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njdowdy / tpt-taxonomy

Foundational taxonomic resources for the TPT project
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Issues in Acari-standardized-v2 #25

Open Jegelewicz opened 1 year ago

Jegelewicz commented 1 year ago

It appears to me that there are some duplicated rows in the Acari-standardized-v2 file, for example:

source taxonID scientificNameID acceptedNameUsageID parentNameUsageID originalNameUsageID nameAccordingToID namePublishedInID taxonConceptID scientificName acceptedNameUsage parentNameUsage originalNameUsage nameAccordingTo namePublishedIn namePublishedInYear higherClassification kingdom phylum class subclass superorder order suborder infraorder parvorder nanorder superfamily family subfamily tribe subtribe genus infragenericEpithet specificEpithet infraspecificEpithet taxonRank verbatimTaxonRank scientificNameAuthorship vernacularName nomenclaturalCode taxonomicStatus nomenclaturalStatus taxonRemarks canonicalName
GBIF acari_2184932     2184982         Argas echinops Hoogstraal, Uilenberg & Blanc, 1967 Argas echinops             Animalia Arthropoda Arachnida     Ixodida           Argasidae       Argas   echinops   species   Hoogstraal, Uilenberg & Blanc, 1967     accepted     Argas echinops
GBIF acari_2184932     2184982         Argas echinops Hoogstraal, Uilenberg & Blanc, 1967 Argas echinops             Animalia Arthropoda Arachnida     Ixodida           Argasidae       Argas   echinops   species   Hoogstraal, Uilenberg & Blanc, 1967     accepted     Argas echinops

Is there a specific reason for this? Or am I missing some slight difference that is meaningful?

njdowdy commented 1 year ago

I don't see a reason why both should be there. Not sure why that happened.

Jegelewicz commented 1 year ago

This one is confusing, because they are essentially the same, but the line with the epithet that doesn't match the canonical or scientific name is listed as doubtful and the one with the mismatch is listed as accepted.

source taxonID scientificNameID acceptedNameUsageID parentNameUsageID originalNameUsageID nameAccordingToID namePublishedInID taxonConceptID scientificName acceptedNameUsage parentNameUsage originalNameUsage nameAccordingTo namePublishedIn namePublishedInYear higherClassification kingdom phylum class subclass superorder order suborder infraorder parvorder nanorder superfamily family subfamily tribe subtribe genus infragenericEpithet specificEpithet infraspecificEpithet taxonRank verbatimTaxonRank scientificNameAuthorship vernacularName nomenclaturalCode taxonomicStatus nomenclaturalStatus taxonRemarks canonicalName
GBIF acari_11088637     2194436         Hoplophorella miranda (Niedbala, 1988)               Animalia Arthropoda Arachnida     Sarcoptiformes           Phthiracaridae       Hoplophorella   mirandus   species   (Niedbala, 1988)     accepted     Hoplophorella miranda
GBIF acari_11088637     2194436         Hoplophorella miranda (Niedbala, 1988)               Animalia Arthropoda Arachnida     Sarcoptiformes           Phthiracaridae       Hoplophorella   miranda   species   (Niedbala, 1988)     doubtful     Hoplophorella miranda
Jegelewicz commented 1 year ago

These are the duplicated taxonIDs in the file - I can't see a reason for this to happen, but perhaps there is?

acari_11088637 acari_2181890 acari_2181958 acari_2181959 acari_2181973 acari_2184932 acari_4547164 acari_4547195 acari_4547201 acari_4547507 acari_4547732 acari_4547738 acari_4547745 acari_4547748 acari_4547751 acari_4547756 acari_4547779 acari_4547862 acari_4547917 (this one is in the file 3 times) acari_4547931 acari_6899321 acari_6901028 acari_6901850 acari_8398357 acari_9323380 acari_9786356

Jegelewicz commented 1 year ago

Sorry to be a pest - I am just coming across this as I try to transform data for loading into Arctos....

njdowdy commented 1 year ago

No, this is good to identify. I just don't have bandwidth to sort through at the moment. But we can leave the issues open until I (or someone) do.

Jegelewicz commented 1 year ago

Totally! No need to rush anything - I can just exclude them or make judgements about what to include and document that on my end. Thanks!!!

