DwC importer assign BiocurationGroup values to rows

[LordFlashmeow]

I have custom BiocurationGroup vocabulary, and I would like to be able to assign those tags via columns in the DwC importer.

Ideally, it would look something like this:

(other columns)	TW:BiocurationGroup:lifestage	TW:BiocurationGroup:sex	TW:BiocurationGroup:caste	TW:BiocurationGroup:subcaste
...	adult	female	queen	alate
...	adult	female	worker	soldier
...	larvae	male	male

[mjy]

@LordFlashmeow I think you could pivot the tables. This is adding Tags (subclasses of actually). So ifeach column is a Keyword, and the value is a 1 if present. Something like 'TW:BiocurationClassification:`.

This should not block merge, but be a feature post merge.

[LordFlashmeow]

True, that could also work. However, I suspect that most curator data isn't going to be pivoted. If the data is stored as	lifestage	sex
adult	male
larvae	female

Then it requires some data manipulation knowledge to convert it to	TW:BiocurationClassification:adult	TW:BiocurationClassification:larvae	TW:BiocurationClassification:male	TW:BiocurationClassification:female
1		1
	1		1

What tool would you recommend for this transformation (besides scripting)?

[LocoDelAssembly]

BTW in https://github.com/SpeciesFileGroup/taxonworks/commit/ff9c22afeaee132f789b3a81640426dd649e4680 I implemented what @LordFlashmeow originally posted. I hope it is better than adding multiple columns with ones and blanks.

Note that sex is mapped and will find or create "sex" BiocurationGroup and map value by finding or creating BiocurationClass. It might collide if both sex and custom TW fields are specified.

TW::BiocurationGroup:* requires both that the BiocurationGroup already exists as well as the BiocurationClassification in field value. In both, column and field value, you may match by either URI or name (URI prioritized when matching).

[LordFlashmeow]

What's the best way to create containers when the CO has multiple individuals with different biocuration classes? Is it to create multiple rows, one for each individual (or group of individuals) with the "Containerize specimen with existing ones when catalog number already exists" setting enabled?

[mjy]

Yes, I believe so. They will be grouped by a Container::Virtual. I'm not sure if prep type also influences when it matches a specific container type.

[mjy]

Side note that the export behaviour has changed to export via a match to the group that groups the attribute. So you can have individual attributes load from the importer, then make them export to a specific DwC field for lifeStage and Sex.

[mjy]

@LordFlashmeow how's the status of this issue?

[LordFlashmeow]

@mjy I don't think we're planning to use this in the near future. Our data is too variable and inconsistent, and we don't think containerizing benefits our dataset.