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feature request #9755

Open issues for cultivar handling

Added by Andreas Müller 3 months ago. Updated 2 months ago.

Status:
In Progress
Priority:
Priority14
Category:
cdmlib
Start date:
09/11/2021
Due date:
% Done:

30%

Severity:
normal

Description

Cultivar names, groups and grex are currently not parsable (#9757)

Cultivar names, groups and grex need to be formatted correctly (#9754)

Decide on related ranks (see also #6387)

Add "Group" or "Gp" and "grex" or "gx" as abbreviation to the according rank terms (similar to #5981 - but not fully correct there)

Handling of cultivars in TaxEditor needs improvement (see #9762)

  • Show cultivar ranks only when ICNCP is selected, do not show any other ranks then #9762
  • Make it possible to select only from certain Codes in NomCode field (e.g. only ICN and ICNCP), alternatively remove ICNCP from Codes as selecting one of the cultivar ranks (#6387) may be enough to decide that ICNCP is meant (ask taxonomists for correctness of this idea)

Handle cultivars correctly in publication

  • cultivar part should not be put in italics (see also formatting)

Questions:

  • is grex only used for cultivars? What about existing grex names in current databases
  • what exactly is rank "denomination class" (see Art. 6), usually it is a genus, should it be moved there?
  • Should graft-chimera be handled similar to hybrids (or general: how to handle them)
  • what is rank convar (see #6387)
  • Should a cultivar name link to the scientific name it is derived from? (see IOPI model https://archive.bgbm.org/biodivinf/docs/iopi_model/iopi_model.pdf page 295)
  • How to handle cultivars using infraspecific scientific name part (the rank can not be defined here as the rank is used for setting the cultivar rank), should rank marker be entered into the infaspecific epi field as this is a rare case, maybe change label in TaxEditor in this case?

What about grex names like "Amblysellus grex" (https://www.cabi.org/isc/datasheet/4880)? Is this a simple species or a cultivated plant name? Similar: Parthenicus grex Van Duzee, 1925

Code: http://www.actahort.org/chronica/pdf/sh_10.pdf

https://de.wikipedia.org/wiki/Internationaler_Code_der_Nomenklatur_der_Kulturpflanzen

https://en.wikipedia.org/wiki/Grex_(horticulture)


Related issues

Related to Edit - feature request #9754: Adapt cache strategy to support cultivar names Closed 09/11/2021
Related to Edit - feature request #6387: [Rule] Rank rule for CultivarPlantNames Closed 01/26/2017
Related to Edit - feature request #5981: Add abbreviation to Rank "Cultivar" Closed 07/15/2016
Related to Edit - feature request #9757: Make cultivars, cultivar groups and grexes parsable Closed 09/14/2021
Related to Edit - feature request #6963: Implement cache strategy for cultivar plant names (done), bacterial names, fungi, etc. In Progress 09/20/2017
Related to Edit - feature request #9761: Add cultivarGroup as field for handling cultivar groups and grex Closed 09/15/2021
Related to Edit - bug #9762: Handle cultivars correctly in TaxEditor Closed 09/15/2021

Associated revisions

Revision bd2f30c9 (diff)
Added by Andreas Müller 3 months ago

ref #9755 add abbrev to cultivar group representation

Revision 6cfc0581 (diff)
Added by Andreas Müller 3 months ago

ref #9755 update cultivarName->cultivarEpithet

Revision c0e9dfbb (diff)
Added by Andreas Müller 3 months ago

ref #9755 adapt taxeditor to cultivarEpi changes

Revision 7c1827b5 (diff)
Added by Andreas Müller 2 months ago

ref #9755 adapt app-import to new cultivar epithet naming

Revision 9585c46e (diff)
Added by Andreas Müller 2 months ago

ref #9778, ref #9755, ref #9754, ref # 9757 split grex and add new ranks lusus, subproles and subgrex

Revision dacb2825 (diff)
Added by Andreas Müller 2 months ago

ref #9755 update script for grex infraspec. representation

Revision d0deb3b0 (diff)
Added by Andreas Müller 2 months ago

ref #9755 add DENOMINATIONCLASS to isCultivar()

Revision 0ea0fdd3 (diff)
Added by Andreas Müller 2 months ago

ref #9762, ref #9755 Add nameCache annotation to cultivar fields

History

#1 Updated by Andreas Müller 3 months ago

  • Description updated (diff)
  • Category set to cdmlib
  • Assignee set to Andreas Müller
  • Target version changed from Unassigned CDM tickets to Release 5.29

#2 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#3 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#4 Updated by Andreas Müller 3 months ago