Jegelewicz commented 1 year ago

These all have some weirdness in the author text

taxonID scientificName scientificNameAuthorship expected authorship
acari_6135175 Nippohermannia parallela (Aoki), 1960 , 1960 (Aoki) (Aoki), 1960
acari_9520887 Rhabdocarpus consanguineus (Athias-Henriot), 1904 , 1904 (Athias-Henriot) (Athias-Henriot), 1904
acari_6135068 Cycetogamasus diviortus (Athias-Henriot), 1967 , 1967 (Athias-Henriot) (Athias-Henriot), 1967
acari_6135227 Platynothrus pelitfer (C. L. Koch), 1989 , 1989 (C. L. Koch) (C. L. Koch), 1989
acari_6135343 Cheletomimus wellsinus (De Leon), 1967 , 1967 (De Leon) (De Leon), 1967
acari_6135088 Lasioseius sugawarae (Ehara), 1964 , 1964 (Ehara) (Ehara), 1964
acari_6135082 Parasitus unicornutus (Ewing), 1909 , 1909 (Ewing) (Ewing), 1909
acari_6135267 Glycycometus malaysiensis (Fain & Nadchatram), 1980 , 1980 (Fain & Nadchatram) (Fain & Nadchatram), 1980
acari_6135167 Gamasolaelaps whartoni (Farrier), 1957 , 1957 (Farrier) (Farrier), 1957
acari_6135408 Zetzellia exserta (Gonzalez), 1963 , 1963 (Gonzalez) (Gonzalez), 1963
acari_6135414 Zetzellia longiseta (Gonzalez), 1963 , 1963 (Gonzalez) (Gonzalez), 1963
acari_6135406 Zetzellia novazelandica (Gonzalez), 1963 , 1963 (Gonzalez) (Gonzalez), 1963
acari_6135412 Zetzellia congolensis (Gonzalez), 1965 , 1965 (Gonzalez) (Gonzalez), 1965
acari_6135410 Zetzellia macrommata (Gonzalez), 1965 , 1965 (Gonzalez) (Gonzalez), 1965
acari_6135405 Zetzellia tucumanensis (Gonzalez), 1965 , 1965 (Gonzalez) (Gonzalez), 1965
acari_2128578 Calacarus carinatus (Green), 1890 , 1890 (Green) (Green), 1890
acari_4337881 Lobohalacarus dolgarae (Green), 1954 , 1954 (Green) (Green), 1954
acari_2180742 Copidognathus oculatus (Hodge, 1863), 1889 , 1889 (Hodge, 1863) (Hodge, 1863), 1889
acari_2180729 Copidognathus granulatus (Hodge, 1863), 1963 , 1963 (Hodge, 1863) (Hodge, 1863), 1963
acari_5738925 Cosell falsus (Huang & Wang), 2009 , 2009 (Huang & Wang) (Huang & Wang), 2009
acari_6135474 Epitrimerus libocedri (Keifer), 1939 , 1939 (Keifer) (Keifer), 1939
acari_6135483 Tegonotus mangiferae (Keifer), 1946 , 1946 (Keifer) (Keifer), 1946
acari_4543942 Aculops pelekassi (Keifer), 1959 , 1959 (Keifer) (Keifer), 1959
acari_6135479 Cosella fleschneri (Keifer), 1959 , 1959 (Keifer) (Keifer), 1959
acari_6135487 Aceria litseae (Keifer), 1972 , 1972 (Keifer) (Keifer), 1972
acari_6135493 Aceria kuko (Kishida), 1927 , 1927 (Kishida) (Kishida), 1927
acari_6135264 Tyreophagus entomophagus (Laboceibene & Robin), 1862 , 1862 (Laboceibene & Robin) (Laboceibene & Robin), 1862
acari_6135484 Tegonotus aegopodii (Liro), 1941 , 1941 (Liro) (Liro), 1941
acari_6135463 Bakerina ziolanensis (Lo & HO), 1989 , 1989 (Lo & HO) (Lo & HO), 1989
acari_4651469 Steneotarsonemus bancrofti (Michael), 1890 , 1890 (Michael) (Michael), 1890
acari_6135243 Cologlyphus berleis (Michael), 1903 , 1903 (Michael) (Michael), 1903
acari_4542791 Lobohalacarus gallicus (Migot), 1926 , 1926 (Migot) (Migot), 1926
acari_6135491 Aceria mikaniae (Nalepa), 1918 , 1918 (Nalepa) (Nalepa), 1918
acari_6135014 Kleemania plumosa (Oudemans), 1902 , 1902 (Oudemans) (Oudemans), 1902
acari_4654328 Eutrombicula wichmanni (Oudemans), 1905 , 1905 (Oudemans) (Oudemans), 1905
acari_6135458 Bryobia rubioculus (Scheuten), 1857 , 1857 (Scheuten) (Scheuten), 1857
acari_6135492 Aceria spicati (Stebbins), 1909 , 1909 (Stebbins) (Stebbins), 1909
acari_6135415 Zetzellia fleschneri (Summers), 1960 , 1960 (Summers) (Summers), 1960
