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Major ranks missing in classification #561

Open mdoering opened 1 year ago

mdoering commented 1 year ago

There are several areas in the COL Classification where there are major Linnean ranks (kpcof) missing, but where intermediate sub- or super ranks are existing. Sometimes this might be for good reasons, but it is odd to have subfamilies without a known family. These cases should be reviewed and fixed where possible.

Attached are reports from the August 2023 COL checklist release. Reports are organised by missing Linnean ranks:

mdoering commented 1 year ago

Missing families:

9JG5G   SUBFAMILY   Heterotrichinae ORDER   Diptera
844NW   SUBFAMILY   Cadenatellinae  SUPERFAMILY Haploporoidea
844PJ   SUBFAMILY   Circopeltinae   ORDER   Camarodonta
7NY79   SUBFAMILY   Syphopsinae SUPERFAMILY [unassigned] Neogastropoda
B3GXF   SUBFAMILY   Microlaimoidea  SUBORDER    Desmodorina
8PRX8   SUBFAMILY   Cretatermitinae INFRAORDER  Isoptera
8NJ76   SUBFAMILY   Lipeurinae  SUPERFAMILY Philopteroidea
8NK3R   SUBFAMILY   Degeeriellinae  SUPERFAMILY Philopteroidea
8NHQK   SUBFAMILY   Goniocotinae    SUPERFAMILY Philopteroidea
8NL2B   SUBFAMILY   Pteroplistinae  SUPERFAMILY Grylloidea
mdoering commented 1 year ago

Missing phyla

J7  CLASS   Sporozoa    KINGDOM Protozoa
BK  CLASS   Filosia KINGDOM Protozoa
77  CLASS   Acantharia  KINGDOM Protozoa
C9  CLASS   Haplosporea KINGDOM Protozoa
622D9   CLASS   Endohelea   KINGDOM Chromista
mdoering commented 1 year ago

missing class:

