isamplesorg / isamples_inabox

Provides functionality intermediate to a collection and central
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A couple of missing values in the previous transformation rules #310

Closed dannymandel closed 9 months ago

dannymandel commented 9 months ago

When porting the old code to the new controlled vocabularies, I noticed the following:

    _soilFloodplainMapper = StringPairedCategoryMapper(
        "Microbiology>Soil", "floodplain", "Subaerial terrestrial biome", vocabulary_mapper.SAMPLED_FEATURE
    )

and Subaerial terrestrial biome doesn't appear in sampledfeature.txt (https://github.com/isamplesorg/isamples_inabox/blob/new_metadata_format/isamples_metadata/vocabularies/sampledfeature.txt)

What should be used instead?

Similarly, Marine biome is gone from here:

_ventBiologyMapper = StringPairedCategoryMapper("Biology", "Vent", "Marine biome", vocabulary_mapper.SAMPLED_FEATURE)

(also expecting to find it here: https://github.com/isamplesorg/isamples_inabox/blob/new_metadata_format/isamples_metadata/vocabularies/sampledfeature.txt)

What should we use instead?

smrgeoinfo commented 9 months ago

marine biome is now "Marine environment" https://w3id.org/isample/vocabulary/sampledfeature/0.9/marinewaterbody

subaerial terrestrial biome is "Subaerial surface environment" https://w3id.org/isample/vocabulary/sampledfeature/0.9/subaerialsurfaceenvironment

dannymandel commented 9 months ago

Thank you!