NHMA variety fullnames don't have "var." in them

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NHMA variety fullnames don't have "var." in them #363

Closed PipBrewer closed 7 months ago

PipBrewer commented 1 year ago

The taxon tree in the NHMA Specify database for entomology does not have "var. " in the fullname for varieties for some unknown reason. This causes problems in the app, which expects this. This probably needs to be changed in the NHMA db and then transferred (synchronized) to the taxon spine in the app. We need to ask NHMA if this is OK.

bhsi-snm commented 1 year ago

ask @PipBrewer to give priority. she knows

PipBrewer commented 1 year ago

I only made the comment into an issue, so this was not originally from me. @FedorSteeman Do you know how NHMA currently puts varieties into Specify?

PipBrewer commented 10 months ago

FYI The workflow at the moment for other collections is that the full trinomial is put into the taxon field and selected. The digitiser goes back and types in var. in the correct place. This will create a new taxon (if it isn't already in there), with variety as the rank. On import to specify, it should add the variety taxon record, with "var." removed.

PipBrewer commented 10 months ago

@FedorSteeman Based on the current db and GREL script, there is no reason why we shouldn't be able to add "var." to NHMA names in future if we want them with no additional development?

FedorSteeman commented 10 months ago

There are currently only three taxa of rank variety in the entire NHMA database.

It would be a problem for the GREL script to deduce rank if " var. " is not in the taxon fullname as supplied by the app.

FedorSteeman commented 10 months ago

And the taxon fullname in the app is taken from Specify db, so by adding " var. " to those fullnames there could make the whole thing work.

PipBrewer commented 10 months ago

@FedorSteeman Thanks. The protocol would be the same - the digitisers would add var. to them name in the app. Just checking that there is no reason why this would not work specifically for NHMA as suggested by the title of this issue. If we expect it to work (either adding var. records to Specify and drawing to app, or for new names put directly into the app, we can add them to Specify during workbench import), I will just close this issue.

FedorSteeman commented 10 months ago

I predict that, unless the fullname in the app includes the " var. " string, that these taxa entered with it will be marked as new taxa.

I would suggest adding the string to the fullnames in NHMA.

FedorSteeman commented 7 months ago

I'll take a final look at this and then it can probably be closed.

FedorSteeman commented 7 months ago

So "var." is still not part of the full name in the NHMA Entomology taxon tree, and I clearly still need to crank up Specify6 to change the relevant settings.

However, looking more closely at this, it is rather odd we even have these cases. The only varieties that are present in the NHMA tree at all are the following bumblebees:

Bombus pascuorum var. mniorum
Bombus pascuorum var. pascuorum
Bombus pascuorum var. tricuspis

According to this checklist that has @DanBIF Isabel as co-author, these are subspecies:

Could there have been a mistake?

FedorSteeman commented 7 months ago

Anyways... The "var. " string is now part of the fullname for varieties in NHMA Entomology:

https://specify-nhma.science.ku.dk/specify/view/taxon/8286/

This will ensure a proper import.