isamplesorg / vocabularies

Vocabularies for categorization of physical samples
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Add Chromista kingdom to the biological vocabulary #17

Closed dannymandel closed 3 weeks ago

dannymandel commented 5 months ago

We have Chromista in our taxon name cache:

isb_2=> select distinct kingdom from taxonomyname;
    kingdom     
----------------
 Archaea
 Bacteria
 Viruses
 incertae sedis
 Fungi
 Chromista
 Animalia
 Plantae
 Protozoa
(9 rows)

And a number of GEOME records have this as their kingdom. We should add it to https://vocabs.ardc.edu.au/repository/api/lda/isamples/biology-extension-basic-taxon-classes-for-biologic/1-0/resource?uri=https://w3id.org/isample/biology/biosampledfeature/1.0/biologicentityvocabulary

smrgeoinfo commented 5 months ago

suggestion from discussion-- add chromista to taxonomy, subclass of Eucaryote note possible overlap with Algae, protista, SEE catalog of life taxonomic backbone, GBIF; There are various identifiers. used in GEOME (GEOME vocabs are controlled by teams, phyla more controlled that kingdom). Assignments are uncertain and change.
Another situation where recording the verbatim taxa, and assigned to most specific subsuming class in controlled vocab.

smrgeoinfo commented 1 month ago

I'm going to merge this into biology_extension main. see https://github.com/isamplesorg/metadata_profile_biology/pull/1

smrgeoinfo commented 3 weeks ago

done, closing