acari_4336854 Agauopsis exornata (Trouessart, 1889), 1899 , 1899 (Trouessart, 1889) (Trouessart, 1889), 1899
acari_4337370 Copidognathus poucheti (Trouessart, 1893), 1983 , 1983 (Trouessart, 1893) (Trouessart, 1893), 1983
acari_2180744 Copidognathus reticulatus (Trouessart, 1893), 1983 , 1983 (Trouessart, 1893) (Trouessart, 1893), 1983
acari_6135074 Parasitus bicornutus (Tseng), 1995 , 1995 (Tseng) (Tseng), 1995
acari_6135079 Parasitus bisiculus (Tseng), 1995 , 1995 (Tseng) (Tseng), 1995
acari_6135075 Parasitus eucervicornis (Tseng), 1995 , 1995 (Tseng) (Tseng), 1995
acari_6135071 Parasitus flagellispinosus (Tseng), 1995 , 1995 (Tseng) (Tseng), 1995
acari_6135080 Parasitus multidenticulatus (Tseng), 1995 , 1995 (Tseng) (Tseng), 1995
acari_6135072 Parasitus scirpiculatus (Tseng), 1995 , 1995 (Tseng) (Tseng), 1995
acari_6135077 Parasitus tonpuensis (Tseng), 1995 , 1995 (Tseng) (Tseng), 1995
acari_6135081 Parasitus trifurcatus (Tseng), 1995 , 1995 (Tseng) (Tseng), 1995
acari_6135073 Parasitus trispinosus (Tseng), 1995 , 1995 (Tseng) (Tseng), 1995
acari_6135070 Parasitus cervicornis (Var Daete), 1975 , 1975 (Var Daete) (Var Daete), 1975
acari_6135169 Ruehmnenteria malayica (Vitathum), 1921 , 1921 (Vitathum) (Vitathum), 1921
acari_6135160 Trichouropoda austroasiatica (Vitzthum), 1921 , 1921 (Vitzthum) (Vitzthum), 1921
acari_6135257 Acotyledon rhizoglyphoides (Zachvatkin), 1937 , 1937 (Zachvatkin) (Zachvatkin), 1937
acari_6902728 Amhyadesia heteromorpha, 1992 , 1992  
acari_2191774 Carabodes translamellatus, 1990 , 1990  
acari_2198677 Ceratozetes gemmula, 1990 , 1990  
acari_2197237 Corynoppia maritima, 1991 , 1991  
acari_2192953 Cosmochthonius monegrensis, 1991 , 1991  
acari_2189394 Ctenobelba parafoliata, 1991 , 1991  
acari_5175196 Damaeus pyrenaicus, 1991 , 1991  
acari_2189908 Hemileius humeralis, 1991 , 1991  
acari_2190525 Lauritzenia sinuata, 1990 , 1990  
acari_2198022 Licneremaeus similis, 1990 , 1990  
acari_2196117 Metabelbella janae, 1991 , 1991  
acari_2196298 Montizetes delamellatus, 1991 , 1991  
acari_2197540 Multioppia integra, 1990 , 1990  
acari_2195209 Oribatella triangulata, 1990 , 1990  
acari_2197940 Passalozetes imperfectus, 1991 , 1991  
acari_2193652 Pergalumna minoricana, 1991 , 1991  
acari_2193744 Pergalumna semistriata, 1990 , 1990  
acari_2197562 Pseudoamerioppia balearica, 1991 , 1991  
acari_2197392 Ramonoppia aequiseta, 1990 , 1990  
acari_2196877 Ramusella subiasi, 1990 , 1990  
acari_6135251 Tyrophagus dinidiatus, 1804 , 1804  
Jegelewicz commented 1 year ago

Here is an apparent misspelling/duplicate in the file:

Name ID
Protomyobia claperedei (Poppe, 1896) acari_8449337
Protomyobia (Protomyobia) claparedei acari_6747
Jegelewicz commented 1 year ago

This file only includes species and lower taxon names. Should it not also include all of the necessary higher taxa? Many mites are only identified to a higher taxon and including those in the file would ensure consistency in the classifications. OK - I see that some are included, but some are missing? Such as these genera:

Orycteroxenus Echinonyssus Euryparasitus Haemogamasus Macronyssus

Jegelewicz commented 1 year ago

As a non-taxonomist, I am asking because I don't know! Should all of these classifications include the subclass Acari?

It seems like they should because some members of the order Mesostigmata include the subclass and others do not...