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https://doi.org/10.21334/marine-db
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Update phytoplankton taxonomy #21

Closed cnrdh closed 2 years ago

cnrdh commented 5 years ago 
./bin/csv-to-ndjson < data/deposit/taxonomy/phytoplankton-2017-12-22.csv | sort | uniq | ndjson-map 'd.species=d.species.replace(/\ssp\.$/, ""),d'  | sort | uniq | wc -l

405 lines => 404 species => 394 after removing " sp." 267 names matches against taxon-db 128 non-matches

To-add:

[ 'Chrysophyta',
'Dinophysis rotundata',
'Dinophyta',
'Favella meunieri',
'Gymnodinium pulchellum',
'Heterokontophyta',
'Myrionecta rubra',
'Nitzschia arctica',
'Pleurochrysis carterae',
'Prorocentrum minimum',
'Protoperidinium marielebourae',
'Scuticociliatida',
'Strobilidium spiralis',
'Strombidium spirale' ]

After { 'taxon-db': 641, candidates: 393, 'to-check': 77, added: 14 }

cnrdh commented 5 years ago

From Philipp Assmy

Check

cnrdh commented 5 years ago

The non-matches are listed here, needs review

cnrdh commented 5 years ago

More corrections from PA: It should be Pseudo-nitzschia pseudodelicatissima instead of Pseudo-nitzschia pseudodelicatisima.

The following species I could neither find in Algaebase nor in WoRMS:

cnrdh commented 5 years ago

From: Agnieszka Tatarek

  1. Gymnodinium gracilientum - should be Gymnodinium gracilentum http://www.marinespecies.org/aphia.php?p=taxdetails&id=232772
    1. Gymnodinium gaelatum - Gymnodinium galeatum http://www.marinespecies.org/aphia.php?p=taxdetails&id=232765
    2. Coxiella pseudoannulata - Coxliella pseudoannulata http://www.marinespecies.org/aphia.php?p=taxdetails&id=427486 (however this has general name issue so the status is: nomen dubium)
    3. Karenia brevis (has the genus name changed?) - no, this is correct name Karenia brevis http://www.marinespecies.org/aphia.php?p=taxdetails&id=233015
    4. Protherythropsis vigilans -Proterythropsis vigilans however the new name is : Nematopsides vigilans http://www.marinespecies.org/aphia.php?p=taxdetails&id=547527
cnrdh commented 5 years ago

This issue is a bit confusing.

  1. Taxonomy-db needs to be fixed.
  2. References in the functional groups need to be fixed, see #22
cnrdh commented 5 years ago

Updated checklist: "Achnanthes longipes" "Actinocyclus" "Actinocyclus tenuissimus" "Ceratium fusus" "Chaetoceros convulutus" "Coccolithophora" "Coscinodiscus centralis" "Coxliella pseudoannulata" "Cylindrotheca gracilis" "Dinoflagellata" "Dinophysis rotundata" "Gonyaulax spinifera" "Gymnodinium elongatum" "Gymnodinium gaelatum" "Gymnodinium galeatum" "Gymnodinium gracilientum" "Heterokontophyta" "Hillea fusiformis" "Karenia" "Karenia brevis" "Myrionecta rubra" "Mesodinium rubrum" "Mesodinium" "Parapedinella reticulata" "Pleurochrysis carterae" "Pleurosigma siberica" "Prorocentrum minimum" "Proterythropsis vigilans" "Nematopsides vigilans" "Pseudo-nitzschia pseudodelicatissima" "Tripos" "Tripos fusus" "Rhoicosphenia" "Uronema marina" "Warnowia"

cnrdh commented 5 years ago

Before { 'taxon-db': 627, candidates: 35, 'to-check': 30, added: 0 } GBIF unknown: { name: 'Chaetoceros convulutus' } GBIF unknown: { name: 'Gymnodinium gracilientum' } GBIF unknown: { name: 'Gymnodinium gaelatum' } GBIF unknown: { name: 'Karenia brevis' }

In taxon-db; known [ 'Chaetoceros convolutus', 'Gymnodinium galeatum', 'Gymnodinium gracilentum' ]

After { 'taxon-db': 653, added: 26 } Added 26 [["Achnanthes longipes","species"],["Actinocyclus","genus"],["Actinocyclus tenuissimus","species"],["Ceratium fusus","species"],["Coccolithophora","genus"],["Coscinodiscus centralis","species"],["Coxliella pseudoannulata","species"],["Cylindrotheca gracilis","species"],["Dinoflagellata","subphylum"],["Dinophysis rotundata","species"],["Gonyaulax spinifera","species"],["Gymnodinium elongatum","species"],["Heterokontophyta","phylum"],["Hillea fusiformis","species"],["Karenia","genus"],["Myrionecta rubra","species"],["Mesodinium","genus"],["Parapedinella reticulata","species"],["Pleurochrysis carterae","species"],["Pleurosigma siberica","species"],["Prorocentrum minimum","species"],["Tripos","genus"],["Tripos fusus","species"],["Rhoicosphenia","genus"],["Uronema marina","species"],["Warnowia","genus"]]

cnrdh commented 5 years ago

Note to self: My local "deposit" version is now updated.

These needs "taxon" key "Ceratium" "Lessardia elongata" "Schmidingerella meunieri" "Ciliophora" "Fossula arctica" "Triconia conifera" "Nitzschia" "Nitzschia levissima"

cnrdh commented 5 years ago

Only "Karenia brevis" now remains to be added, for some reason unknown to GBIF.

cnrdh commented 5 years ago

Hmm Coccolithophora is (also) a genus of Protozoa

cnrdh commented 5 years ago

Updated the Google docs version