Taxonomic Spine for botany

[jlegind]

Issue

Creation of the first taxonomic spine for Vascular Plants.

The Taxonomic Spine is the canonical taxon list drawn from both Specify and authoritative checklists, including synonyms, so that 99% of taxa we will come across will be in the there.

Basic requirements:

• A flattened list of taxon names only and no (foreign) keys
• separate columns for each higher taxon level
• separate records for each taxon, including all higher taxa above family level
• extract missing taxon records from Jan's DB (c. 29,000)
• import missing taxon records into Specify 7

Missing taxon records are in the shared drive:
N:\SCI-SNM-DigitalCollections\DaSSCo\missing_names_botany_august2022.xlsx

[jlegind]

Estimated work days: 5 WD

[jlegind]

Update: Botanical Taxonomy from Christian Lange & Olof is still an outstanding issue (they have been contacted)
B. taxonomy from Aarhus is yet to be obtained (they have been contacted)
With POWO (Kew) taxonomy, we are at 1.2M names including synonyms.

[jlegind]

I consider this item finished. It was completed 10-06-2022.

[FedorSteeman]

While working on #11 several issues with the taxonomy were uncovered that are now moved into tickets:
#27 #28 DanSpecify#172

This ticket will remain open until the Full Taxonomy has been prepared (#28), imported into Specify (DanSpecify#173) and into the app's local database.

[FedorSteeman]

To prevent further confusion of terms, I suggest we call this, the compendium of taxa (restricted to botany for now), the actual Taxonomic Spine. Of course this is supposed to be the source of taxon names residing in the digitization app's local database. I noticed that the latter is often referred to as "taxonomic spine", which makes no sense to me and I'd like to keep these concepts separate.

I will rename tickets accordingly.

[FedorSteeman]

I renamed this ticket and edited the description for clarity. Removed the requirement for synonyms. These will be dealt with later and separate tickets ought to be created for this and hybrids.

[FedorSteeman]

Reopening as @PipBrewer discovered some issues with the taxon spine that needs investigation.

[jlegind]

I am investigating the missing names that Kim highlighted in mail from 29-08-2022.
Specifically it is vascular plant names in the word doc that Olof Ryding sent in June.

[jlegind]

The number of missing names turned out to be 12,641 total.