#5 Updated by Andreas Müller 3 months ago

#6 Updated by Andreas Müller 3 months ago

#7 Updated by Andreas Müller 3 months ago

  • Tags set to cultivar, mexico

#8 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#9 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#10 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#11 Updated by Andreas Müller 3 months ago

#12 Updated by Andreas Müller 3 months ago

  • Related to feature request #6963: Implement cache strategy for cultivar plant names (done), bacterial names, fungi, etc. added

#13 Updated by Andreas Müller 3 months ago

  • Status changed from New to In Progress

Existing cases:

SELECT *
FROM TaxonName tn INNER JOIN DefinedTermBase r ON r.id = tn.rank_id
WHERE r.uuid = '08dcb4ff-ac58-48a3-93af-efb3d836ac84';

SELECT *
FROM TaxonName tn 
WHERE tn.titleCache LIKE '% grex%' OR tn.fullTitleCache LIKE '% grex%' OR tn.nameCache LIKE '% grex%' 

Most of them are in Hieracium

Currently records exist in Cichorieae, E+M, RL Plantae, RL Standardliste, FdAC, FM

#14 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#15 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#16 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#17 Updated by Andreas Müller 3 months ago

  • Related to feature request #9761: Add cultivarGroup as field for handling cultivar groups and grex added

#18 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#19 Updated by Andreas Müller 3 months ago

  • Related to bug #9762: Handle cultivars correctly in TaxEditor added

#20 Updated by Andreas Müller 3 months ago

  • Description updated (diff)

#21 Updated by Andreas Müller 2 months ago

  • Status changed from In Progress to Resolved

Not yet fully resolved but set to resolved to not forget

#22 Updated by Andreas Müller 2 months ago

  • Priority changed from New to Highest

#23 Updated by Andreas Müller 2 months ago

  • Target version changed from Release 5.29 to Release 5.27

#24 Updated by Andreas Müller 2 months ago

  • Description updated (diff)
  • Priority changed from Highest to New
  • Target version changed from Release 5.27 to Release 5.29

#25 Updated by Andreas Müller 2 months ago

  • Priority changed from New to Highest
  • Target version changed from Release 5.29 to Release 5.27

#26 Updated by Andreas Müller 2 months ago

  • Description updated (diff)

#27 Updated by Andreas Müller 2 months ago

  • Description updated (diff)

#28 Updated by Andreas Müller 2 months ago

  • Description updated (diff)
  • % Done changed from 0 to 20

#29 Updated by Andreas Müller 2 months ago

  • Tracker changed from bug to feature request

#30 Updated by Andreas Müller 2 months ago

  • Description updated (diff)

#31 Updated by Andreas Müller 2 months ago

  • Description updated (diff)

#32 Updated by Andreas Müller 2 months ago

  • Subject changed from Fix and improve cultivar handling to Open issues for cultivar handling
  • Status changed from Resolved to In Progress
  • Priority changed from Highest to Priority14
  • Target version changed from Release 5.27 to Reviewed Next Major Release
  • % Done changed from 20 to 30

The important issues have been fixed with 5.27 mostly using separate tickets.

#33 Updated by Andreas Müller 2 months ago

AM:

Verwendung von nom. Author and nom. Ref. (und evtl. andere Zusätze):
Article 28.2 verstehe ich so, dass ein Autor angegeben werden kann nach dem Namen (aber weniger zwingend als bei Wildpflanzen), es aber keine Basionym oder Ex-Autoren gibt. Korrekt?
Wie sieht es mit der Angabe von nomenklatorischen Referenzen aus. Erfolgt das genauso wie bei Wildplanzen oder werden nom.Refs. anders oder gar nicht angegeben? (Ich habe keine Beispiele mit nom. ref. gefunden, lediglich die Recommendation 27B.1., die aber allgemeinerer Natur ist)

WGB:

Ich denke, es gelten die gleichen Regeln bei einer Autorenangabe wie im Bot. Code.
Das Literaturzitat wird (vermutlich) eher nicht verwandt.

#34 Updated by Andreas Müller 2 months ago

AM

Denomination class:
Verstehe ich es richtig, dass das in der Regel Taxa vom Rang „Genus“ sind, und in seltenen Fällen auch andere Ränge? Wie unterscheidet sich die denomination class von der „normalen“ Gattung? Gibt es denomination classes, die nicht Taxa sind, die dem ICNafp folgen? Wenn ja, gibt es Beispiele.
Auch hier müssen wir den Rang nicht unbedingt unterstützen, ich würde ihn aber zumindest gerne kommentieren. Ich nehme an, beim Parsen lässt er sich sowieso nicht von einer Gattung unterscheiden.

WGB:

Muss ich mir ansehen, aber man sollte jemanden aus der Cultivated Plant Community solche Sachen fragen.

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