Adding phylum Myzozoa to dataset

Author: mdoering

README.md

@@ -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).

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