MOSJ2016 taxonomy issues

[cnrdh]

Phytoplankton Checked 235 names, found 91 in local taxonomy, unknown: 144 [!]

$ cat data/deposit/2016/MOSJ2016/mosj2016_phytoplankton_all_datajw.tsv | ./bin/csv-transform --ndjson | ndjson-map d.takson | sort |uniq | ./bin/gbif-validate-taxon 

cat data/deposit/2016/MOSJ2016/mosj2016_phytoplankton_all_datajw.tsv | ./bin/dwc-occurrence-csv-transform |ndjson-filter 'd.errors' | ndjson-split 'd.errors' | sort | uniq

{"value":"aff. Telonema sp.","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"aff. Telonema sp.","dataPath":".scientificName","message":"should match pattern \"^[A-Z][a-z\\s-]\""}
{"value":"Bifagellates","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Calycomonas wulffii","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Chaetoceros convolutus f. trisetosa","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Chaetoceros holsaticus","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Chrysophycean","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Coccolithophores","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Contricibra","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"","dataPath":".scientificName","message":"should match pattern \"^[A-Z][a-z\\s-]\""}
{"value":"Dinohyceae","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Dinophycean","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Dunaliella salina","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Fecal pellets","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Fourfagellates","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Gyrodinium lahryma","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Heliozoa","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Incertae taxa","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Leprotintinnus","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Pelagococcus","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Spora","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Stenoneis inconspicua","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Strobilidium conicum","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Strobilidium spiralis","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Symbiont Mesodinium rubrum","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Telonema antarctica","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Tintinidae","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Tintinnus","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Uniflagellates","dataPath":".scientificName","message":"should be equal to one of the allowed values"}

[cnrdh]

Handnet

Checked 70 names, found 42 in local taxonomy, unknown: 28 [ 'Alexandrium sp.',
  'Chaetoceros brevipes',
  'Ciliophora indet. 30-40um',
  'Ciliophora indet. 40-50um',
  'Ciliophora indet. 50-60um',
  'Cochlodinium sp.',
  'Dictiocha speculum',
  'Didinium sp.',
  'Dinophyceae indet. cyst',
  'Dinphyceae indet. cyst',
  'Fecal pellets',
  'Gonyaulax sp.',
  'Gymnodiniales indet. 20-30um',
  'Gymnodiniales indet. 30-40um',
  'Gymnodiniales indet. 40-50um',
  'Gymnodiniales indet. 50-60um',
  'Gymnodinium sp. 30-40um',
  'Leprotintinnopsis sp.',
  'Licmophora sp.',
  'Polarella glacialis cyst',
  'Protoperidinium conicum',
  'Pseudo-nitzschia delicatissima/pseudodelicatissima',
  'Pterosperma sp.',
  'Scrippsiella sp.',
  'Strombidium sp.',
  'Thalassiosira gravida/antarctica',
  'Tintinnopsis sp.',
  'Tintinnpsis sp.' ]

$ cat data/deposit/2016/MOSJ2016/mosj2016-handnet-biodiversity.tsv | ./bin/dwc-occurrence-csv-transform | ndjson-split 'd.errors' | sort | uniq

{"value":"20 – 0","dataPath":".maximumDepthInMeters","message":"should be number,null"}
{"value":"Chaetoceros brevipes","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Dictiocha speculum","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Dinphyceae","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Fecal pellets","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Leprotintinnopsis","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Protoperidinium conicum","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Tintinnpsis","dataPath":".scientificName","message":"should be equal to one of the allowed values"}

[cnrdh]

Microplankton

Checked 71 names, found 43 in local taxonomy, unknown: 28 [ 'Alexandrium sp.',
  'Chaetoceros furcellatus spores',
  'Chaetoceros holsaticus',
  'Ciliophora indet. 20-30um',
  'Ciliophora indet. 30-40um',
  'Ciliophora indet. 40-50um',
  'Ciliophora indet. 60-70um',
  'Cochlodinium sp.',
  'Didinium sp.',
  'Dinophyceae indet. cyst',
  'Euplotes sp.',
  'Fecal pellets',
  'Gymnodiniales indet. 20-30um',
  'Gymnodiniales indet. 30-40um',
  'Gymnodiniales indet. 40-50um',
  'Gymnodiniales indet. 50-60um',
  'Heliozoa indet.',
  'Leprotintinnopsis sp.',
  'Licmophora sp.',
  'Pleurosigma sp.',
  'Polarella glacialis cyst',
  'Protoperidinium conicum',
  'Pterosperma sp.',
  'Scrippsiella sp.',
  'Strombidium sp.',
  'Thalassiosira gravida/antarctica',
  'Tintinnopsis sp.',
  'empty' ]

cat data/deposit/2016/MOSJ2016/mosj2016-microplankton-biodiversity.tsv | ./bin/dwc-occurrence-csv-transform |ndjson-filter 'd.errors'| ndjson-split 'd.errors' | sort | uniq

{"value":"25/5","dataPath":".maximumDepthInMeters","message":"should be number,null"}
{"value":"Chaetoceros holsaticus","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"","dataPath":".scientificName","message":"should match pattern \"^[A-Z][a-z\\s-]\""}
{"value":"Fecal pellets","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Heliozoa","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Leprotintinnopsis","dataPath":".scientificName","message":"should be equal to one of the allowed values"}
{"value":"Protoperidinium conicum","dataPath":".scientificName","message":"should be equal to one of the allowed values"}

[cnrdh]

Status now:

Phyto unknown: 20 [ 'Bifagellates', 'Calycomonas wulffii', 'Chaetoceros convolutus f. trisetosa', 'Chrysophycean', 'Coccolithophores', 'Contricibra', 'Dinohyceae', 'Dinophycean', 'Dunaliella salina', 'Fecal pellets', 'Fourfagellates', 'Gyrodinium lahryma', 'Incertae taxa', 'Pelagococcus', 'Strobilidium conicum', 'Strobilidium spiralis', 'Telonema antarctica', 'Tintinidae', 'Tintinnus', 'Uniflagellates' ]

Hand: unknown: 7 [ 'Chaetoceros brevipes', 'Dictiocha speculum', 'Dinphyceae', 'Fecal pellets', 'Leprotintinnopsis', 'Protoperidinium conicum', 'Tintinnpsis' ]

Micro: unknown: 3 [ 'Fecal pellets', 'Leprotintinnopsis', 'Protoperidinium conicum' ]

[cnrdh]

See also #48 – way better now

MOSJ2016 mosj2016_pht.ndjson Checked 158 names, found 144 in local taxonomy, unknown: 14

MOSJ2016 mosj2016_mit.ndjson Checked 63 names, found 62 in local taxonomy, unknown: 1

MOSJ2016 mosj2016_han.ndjson Checked 64 names, found 59 in local taxonomy, unknown: 5