8ZXX3   ORDER   Entomoplasmatales   PHYLUM  Tenericutes
8ZXVP   ORDER   Anaeroplasmatales   PHYLUM  Tenericutes
92ZQQ   ORDER   Haloplasmatales PHYLUM  Tenericutes
8ZXVF   ORDER   Acholeplasmatales   PHYLUM  Tenericutes
8ZXXV   ORDER   Mycoplasmatales PHYLUM  Tenericutes
LC  SUBCLASS    Rubrobacteridae PHYLUM  Actinobacteria
L7  SUBCLASS    Nitriliruptoridae   PHYLUM  Actinobacteria
KV  SUBCLASS    Coriobacteridae PHYLUM  Actinobacteria
KQ  SUBCLASS    Actinobacteridae    PHYLUM  Actinobacteria
8ZXVH   ORDER   Acidobacteriales    PHYLUM  Acidobacteria
3HR ORDER   Mantamonadida   SUBPHYLUM   Apusozoa
623D8   ORDER   Nephridiophagales   PHYLUM  Chytridiomycota
3F3 ORDER   Lahmiales   PHYLUM  Ascomycota
623DG   ORDER   Lauriomycetales PHYLUM  Ascomycota
4BL ORDER   Wiesneriomycetales  PHYLUM  Ascomycota
4B6 ORDER   Vezdaeales  PHYLUM  Ascomycota
494 ORDER   Triblidiales    PHYLUM  Ascomycota
47P ORDER   Thelocarpales   PHYLUM  Ascomycota
SR  ORDER   Basidiobolales  PHYLUM  Zygomycota
RJ  ORDER   Asellariales    PHYLUM  Mucoromycota
62239   ORDER   Dimargaritales  PHYLUM  Mucoromycota
Z4  ORDER   Coloniales  PHYLUM  Entoprocta
442 ORDER   Solitaria   PHYLUM  Entoprocta
62228   ORDER   Centrohelida    PHYLUM  Heliozoa
347 ORDER   Desmothoracida  PHYLUM  Heliozoa
3K9 ORDER   Microhelida PHYLUM  Heliozoa
6229F   ORDER   Bursovaginoidea PHYLUM  Gnathostomulida
38D ORDER   Filospermoidea  PHYLUM  Gnathostomulida
B6LFB   ORDER   Macrodasyida    PHYLUM  Gastrotricha
7NF8N   ORDER   Chaetonotida    PHYLUM  Gastrotricha
MK  ORDER   Acoela  SUBPHYLUM   Acoelomorpha
B6LMY   ORDER   Nemertodermatida    SUBPHYLUM   Acoelomorpha
B6LN6   ORDER   Priapulomorpha  PHYLUM  Priapulida
B6LNF   ORDER   Seticoronaria   PHYLUM  Priapulida
B3FYH   ORDER   Halicryptomorpha    PHYLUM  Priapulida
B3FYK   ORDER   Meiopriapulomorpha  PHYLUM  Priapulida
7NF4G   SUPERORDER  Macrostomorpha  SUBPHYLUM   Rhabditophora
62245   ORDER   Gnosonesimida   SUBPHYLUM   Rhabditophora
7NG9J   ORDER   Prorhynchida    SUBPHYLUM   Rhabditophora
7NG6G   ORDER   Fecampiida  SUBPHYLUM   Rhabditophora
7NFH2   ORDER   Bothrioplanida  SUBPHYLUM   Rhabditophora
B6LN7   ORDER   Prolecithophora SUBPHYLUM   Rhabditophora
7NFFB   ORDER   Polycladida SUBPHYLUM   Rhabditophora
7NFL2   ORDER   Rhabdocoela SUBPHYLUM   Rhabditophora
8ZDRS   ORDER   Mariplanellida  SUBPHYLUM   Rhabditophora
B6L64   ORDER   Tricladida  SUBPHYLUM   Rhabditophora
B6LN8   ORDER   Proseriata  SUBPHYLUM   Rhabditophora
B3FYL   ORDER   Nanaloricida    PHYLUM  Loricifera
NH  ORDER   Albuliformes    GIGACLASS   Actinopterygii
NX  ORDER   Amiiformes  GIGACLASS   Actinopterygii
622V4   ORDER   Pleuronectiformes   GIGACLASS   Actinopterygii
SV  ORDER   Batrachoidiformes   GIGACLASS   Actinopterygii
394 ORDER   Gasterosteiformes   GIGACLASS   Actinopterygii
3F6 ORDER   Lampriformes    GIGACLASS   Actinopterygii
X2  ORDER   Characiformes   GIGACLASS   Actinopterygii
3VN ORDER   Polypteriformes GIGACLASS   Actinopterygii
YR  ORDER   Clupeiformes    GIGACLASS   Actinopterygii
42M ORDER   Scorpaeniformes GIGACLASS   Actinopterygii
6223X   ORDER   Gonorynchiformes    GIGACLASS   Actinopterygii
3NQ ORDER   Notacanthiformes    GIGACLASS   Actinopterygii
46T ORDER   Syngnathiformes GIGACLASS   Actinopterygii
6228Z   ORDER   Beryciformes    GIGACLASS   Actinopterygii
3ZM ORDER   Saccopharyngiformes GIGACLASS   Actinopterygii
PJ  ORDER   Anguilliformes  GIGACLASS   Actinopterygii
MJ  ORDER   Acipenseriformes    GIGACLASS   Actinopterygii
335 ORDER   Cyprinodontiformes  GIGACLASS   Actinopterygii
4BY ORDER   Zeiformes   GIGACLASS   Actinopterygii
3LN ORDER   Myctophiformes  GIGACLASS   Actinopterygii
6236K   ORDER   Siluriformes    GIGACLASS   Actinopterygii
3QH ORDER   Osteoglossiformes   GIGACLASS   Actinopterygii
WQ  ORDER   Cetomimiformes  GIGACLASS   Actinopterygii
62246   ORDER   Gobiesociformes GIGACLASS   Actinopterygii
463 ORDER   Stomiiformes    GIGACLASS   Actinopterygii
334 ORDER   Cypriniformes   GIGACLASS   Actinopterygii
3QF ORDER   Osmeriformes    GIGACLASS   Actinopterygii
3LB ORDER   Mugiliformes    GIGACLASS   Actinopterygii
47D ORDER   Tetraodontiformes   GIGACLASS   Actinopterygii
RW  ORDER   Ateleopodiformes    GIGACLASS   Actinopterygii
623BF   ORDER   Gymnotiformes   GIGACLASS   Actinopterygii
3FS ORDER   Lepisosteiformes    GIGACLASS   Actinopterygii
RY  ORDER   Atheriniformes  GIGACLASS   Actinopterygii
3ZR ORDER   Salmoniformes   GIGACLASS   Actinopterygii
S8  ORDER   Aulopiformes    GIGACLASS   Actinopterygii
3GY ORDER   Lophiiformes    GIGACLASS   Actinopterygii
3PT ORDER   Ophidiiformes   GIGACLASS   Actinopterygii
46Q ORDER   Synbranchiformes    GIGACLASS   Actinopterygii
T6  ORDER   Beloniformes    GIGACLASS   Actinopterygii
37D ORDER   Esociformes GIGACLASS   Actinopterygii
38T ORDER   Gadiformes  GIGACLASS   Actinopterygii
45N ORDER   Stephanoberyciformes    GIGACLASS   Actinopterygii
36H ORDER   Elopiformes GIGACLASS   Actinopterygii
PC  ORDER   Perciformes GIGACLASS   Actinopterygii
3VJ ORDER   Polymixiiformes GIGACLASS   Actinopterygii
3SB ORDER   Percopsiformes  GIGACLASS   Actinopterygii
QQ  ORDER   Archaeolithophyllales   PHYLUM  Rhodophyta
6236G   ORDER   Schizopyrenida  PHYLUM  Amoebozoa
3S3 ORDER   Pelobiontida    PHYLUM  Amoebozoa
B6MTV   ORDER   Eugregarinida   PHYLUM  Miozoa
6227K   ORDER   Archigregarinida    PHYLUM  Miozoa
N6  ORDER   Againococcidiida    PHYLUM  Miozoa
3N5 ORDER   Neogregarinida  PHYLUM  Miozoa
3WQ ORDER   Protococcidiida PHYLUM  Miozoa
623FH   ORDER   Piroplasmida    PHYLUM  Miozoa
6222H   ORDER   Eucoccidiida    PHYLUM  Miozoa
RC  SUBCLASS    Arachnida   PHYLUM  Arthropoda
B8WKR   SUBCLASS    Mystacocarida   PHYLUM  Arthropoda
mdoering commented 1 year ago

See also https://github.com/CatalogueOfLife/data/issues/484

mdoering commented 1 year ago

SQL used to generate the family report:

\copy (SELECT u.id, n.rank, n.scientific_name, pn.rank as parent_rank, pn.scientific_name as parent
 FROM name_usage u 
    JOIN name n ON u.name_id=n.id AND u.dataset_key=n.dataset_key
    JOIN name_usage p ON u.parent_id=p.id AND u.dataset_key=p.dataset_key
    JOIN name pn ON p.name_id=pn.id AND u.dataset_key=pn.dataset_key
 WHERE u.dataset_key=3 AND NOT is_synonym(u.status)
    AND n.rank <= 'FAMILY' AND n.rank > 'ORDER'
    AND pn.rank < 'ORDER'
 ) to 'order.tsv';