steps needed when a taxon is finally published

[mfrasca]

As a collection manager, I want to insert publication information about a species that has been in our collection under a temporary name, so that both names are found, so that all accessions now point to the published name, so that this change is only visible from the species, not in the accessions.

(@RoDuth, original reporter of the issue #444, can you correct the above and make your goal more explicit?)

Expected behaviour

We had a species collected by the team, and we had it in the database as Actephila sp. Koumala (I.G Champion 870). A couple of years ago this species was finally formally named: Actephila sp. Koumala (I.G Champion 870) became Actephila championiae, and the temporary name stays in the database as a synonym of the new published name.

Actual behaviour

using that example the workflow went like this:

1. search for gen='Actephila'

• expand the genus

2. open Actephila sp. Koumala (I.G Champion 870),

• copy the species name to avoid misspellings and
• change it to championiae
• close/save

3. right click Actephila,

• add species and
• create a new sp. Koumala (I.G Champion 870)
• close/save

3. open Actephila championiae and

• add Actephila sp. Koumala (I.G Champion 870) as a synonym

Opinions and suggestions

can you describe how you wish it works? with more words than "I click on »do what I'm thinking of« and it does what I want."

my guess is that you want:

• temporary names are recognized as such by the program,
• the species editor offers an extra button for the above operation,
• that the above operation is only available for species with a temporary name and no accepted synonym,

[mfrasca]

but why don't you simply add an epithet and author, keep the temporary information, and request that the species shows itself as you need it, without messing with the database? I'm sure you have considered this, so I'm asking why you're not doing it.

[RoDuth]

The example was not meant to be specific to provisional names it was meant to be about work flow. What I want is the temporary name to remaining in the database and being nothing more than a synonym to the now accepted name. This is no different to any species name change. The complication comes about from all the data that is attached to the species. If we have been in the process of formal identification we have accumulated herbarium vouchers, multiple accessions and plantings, species level photographs and notes, etc.

The only other way to make this change is to create a new epithet for Actephila championiae and then one by one open each accession of Actephila sp. Koumala (I.G Champion 870) and change the species name to Actephila championiae. Problem is if, rather than leave it buried in the now synonym, you want to keep any of the data attached at species level (pictures, notes, etc.) you need do it manually. That is a hell of a lot more clicks than the 3 step method I gave above.

What would I like?:
At step 2 I would like to just change the epithet to championiae click save and have ghini offers to recreate Actephila sp. Koumala (I.G Champion 870) (using just the taxanomic data (genus, species, infraspecific parts, author, hybrid flag, cultivar group, species qualifier) and link it as a synonym to Actephila championiae. This would be the same as any other renaming of a species.

[mfrasca]

parenthesis:
you are talking of adding this to the current database structure, not to plan it for 3.2.
in 3.2 there are no infraspecific parts, each taxon has its own rank and that is one, not many as it is now.

I'm not sure I'm reading you correctly, but sounds like that of the three points in my "guess" you are only confirming the middle one.

so my updated understanding:

• for any given species X in a 1.0/3.1 database, I want to be able to
  • add a new accepted name (a new Species object Y),
  • open the Species Editor on Y, and —on confirming the edit—
  • change all accessions previously associated to X so that they become accessions of Y, and
  • copy all notes (and pictures, what else?) from X to Y, and
  • make sure that X is now a synonym for Y.
• the option could be offered in the species context menu
• the option could be included as an extra button in the Species Editor

[RoDuth]

moving this to #444 as I believe this can be closed...

But

in 3.2 there are no infraspecific parts, each taxon has its own rank and that is one, not many as it is now.

I'm not sure where you are going with all this but my understanding is that each species should end with a binomial (including infraspecific name etc..) not a uninomial.

Note this quirk of taxonomy, (and this happens a lot) if a subspecies, etc. is created of a species then the type species automatically gets a subsp. name that mirrors the species epithet. E.g. when they decided that the Araucaria cunninghamii from PNG was a variety and named it Araucaria cunninghamii var. papuana then all other Araucaria cunninghamii automatically became Araucaria cunninghamii var cunninghamii.

it is the whole Araucaria cunninghamii var cunninghamii not var cunninghamii that is the full name, nor is Araucaria cunninghamii any longer accepted as it is ambiguous. The full name must be unique in the order and unambiguous so with this you don't need any other rank information other than the "full scientific name" as ABCD calls it to be clear what you'rw talking about. You could think of the whole scientific name as the key in the database...

Uninomials are only used for all ranks above species.

[mfrasca]

@RoDuth , you are commenting here something that belongs in #92.