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npolar / marine-db

https://doi.org/10.21334/marine-db
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Protist taxonomy issues from N-ICE2015 #30

Open cnrdh opened 5 years ago

cnrdh commented 5 years ago

Common: "Genus sp1/sp2" => "cf. sp1/sp2" ? Chaetoceros convolutus/concavicornis

Some problems:

"var." "Bacillaria paxillifer var.tumidula" 32 ["aff Catenula",null,null] "Chrysophyceae cyst 1" Cocal sphere 67 Spora 1 "Deformed Ciliophora with endosymbionts 1 ["Empty dinophyceae",null,"spores"] 1 ["Empty unknown",null,"cysts"] 1 ["Encysting protist on stem",null,null] 5 ["Fragilariopsis cylindrus/F. Reginae-jahniae",null,null] 99 Incertains taxa 5 ["Unknown",null,"cysts"] 2 ["Unknown",null,"spores"] 11 ["Unknown taxon",null,null]

cnrdh commented 5 years ago

ndjson-join --left 'd.scientificName' data/deposit/2015/N-ICE2015/biodiversity/n-ice2015-ice-algae-taxonomy.ndjson data/master/taxonomy/taxonomy-db.ndjson | ndjson-filter '!d[1]' | ndjson-map 'd[0]' | ./bin/ndjson-transform --tsv | ./bin/gbif-validate-species

cnrdh commented 5 years ago

cat data/deposit/iopan/protist-biodiversity/n-ice2015_phytopl_micrpl_taxonomy-iopan.tsv | ./bin/dwc-occurrence-csv-transform 2> /tmp/e |ndjson-filter d.errors | ndjson-split d.errors | sort | ndjson-map '[d.dataPath,d.value]' | sort | uniq [".individualCount","#DIV/0!"] [".maximumDepthInMeters","in log does not exist"] [".organismQuantity","#DIV/0!"] [".organismQuantity","#VERDI!"] [".scientificName","Autotrophic flagellates"] [".scientificName","Bifagellates"] [".scientificName","Chrysophycean"] [".scientificName","Cocal sphere"] [".scientificName","Ebria tripartita"] [".scientificName","Entomoneis kjellmanii var kariana"] [".scientificName","Fagellatae"] [".scientificName","Gonyaulax gracilis (aff. Poulin)"] [".scientificName","Gymndinium arcticum"] [".scientificName","Gymndinium galeatum"] [".scientificName","Gymndinium gracilentum"] [".scientificName","Gymndinium/Gyrodinium"] [".scientificName","Gymndinium simplex"] [".scientificName","Oligotrichea"] [".scientificName","Pennales"] [".scientificName","Spora"] [".scientificName","Symbiont Mesodinium rubrum"]

cnrdh commented 2 years ago

$ ndjson-join --left 'd.scientificName' data/input/iopan/protist-biodiversity/ndjson/n-ice2015_pht.ndjson data/master/taxonomy/taxonomy-db.ndjson | ndjson-filter '!d[1]' | ndjson-map 'd[0]' | ./bin/gbif-validate-taxon | ./bin/gbif-validate-taxon | grep Chromista

cnrdh commented 2 years ago

See #57