213 19542 Order Syndiniales 1
+582437 146213 Order Syndinida
+109401 146213 Family Amoebophryaceae 1
+562663 146213 Family Syndinidae 1 0 0
+146212 146213 Suborder Syndiniophycidae 1
+836374 19542 Family Thalassomycetaceae
+146211 19542 Order Thalassomycetales 1
+231814 19542 Order Thoracosphaerales 1
+591150 231814 Order Thoracosphaeida
+109438 231814 Family Thoracosphaeraceae 1
+591143 562620 Class Noctilucea
+562634 562620 Class Peridinea 1 0 1
+591147 562634 Order Dinamoebida
+599634 591147 Family Dinamoebaceae
+591153 562634 Subclass Dinophysoidia
+591155 591153 Order Nannoceratopsida
+591156 562634 Subclass Gonyaulacoidia
+591161 562634 Subclass Oxyrrhia
+562635 562634 Subclass Peridinoidia 1 0 1
+591159 562634 Subclass Suessioidia
+562662 562620 Class Syndinea
+591136 562620 Class Colponemea
+591138 591136 Order Algovorida
+591137 591136 Order Colponemida
+562624 562620 Class Ellobiopsea 1 0 0
+562625 562624 Order Ellobiopsida 1 0 0
+562626 562625 Family Ellobiopsidae 1 0 0
+160466 562626 Family Ellobiospidae
+591139 562620 Class Myzomonadea
+591140 591139 Order Chilovorida
+591141 591139 Order Voromonadida
+178968 562620 Class Perkinsea 1
+103337 178968 Class Perkinsasida 1
+591142 178968 Order Perkinsida
+103338 591142 Order Perkinsorida 1
+103339 591142 Family Perkinsidae 1 0 0
+
pc1 3 Phylum Cercozoa
pc2 pc1 Class Chlorarachniophyceae Hibberd & Norris, 1984
pc2b pc2 Class Chlorarachnea
-pc3 pc2 Order Chlorarachniales
+pc3 pc2 Order Chlorarachniales
pc3b pc3 Order Chlorachniida
pc4 pc3 Family Chlorarachniaceae Ishida & Y. Hara, 1996
pc4b pc4 Family Chlorarachniidae Hibberd & Norris, 1984

0 comments on commit afccc62

Please sign in to comment.